Preface

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About *Microbiology*

*Microbiology* is designed to cover the scope and sequence requirements for the single-semester Microbiology course for non-majors. The book presents the core concepts of microbiology with a focus on applications for careers in allied health. The pedagogical features of *Microbiology* make the material interesting and accessible to students while maintaining the career-application focus and scientific rigor inherent in the subject matter.

Additional Resources

About the Authors

An Invisible World

Introduction

What Our Ancestors Knew

Fermented Foods and Beverages

People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from rice, honey, and fruit as early as 7000 BC.[footnote]

P.E. McGovern et al. “Fermented Beverages of Pre- and Proto-Historic China.” *Proceedings of the National Academy of Sciences of the United States of America* 1 no. 51 (2004):17593–17598. doi:10.1073/pnas.0407921102.

The Iceman and Evidence of Early Treatments

Prehistoric humans had a very limited understanding of the causes of disease, and various cultures developed different beliefs and explanations. While many believed that illness was punishment for angering the gods or was simply the result of fate, archaeological evidence suggests that prehistoric people attempted to treat illnesses and infections. One example of this is Ötzi the Iceman, a 5300-year-old mummy found frozen in the ice of the Ötzal Alps on the Austrian-Italian border in 1991. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite *Trichuris trichiura*, which may have caused him to have abdominal pain and anemia. Researchers also found evidence of *Borrelia burgdorferi*, a bacterium that causes Lyme disease.[footnote] Some researchers think Ötzi may have been trying to treat his infections with the woody fruit of the *Fomitopsis betulinus* fungus, which was discovered tied to his belongings.[footnote] This fungus has both laxative and antibiotic properties. Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then burning the herbs.[footnote] There is speculation that this may have been another attempt to treat his health ailments.

A. Keller et al. “New Insights into the Tyrolean Iceman's Origin and Phenotype as Inferred by Whole-Genome Sequencing.” *Nature Communications*, 3 (2012): 698. doi:10.1038/ncomms1701.L. Capasso. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” *The Lancet*, 352 (1998) 9143: 1864. doi: 10.1016/s0140-6736(05)79939-6.L. Capasso, L. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” *The Lancet*, 352 no. 9143 (1998): 1864. doi: 10.1016/s0140-6736(05)79939-6.

Early Notions of Disease, Contagion, and Containment

Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. This is especially evident in historical attempts to contain the spread of disease. For example, the Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. Ironically, while leprosy is communicable, it is also a disease that progresses slowly. This means that people were likely quarantined after they had already spread the disease to others.

The Birth of Microbiology

While the ancients may have suspected the existence of invisible “minute creatures,” it wasn’t until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as “animalcules” or “wee little beasties,” swimming in a drop of rain water. From his drawings of these little organisms, we now know he was looking at bacteria and protists. (We will explore Leeuwenhoek’s contributions to microscopy further in How We See the Invisible World.)

A Systematic Approach

The Science of Taxonomy

Taxonomy is the classification, description, identification, and naming of living organisms. Classification is the practice of organizing organisms into different groups based on their shared characteristics. The most famous early taxonomist was a Swedish botanist, zoologist, and physician named Carolus Linnaeus (1701–1778). In 1735, Linnaeus published *Systema Naturae*, an 11-page booklet in which he proposed the Linnaean taxonomy, a system of categorizing and naming organisms using a standard format so scientists could discuss organisms using consistent terminology. He continued to revise and add to the book, which grew into multiple volumes ([link]).

Types of Microorganisms

Prokaryotic Microorganisms

Bacteria are found in nearly every habitat on earth, including within and on humans. Most bacteria are harmless or helpful, but some are pathogen**s**, causing disease in humans and other animals. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have cell walls that contain peptidoglycan.

Eukaryotic Microorganisms

The domain Eukarya contains all eukaryotes, including uni- or multicellular eukaryotes such as protists, fungi, plants, and animals. The major defining characteristic of eukaryotes is that their cells contain a nucleus.

Helminths

Multicellular parasitic worms called helminth**s** are not technically microorganisms, as most are large enough to see without a microscope. However, these worms fall within the field of microbiology because diseases caused by helminths involve microscopic eggs and larvae. One example of a helminth is the guinea worm, or *Dracunculus medinensis*, which causes dizziness, vomiting, diarrhea, and painful ulcers on the legs and feet when the worm works its way out of the skin ([link]). Infection typically occurs after a person drinks water containing water fleas infected by guinea-worm larvae. In the mid-1980s, there were an estimated 3.5 million cases of guinea-worm disease, but the disease has been largely eradicated. In 2014, there were only 126 cases reported, thanks to the coordinated efforts of the World Health Organization (WHO) and other groups committed to improvements in drinking water sanitation.[footnote][footnote]

C. Greenaway “Dracunculiasis (Guinea Worm Disease).” *Canadian Medical Association Journal* 170 no. 4 (2004):495–500.World Health Organization. “Dracunculiasis (Guinea-Worm Disease).” *WHO*. 2015. http://www.who.int/mediacentre/factsheets/fs359/en/. Accessed October 2, 2015.

Viruses

Virus**es** are acellular microorganisms, which means they are not composed of cells. Essentially, a virus consists of proteins and genetic material—either DNA or RNA, but never both—that are inert outside of a host organism. However, by incorporating themselves into a host cell, viruses are able to co-opt the host’s cellular mechanisms to multiply and infect other hosts.

Microbiology as a Field of Study

Microbiology is a broad term that encompasses the study of all different types of microorganisms. But in practice, microbiologists tend to specialize in one of several subfields. For example, bacteriology is the study of bacteria; mycology is the study of fungi; protozoology is the study of protozoa; parasitology is the study of helminths and other parasites; and virology is the study of viruses ([link]). Immunology, the study of the immune system, is often included in the study of microbiology because host–pathogen interactions are central to our understanding of infectious disease processes. Microbiologists can also specialize in certain areas of microbiology, such as clinical microbiology, environmental microbiology, applied microbiology, or food microbiology.

How We See the Invisible World

Introduction

The Properties of Light

Interactions of Light

Light waves interact with materials by being reflected, absorbed, or transmitted. Reflection occurs when a wave bounces off of a material. For example, a red piece of cloth may reflect red light to our eyes while absorbing other colors of light. Absorbance occurs when a material captures the energy of a light wave. In the case of glow-in-the-dark plastics, the energy from light can be absorbed and then later re-emitted as another form of phosphorescence. Transmission occurs when a wave travels through a material, like light through glass (the process of transmission is called transmittance). When a material allows a large proportion of light to be transmitted, it may do so because it is thinner, or more transparent (having more transparency and less opacity). [link] illustrates the difference between transparency and opacity.

Lenses and Refraction

In the context of microscopy, refraction is perhaps the most important behavior exhibited by light waves. Refraction occurs when light waves change direction as they enter a new medium ([link]). Different transparent materials transmit light at different speeds; thus, light can change speed when passing from one material to another. This change in speed usually also causes a change in direction (refraction), with the degree of change dependent on the angle of the incoming light.

Electromagnetic Spectrum and Color

Visible light is just one form of electromagnetic radiation (EMR), a type of energy that is all around us. Other forms of EMR include microwaves, X-rays, and radio waves, among others. The different types of EMR fall on the electromagnetic spectrum, which is defined in terms of wavelength and frequency. The spectrum of visible light occupies a relatively small range of frequencies between infrared and ultraviolet light ([link]).

Magnification, Resolution, and Contrast

Microscopes magnify images and use the properties of light to create useful images of small objects. Magnification is defined as the ability of a lens to enlarge the image of an object when compared to the real object. For example, a magnification of 10⨯ means that the image appears 10 times the size of the object as viewed with the naked eye.

Peering Into the Invisible World

Early Microscopes

Antonie van Leeuwenhoek, sometimes hailed as “the Father of Microbiology,” is typically credited as the first person to have created microscopes powerful enough to view microbes ([link]). Born in the city of Delft in the Dutch Republic, van Leeuwenhoek began his career selling fabrics. However, he later became interested in lens making (perhaps to look at threads) and his innovative techniques produced microscopes that allowed him to observe microorganisms as no one had before. In 1674, he described his observations of single-celled organisms, whose existence was previously unknown, in a series of letters to the Royal Society of London. His report was initially met with skepticism, but his claims were soon verified and he became something of a celebrity in the scientific community.

Instruments of Microscopy

Light Microscopy

Many types of microscopes fall under the category of light microscopes, which use light to visualize images. Examples of light microscopes include brightfield microscopes, darkfield microscopes, phase-contrast microscopes, differential interference contrast microscopes, fluorescence microscopes, confocal scanning laser microscopes, and two-photon microscopes. These various types of light microscopes can be used to complement each other in diagnostics and research.

Electron Microscopy

The maximum theoretical resolution of images created by light microscopes is ultimately limited by the wavelengths of visible light. Most light microscopes can only magnify 1000⨯, and a few can magnify up to 1500⨯, but this does not begin to approach the magnifying power of an electron microscope **(EM)**, which uses short-wavelength electron beams rather than light to increase magnification and resolution.

Scanning Probe Microscopy

A scanning probe microscope does not use light or electrons, but rather very sharp probes that are passed over the surface of the specimen and interact with it directly. This produces information that can be assembled into images with magnifications up to 100,000,000⨯. Such large magnifications can be used to observe individual atoms on surfaces. To date, these techniques have been used primarily for research rather than for diagnostics.

Staining Microscopic Specimens

Preparing Specimens for Light Microscopy

In clinical settings, light microscopes are the most commonly used microscopes. There are two basic types of preparation used to view specimens with a light microscope: wet mounts and fixed specimens.

Gram Staining

The Gram stain procedure is a differential staining procedure that involves multiple steps. It was developed by Danish microbiologist Hans Christian Gram in 1884 as an effective method to distinguish between bacteria with different types of cell walls, and even today it remains one of the most frequently used staining techniques. The steps of the Gram stain procedure are listed below and illustrated in [link].

Acid-Fast Stains

Acid-fast staining is another commonly used, differential staining technique that can be an important diagnostic tool. An acid-fast stain is able to differentiate two types of gram-positive cells: those that have waxy mycolic acids in their cell walls, and those that do not. Two different methods for acid-fast staining are the Ziehl-Neelsen technique and the Kinyoun technique. Both use carbolfuchsin as the primary stain. The waxy, acid-fast cells retain the carbolfuchsin even after a decolorizing agent (an acid-alcohol solution) is applied. A secondary counterstain, methylene blue, is then applied, which renders non–acid-fast cells blue.

Capsule Staining

Certain bacteria and yeasts have a protective outer structure called a capsule. Since the presence of a capsule is directly related to a microbe’s virulence (its ability to cause disease), the ability to determine whether cells in a sample have capsules is an important diagnostic tool. Capsules do not absorb most basic dyes; therefore, a negative staining technique (staining around the cells) is typically used for capsule staining. The dye stains the background but does not penetrate the capsules, which appear like halos around the borders of the cell. The specimen does not need to be heat-fixed prior to negative staining.

Endospore Staining

Endospores are structures produced within certain bacterial cells that allow them to survive harsh conditions. Gram staining alone cannot be used to visualize endospores, which appear clear when Gram-stained cells are viewed. Endospore staining uses two stains to differentiate endospores from the rest of the cell. The Schaeffer-Fulton method (the most commonly used endospore-staining technique) uses heat to push the primary stain (malachite green) into the endospore. Washing with water decolorizes the cell, but the endospore retains the green stain. The cell is then counterstained pink with safranin. The resulting image reveals the shape and location of endospores, if they are present. The green endospores will appear either within the pink vegetative cells or as separate from the pink cells altogether. If no endospores are present, then only the pink vegetative cells will be visible ([link]).

Flagella Staining

Flagella (singular: flagellum) are tail-like cellular structures used for locomotion by some bacteria, archaea, and eukaryotes. Because they are so thin, flagella typically cannot be seen under a light microscope without a specialized flagella staining technique. Flagella staining thickens the flagella by first applying mordant (generally tannic acid, but sometimes potassium alum), which coats the flagella; then the specimen is stained with pararosaniline (most commonly) or basic fuchsin ([link]).

Preparing Specimens for Electron Microscopy

Samples to be analyzed using a TEM must have very thin sections. But cells are too soft to cut thinly, even with diamond knives. To cut cells without damage, the cells must be embedded in plastic resin and then dehydrated through a series of soaks in ethanol solutions (50%, 60%, 70%, and so on). The ethanol replaces the water in the cells, and the resin dissolves in ethanol and enters the cell, where it solidifies. Next, thin sections are cut using a specialized device called an ultramicrotome ([link]). Finally, samples are fixed to fine copper wire or carbon-fiber grids and stained—not with colored dyes, but with substances like uranyl acetate or osmium tetroxide, which contain electron-dense heavy metal atoms.

Preparation and Staining for Other Microscopes

Samples for fluorescence and confocal microscopy are prepared similarly to samples for light microscopy, except that the dyes are fluorochromes. Stains are often diluted in liquid before applying to the slide. Some dyes attach to an antibody to stain specific proteins on specific types of cells (immunofluorescence); others may attach to DNA molecules in a process called fluorescence in situ hybridization (FISH), causing cells to be stained based on whether they have a specific DNA sequence.

The Cell

Introduction

Spontaneous Generation

The Theory of Spontaneous Generation

The Greek philosopher Aristotle (384–322 BC) was one of the earliest recorded scholars to articulate the theory of spontaneous generation, the notion that life can arise from nonliving matter. Aristotle proposed that life arose from nonliving material if the material contained *pneuma* (“spirit” or “breath”). As evidence, he noted several instances of the appearance of animals from environments previously devoid of such animals, such as the seemingly sudden appearance of fish in a new puddle of water.[footnote]

K. Zwier. “Aristotle on Spontaneous Generation.” http://www.sju.edu/int/academics/cas/resources/gppc/pdf/Karen%20R.%20Zwier.pdf

Disproving Spontaneous Generation

The debate over spontaneous generation continued well into the 19th century, with scientists serving as proponents of both sides. To settle the debate, the Paris Academy of Sciences offered a prize for resolution of the problem. Louis Pasteur, a prominent French chemist who had been studying microbial fermentation and the causes of wine spoilage, accepted the challenge. In 1858, Pasteur filtered air through a gun-cotton filter and, upon microscopic examination of the cotton, found it full of microorganisms, suggesting that the exposure of a broth to air was not introducing a “life force” to the broth but rather airborne microorganisms.

Foundations of Modern Cell Theory

The Origins of Cell Theory

The English scientist Robert Hooke first used the term “cells” in 1665 to describe the small chambers within cork that he observed under a microscope of his own design. To Hooke, thin sections of cork resembled “Honey-comb,” or “small Boxes or Bladders of Air.” He noted that each “Cavern, Bubble, or Cell” was distinct from the others ([link]). At the time, Hooke was not aware that the cork cells were long dead and, therefore, lacked the internal structures found within living cells.

Endosymbiotic Theory

As scientists were making progress toward understanding the role of cells in plant and animal tissues, others were examining the structures within the cells themselves. In 1831, Scottish botanist Robert Brown (1773–1858) was the first to describe observations of nuclei, which he observed in plant cells. Then, in the early 1880s, German botanist Andreas Schimper (1856–1901) was the first to describe the chloroplasts of plant cells, identifying their role in starch formation during photosynthesis and noting that they divided independent of the nucleus.

The Germ Theory of Disease

Prior to the discovery of microbes during the 17th century, other theories circulated about the origins of disease. For example, the ancient Greeks proposed the miasma theory, which held that disease originated from particles emanating from decomposing matter, such as that in sewage or cesspits. Such particles infected humans in close proximity to the rotting material. Diseases including the Black Death, which ravaged Europe’s population during the Middle Ages, were thought to have originated in this way. In the 11th Century, Persian physician Ibn Sina (sometimes referred to as Avicenna) proposed that tuberculosis was likely spread by people's breath when in close proximity. Arab physician Ibn Zuhr, writing in about 1155, documented that the common skin condition scabies was caused by tiny mites that bored into the skin. Though scabies mites are about half a millimeter long (and therefore not technically microscopic) and their skin tunnels are often visible, Ibn Zuhr's discovery gave more evidence that unseen substances or creatures caused diseases.

Unique Characteristics of Prokaryotic Cells

Common Cell Morphologies and Arrangements

Individual cells of a particular prokaryotic organism are typically similar in shape, or **cell** morphology. Although thousands of prokaryotic organisms have been identified, only a handful of cell morphologies are commonly seen microscopically. [link] names and illustrates cell morphologies commonly found in prokaryotic cells. In addition to cellular shape, prokaryotic cells of the same species may group together in certain distinctive arrangements depending on the plane of cell division. Some common arrangements are shown in [link].

The Nucleoid

All cellular life has a DNA genome organized into one or more chromosomes. Prokaryotic chromosomes are typically circular, haploid (unpaired), and not bound by a complex nuclear membrane. Prokaryotic DNA and DNA-associated proteins are concentrated within the nucleoid region of the cell ([link]). In general, prokaryotic DNA interacts with nucleoid-associated proteins (NAPs) that assist in the organization and packaging of the chromosome. In bacteria, NAPs function similar to histones, which are the DNA-organizing proteins found in eukaryotic cells. In archaea, the nucleoid is organized by either NAPs or histone-like DNA organizing proteins.

Plasmids

Prokaryotic cells may also contain extrachromosomal DNA, or DNA that is not part of the chromosome. This extrachromosomal DNA is found in plasmid**s**, which are small, circular, double-stranded DNA molecules. Cells that have plasmids often have hundreds of them within a single cell. Plasmids are more commonly found in bacteria; however, plasmids have been found in archaea and eukaryotic organisms. Plasmids often carry genes that confer advantageous traits such as antibiotic resistance; thus, they are important to the survival of the organism. We will discuss plasmids in more detail in Mechanisms of Microbial Genetics.

Ribosomes

All cellular life synthesizes proteins, and organisms in all three domains of life possess ribosomes, structures responsible for protein synthesis. However, ribosomes in each of the three domains are structurally different. Ribosomes, themselves, are constructed from proteins, along with ribosomal RNA (rRNA). Prokaryotic ribosomes are found in the cytoplasm. They are called 70S ribosome**s** because they have a size of 70S ([link]), whereas eukaryotic cytoplasmic ribosomes have a size of 80S. (The S stands for Svedberg unit, a measure of sedimentation in an ultracentrifuge, which is based on size, shape, and surface qualities of the structure being analyzed). Although they are the same size, bacterial and archaeal ribosomes have different proteins and rRNA molecules, and the archaeal versions are more similar to their eukaryotic counterparts than to those found in bacteria.

Inclusions

As single-celled organisms living in unstable environments, some prokaryotic cells have the ability to store excess nutrients within cytoplasmic structures called inclusions. Storing nutrients in a polymerized form is advantageous because it reduces the buildup of osmotic pressure that occurs as a cell accumulates solutes. Various types of inclusions store glycogen and starches, which contain carbon that cells can access for energy. Volutin granules, also called metachromatic granules because of their staining characteristics, are inclusions that store polymerized inorganic phosphate that can be used in metabolism and assist in the formation of biofilms. Microbes known to contain volutin granules include the archaea *Methanosarcina*, the bacterium *Corynebacterium diphtheriae*, and the unicellular eukaryotic alga *Chlamydomonas*. Sulfur granules, another type of inclusion, are found in sulfur bacteria of the genus *Thiobacillus*; these granules store elemental sulfur, which the bacteria use for metabolism.

Endospores

Bacterial cells are generally observed as vegetative cells, but some genera of bacteria have the ability to form endospores, structures that essentially protect the bacterial genome in a dormant state when environmental conditions are unfavorable. Endospores (not to be confused with the reproductive spores formed by fungi) allow some bacterial cells to survive long periods without food or water, as well as exposure to chemicals, extreme temperatures, and even radiation. [link] compares the characteristics of vegetative cells and endospores.

Plasma Membrane

Structures that enclose the cytoplasm and internal structures of the cell are known collectively as the cell envelope. In prokaryotic cells, the structures of the cell envelope vary depending on the type of cell and organism. Most (but not all) prokaryotic cells have a cell wall, but the makeup of this cell wall varies. All cells (prokaryotic and eukaryotic) have a plasma membrane (also called cytoplasmic membrane or cell membrane) that exhibits selective permeability, allowing some molecules to enter or leave the cell while restricting the passage of others.

Cell Wall

The primary function of the cell wall is to protect the cell from harsh conditions in the outside environment. When present, there are notable similarities and differences among the cell walls of archaea, bacteria, and eukaryotes.

Glycocalyces and S-Layers

Although most prokaryotic cells have cell walls, some may have additional cell envelope structures exterior to the cell wall, such as glycocalyces and S-layers. A glycocalyx is a sugar coat, of which there are two important types: capsules and slime layers. A capsule is an organized layer located outside of the cell wall and usually composed of polysaccharides or proteins ([link]). A slime layer is a less tightly organized layer that is only loosely attached to the cell wall and can be more easily washed off. Slime layers may be composed of polysaccharides, glycoproteins, or glycolipids.

Filamentous Appendages

Many bacterial cells have protein appendages embedded within their cell envelopes that extend outward, allowing interaction with the environment. These appendages can attach to other surfaces, transfer DNA, or provide movement. Filamentous appendages include fimbriae, pili, and flagella.

Unique Characteristics of Eukaryotic Cells

Cell Morphologies

Eukaryotic cells display a wide variety of different cell morphologies. Possible shapes include spheroid, ovoid, cuboidal, cylindrical, flat, lenticular, fusiform, discoidal, crescent, ring stellate, and polygonal ([link]). Some eukaryotic cells are irregular in shape, and some are capable of changing shape. The shape of a particular type of eukaryotic cell may be influenced by factors such as its primary function, the organization of its cytoskeleton, the viscosity of its cytoplasm, the rigidity of its cell membrane or cell wall (if it has one), and the physical pressure exerted on it by the surrounding environment and/or adjoining cells.

Nucleus

Unlike prokaryotic cells, in which DNA is loosely contained in the nucleoid region, eukaryotic cells possess a nucleus, which is surrounded by a complex nuclear membrane that houses the DNA genome ([link]). By containing the cell’s DNA, the nucleus ultimately controls all activities of the cell and also serves an essential role in reproduction and heredity. Eukaryotic cells typically have their DNA organized into multiple linear chromosomes. The DNA within the nucleus is highly organized and condensed to fit inside the nucleus, which is accomplished by wrapping the DNA around proteins called histones.

Ribosomes

Ribosomes found in eukaryotic organelles such as mitochondria or chloroplasts have 70S ribosomes—the same size as prokaryotic ribosomes. However, nonorganelle-associated ribosomes in eukaryotic cells are 80S ribosomes, composed of a 40S small subunit and a 60S large subunit. In terms of size and composition, this makes them distinct from the ribosomes of prokaryotic cells.

Endomembrane System

The endomembrane system, unique to eukaryotic cells, is a series of membranous tubules, sacs, and flattened disks that synthesize many cell components and move materials around within the cell ([link]). Because of their larger cell size, eukaryotic cells require this system to transport materials that cannot be dispersed by diffusion alone. The endomembrane system comprises several organelles and connections between them, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles.

Peroxisomes

Christian de Duve is also credited with the discovery of peroxisomes, membrane-bound organelles that are not part of the endomembrane system ([link]). Peroxisomes form independently in the cytoplasm from the synthesis of peroxin proteins by free ribosomes and the incorporation of these peroxin proteins into existing peroxisomes. Growing peroxisomes then divide by a process similar to binary fission.

Cytoskeleton

Eukaryotic cells have an internal cytoskeleton made of microfilaments, intermediate filaments, and microtubules. This matrix of fibers and tubes provides structural support as well as a network over which materials can be transported within the cell and on which organelles can be anchored ([link]). For example, the process of exocytosis involves the movement of a vesicle via the cytoskeletal network to the plasma membrane, where it can release its contents.

Mitochondria

The large, complex organelles in which aerobic cellular respiration occurs in eukaryotic cells are called mitochondria ([link]). The term “mitochondrion” was first coined by German microbiologist Carl Benda in 1898 and was later connected with the process of respiration by Otto Warburg in 1913. Scientists during the 1960s discovered that mitochondria have their own genome and 70S ribosomes. The mitochondrial genome was found to be bacterial, when it was sequenced in 1976. These findings ultimately supported the endosymbiotic theory proposed by Lynn Margulis, which states that mitochondria originally arose through an endosymbiotic event in which a bacterium capable of aerobic cellular respiration was taken up by phagocytosis into a host cell and remained as a viable intracellular component.

Chloroplasts

Plant cells and algal cells contain chloroplasts, the organelles in which photosynthesis occurs ([link]). All chloroplasts have at least three membrane systems: the outer membrane, the inner membrane, and the thylakoid membrane system. Inside the outer and inner membranes is the chloroplast stroma, a gel-like fluid that makes up much of a chloroplast’s volume, and in which the thylakoid system floats. The thylakoid system is a highly dynamic collection of folded membrane sacs. It is where the green photosynthetic pigment chlorophyll is found and the light reactions of photosynthesis occur. In most plant chloroplasts, the thylakoids are arranged in stacks called grana (singular: granum), whereas in some algal chloroplasts, the thylakoids are free floating.

Plasma Membrane

The plasma membrane of eukaryotic cells is similar in structure to the prokaryotic plasma membrane in that it is composed mainly of phospholipids forming a bilayer with embedded peripheral and integral proteins ([link]). These membrane components move within the plane of the membrane according to the fluid mosaic model. However, unlike the prokaryotic membrane, eukaryotic membranes contain sterols, including cholesterol, that alter membrane fluidity. Additionally, many eukaryotic cells contain some specialized lipids, including sphingolipids, which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell-to-cell communication.

Cell Wall

In addition to a plasma membrane, some eukaryotic cells have a cell wall. Cells of fungi, algae, plants, and even some protists have cell walls. Depending upon the type of eukaryotic cell, cell walls can be made of a wide range of materials, including cellulose (fungi and plants); biogenic silica, calcium carbonate, agar, and carrageenan (protists and algae); or chitin (fungi). In general, all cell walls provide structural stability for the cell and protection from environmental stresses such as desiccation, changes in osmotic pressure, and traumatic injury.[footnote]

M. Dudzick. “Protists.” OpenStax CNX. November 27, 2013. http://cnx.org/contents/f7048bb6-e462-459b-805c-ef291cf7049c@1

Extracellular Matrix

Cells of animals and some protozoans do not have cell walls to help maintain shape and provide structural stability. Instead, these types of eukaryotic cells produce an extracellular matrix for this purpose. They secrete a sticky mass of carbohydrates and proteins into the spaces between adjacent cells ([link]). Some protein components assemble into a basement membrane to which the remaining extracellular matrix components adhere. Proteoglycans typically form the bulky mass of the extracellular matrix while fibrous proteins, like collagen, provide strength. Both proteoglycans and collagen are attached to fibronectin proteins, which, in turn, are attached to integrin proteins. These integrin proteins interact with transmembrane proteins in the plasma membranes of eukaryotic cells that lack cell walls.

Flagella and Cilia

Some eukaryotic cells use flagella for locomotion; however, eukaryotic flagella are structurally distinct from those found in prokaryotic cells. Whereas the prokaryotic flagellum is a stiff, rotating structure, a eukaryotic flagellum is more like a flexible whip composed of nine parallel pairs of microtubules surrounding a central pair of microtubules. This arrangement is referred to as a 9+2 array ([link]). The parallel microtubules use dynein motor proteins to move relative to each other, causing the flagellum to bend.

Prokaryotic Diversity

Introduction

Prokaryote Habitats, Relationships, and Microbiomes

Prokaryote Habitats and Functions

Prokaryotes are ubiquitous. They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water. One bacterium, *Paracoccus denitrificans*, has even been shown to survive when scientists removed it from its native environment (soil) and centrifuged it to 2.4 g, equivalent to the gravitational force on the surface of Jupiter.

Symbiotic Relationships

As we have learned, prokaryotic microorganisms can associate with plants and animals. Often, this association results in unique relationships between organisms. For example, bacteria living on the roots or leaves of a plant get nutrients from the plant and, in return, produce substances that protect the plant from pathogens. On the other hand, some bacteria are plant pathogens that use mechanisms of infection similar to bacterial pathogens of animals and humans.

Taxonomy and Systematics

Assigning prokaryotes to a certain species is challenging. They do not reproduce sexually, so it is not possible to classify them according to the presence or absence of interbreeding. Also, they do not have many morphological features. Traditionally, the classification of prokaryotes was based on their shape, staining patterns, and biochemical or physiological differences. More recently, as technology has improved, the nucleotide sequences in genes have become an important criterion of microbial classification.

Proteobacteria

Alphaproteobacteria

The first class of Proteobacteria is the Alphaproteobacteria, many of which are obligate or facultative intracellular bacteria. Some species are characterized as oligotrophs, organisms capable of living in low-nutrient environments such as deep oceanic sediments, glacial ice, or deep undersurface soil.

Betaproteobacteria

Betaproteobacteria are a diverse group of bacteria. The different bacterial species within this group utilize a wide range of metabolic strategies and can survive in a range of environments. Some genera include species that are human pathogens, able to cause severe, sometimes life-threatening disease. The genus *Neisseria*, for example, includes the bacteria *N. gonorrhoeae,* the causative agent of the STI gonorrhea, and *N. meningitides*, the causative agent of bacterial meningitis.

Gammaproteobacteria

The most diverse class of gram-negative bacteria is Gammaproteobacteria, and it includes a number of human pathogens. For example, a large and diverse family, *Pseudomonaceae*, includes the genus *Pseudomonas*. Within this genus is the species *P. aeruginosa*, a pathogen responsible for diverse infections in various regions of the body. *P. aeruginosa* is a strictly aerobic, nonfermenting, highly motile bacterium. It often infects wounds and burns, can be the cause of chronic urinary tract infections, and can be an important cause of respiratory infections in patients with cystic fibrosis or patients on mechanical ventilators. Infections by *P. aeruginosa* are often difficult to treat because the bacterium is resistant to many antibiotics and has a remarkable ability to form biofilms. Other representatives of *Pseudomonas* include the fluorescent (glowing) bacterium *P. fluorescens* and the soil bacteria *P. putida*, which is known for its ability to degrade xenobiotics (substances not naturally produced or found in living organisms).

Deltaproteobacteria

The Deltaproteobacteria is a small class of gram-negative Proteobacteria that includes sulfate-reducing bacteria (SRBs), so named because they use sulfate as the final electron acceptor in the electron transport chain. Few SRBs are pathogenic. However, the SRB *Desulfovibrio orale* is associated with periodontal disease (disease of the gums).

Epsilonproteobacteria

The smallest class of Proteobacteria is Epsilonproteobacteria, which are gram-negative microaerophilic bacteria (meaning they only require small amounts of oxygen in their environment). Two clinically relevant genera of Epsilonproteobacteria are *Campylobacter* and *Helicobacter*, both of which include human pathogens. *Campylobacter* can cause food poisoning that manifests as severe enteritis (inflammation in the small intestine). This condition, caused by the species *C. jejuni*, is rather common in developed countries, usually because of eating contaminated poultry products. Chickens often harbor *C. jejuni* in their gastrointestinal tract and feces, and their meat can become contaminated during processing.

Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria

Chlamydia

*C. trachomatis* is a human pathogen that causes trachoma, a disease of the eyes, often leading to blindness. *C. trachomatis* also causes the sexually transmitted disease lymphogranuloma venereum (LGV). This disease is often mildly symptomatic, manifesting as regional lymph node swelling, or it may be asymptomatic, but it is extremely contagious and is common on college campuses.

Spirochetes

Spirochetes are characterized by their long (up to 250 μm), spiral-shaped bodies. Most spirochetes are also very thin, which makes it difficult to examine gram-stained preparations under a conventional brightfield microscope. Darkfield fluorescent microscopy is typically used instead. Spirochetes are also difficult or even impossible to culture. They are highly motile, using their axial filament to propel themselves. The axial filament is similar to a flagellum, but it wraps around the cell and runs inside the cell body of a spirochete in the periplasmic space between the outer membrane and the plasma membrane ([link]).

*Cytophaga*, *Fusobacterium*, and *Bacteroides*

The gram-negative nonproteobacteria of the genera *Cytophaga*, *Fusobacterium*, and *Bacteroides* are classified together as a phylum and called the CFB group. Although they are phylogenetically diverse, bacteria of the CFB group share some similarities in the sequence of nucleotides in their DNA. They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals. CFB bacteria are avid fermenters, able to process cellulose in rumen, thus enabling ruminant animals to obtain carbon and energy from grazing.

Planctomycetes

The Planctomycetes are found in aquatic environments, inhabiting freshwater, saltwater, and brackish water. Planctomycetes are unusual in that they reproduce by budding, meaning that instead of one maternal cell splitting into two equal daughter cells in the process of binary fission, the mother cell forms a bud that detaches from the mother cell and lives as an independent cell. These so-called swarmer cells are motile and not attached to a surface. However, they will soon differentiate into sessile (immobile) cells with an appendage called a holdfast that allows them to attach to surfaces in the water ([link]). Only the sessile cells are able to reproduce.

Phototrophic Bacteria

The phototrophic bacteria are a large and diverse category of bacteria that do not represent a taxon but, rather, a group of bacteria that use sunlight as their primary source of energy. This group contains both Proteobacteria and nonproteobacteria. They use solar energy to synthesize ATP through photosynthesis. When they produce oxygen, they perform oxygenic photosynthesis. When they do not produce oxygen, they perform anoxygenic photosynthesis. With the exception of some cyanobacteria, the majority of phototrophic bacteria perform anoxygenic photosynthesis.

Gram-Positive Bacteria

Actinobacteria: High G+C Gram-Positive Bacteria

The name Actinobacteria comes from the Greek words for *rays* and *small rod*, but Actinobacteria are very diverse. Their microscopic appearance can range from thin filamentous branching rods to coccobacilli. Some Actinobacteria are very large and complex, whereas others are among the smallest independently living organisms. Most Actinobacteria live in the soil, but some are aquatic. The vast majority are aerobic. One distinctive feature of this group is the presence of several different peptidoglycans in the cell wall.

Low G+C Gram-positive Bacteria

The low G+C gram-positive bacteria have less than 50% guanine and cytosine in their DNA, and this group of bacteria includes a number of genera of bacteria that are pathogenic.

Deeply Branching Bacteria

Archaea

Crenarchaeota

Crenarchaeota is a class of Archaea that is extremely diverse, containing genera and species that differ vastly in their morphology and requirements for growth. All Crenarchaeota are aquatic organisms, and they are thought to be the most abundant microorganisms in the oceans. Most, but not all, Crenarchaeota are hyperthermophiles; some of them (notably, the genus *Pyrolobus*) are able to grow at temperatures up to 113 °C.[footnote]

E. Blochl et al.“*Pyrolobus fumani*, gen. and sp. nov., represents a novel group of Archaea, extending the upper temperature limit for life to 113°C.” *Extremophiles* 1 (1997):14–21.

Euryarchaeota

The phylum Euryarchaeota includes several distinct classes. Species in the classes Methanobacteria, Methanococci, and Methanomicrobia represent Archaea that can be generally described as methanogens. Methanogens are unique in that they can reduce carbon dioxide in the presence of hydrogen, producing methane. They can live in the most extreme environments and can reproduce at temperatures varying from below freezing to boiling. Methanogens have been found in hot springs as well as deep under ice in Greenland. Methanogens also produce gases in ruminants and humans. Some scientists have even hypothesized that methanogen**s** may inhabit the planet Mars because the mixture of gases produced by methanogens resembles the makeup of the Martian atmosphere.[footnote]

R.R. Britt “Crater Critters: Where Mars Microbes Might Lurk.” http://www.space.com/1880-crater-critters-mars-microbes-lurk.html. Accessed April 7, 2015.

The Eukaryotes of Microbiology

Introduction

Unicellular Eukaryotic Parasites

Characteristics of Protists

The word *protist* is a historical term that is now used informally to refer to a diverse group of microscopic eukaryotic organisms. It is not considered a formal taxonomic term because the organisms it describes do not have a shared evolutionary origin. Historically, the protists were informally grouped into the “animal-like” protozoans, the “plant-like” algae, and the “fungus-like” protists such as water molds. These three groups of protists differ greatly in terms of their basic characteristics. For example, algae are photosynthetic organisms that can be unicellular or multicellular. Protozoa, on the other hand, are nonphotosynthetic, motile organisms that are always unicellular. Other informal terms may also be used to describe various groups of protists. For example, microorganisms that drift or float in water, moved by currents, are referred to as plankton. Types of plankton include zooplankton, which are motile and nonphotosynthetic, and phytoplankton, which are photosynthetic.

Taxonomy of Protists

The protists are a polyphyletic group, meaning they lack a shared evolutionary origin. Since the current taxonomy is based on evolutionary history (as determined by biochemistry, morphology, and genetics), protists are scattered across many different taxonomic groups within the domain Eukarya. Eukarya is currently divided into six supergroups that are further divided into subgroups, as illustrated in ([link]). In this section, we will primarily be concerned with the supergroups Amoebozoa, Excavata, and Chromalveolata; these supergroups include many protozoans of clinical significance. The supergroups Opisthokonta and Rhizaria also include some protozoans, but few of clinical significance. In addition to protozoans, Opisthokonta also includes animals and fungi, some of which we will discuss in Parasitic Helminths and Fungi. Some examples of the Archaeplastida will be discussed in Algae. [link] and [link] summarize the characteristics of each supergroup and subgroup and list representatives of each.

Parasitic Helminths

Nematoda (Roundworms)

Phylum Nematoda (the roundworms) is a diverse group containing more than 15,000 species, of which several are important human parasites ([link]). These unsegmented worms have a full digestive system even when parasitic. Some are common intestinal parasites, and their eggs can sometimes be identified in feces or around the anus of infected individuals. *Ascaris* *lumbricoides* is the largest nematode intestinal parasite found in humans; females may reach lengths greater than 1 meter. *A.* *lumbricoides* is also very widespread, even in developed nations, although it is now a relatively uncommon problem in the United States. It may cause symptoms ranging from relatively mild (such as a cough and mild abdominal pain) to severe (such as intestinal blockage and impaired growth).

Platyhelminths (Flatworms)

Phylum Platyhelminthes (the platyhelminths) are flatworms. This group includes the flukes, tapeworms, and the turbellarians, which include planarians. The flukes and tapeworms are medically important parasites ([link]).

Fungi

Characteristics of Fungi

Fungi have well-defined characteristics that set them apart from other organisms. Most multicellular fungal bodies, commonly called molds, are made up of filaments called hyphae. Hyphae can form a tangled network called a mycelium and form the thallus (body) of fleshy fungi. Hyphae that have walls between the cells are called septate hyphae; hyphae that lack walls and cell membranes between the cells are called nonseptate or coenocytic hyphae). ([link]).

Fungal Diversity

The fungi are very diverse, comprising seven major groups. Not all of the seven groups contain pathogens. Some of these groups are generally associated with plants and include plant pathogens. For example, Urediniomycetes and Ustilagomycetes include the plant rusts and smuts, respectively. These form reddish or dark masses, respectively, on plants as rusts (red) or smuts (dark). Some species have substantial economic impact because of their ability to reduce crop yields. Glomeromycota includes the mycorrhizal fungi, important symbionts with plant roots that can promote plant growth by acting like an extended root system. The Glomeromycota are obligate symbionts, meaning that they can only survive when associated with plant roots; the fungi receive carbohydrates from the plant and the plant benefits from the increased ability to take up nutrients and minerals from the soil. The Chytridiomycetes (chytrids) are small fungi, but are extremely ecologically important. Chytrids are generally aquatic and have flagellated, motile gametes; specific types are implicated in amphibian declines around the world. Because of their medical importance, we will focus on Zygomycota, Ascomycota, Basidiomycota, and Microsporidia. [link] summarizes the characteristics of these medically important groups of fungi.

Algae

Algal Diversity

Although the algae and protozoa were formerly separated taxonomically, they are now mixed into supergroups. The algae are classified within the Chromalveolata and the Archaeplastida. Although the Euglenozoa (within the supergroup Excavata) include photosynthetic organisms, these are not considered algae because they feed and are motile.

Lichens

Characteristics

A lichen is a combination of two organisms, a green alga or cyanobacterium and fungus, living in a symbiotic relationship. Whereas algae normally grow only in aquatic or extremely moist environments, lichens can potentially be found on almost any surface (especially rocks) or as epiphytes (meaning that they grow on other plants).

Lichen Diversity

Lichens are classified as fungi and the fungal partners belong to the Ascomycota and Basidiomycota. Lichens can also be grouped into types based on their morphology. There are three major types of lichens, although other types exist as well. Lichens that are tightly attached to the substrate, giving them a crusty appearance, are called crustose lichens. Those that have leaf-like lobes are foliose lichens; they may only be attached at one point in the growth form, and they also have a second cortex below the medulla. Finally, fruticose lichens have rounded structures and an overall branched appearance. [link] shows an example of each of the forms of lichens.

Acellular Pathogens

Introduction

Viruses

Hosts and Viral Transmission

Viruses can infect every type of host cell, including those of plants, animals, fungi, protists, bacteria, and archaea. Most viruses will only be able to infect the cells of one or a few species of organism. This is called the host range. However, having a wide host range is not common and viruses will typically only infect specific hosts and only specific cell types within those hosts. The viruses that infect bacteria are called bacteriophage**s**, or simply phages. The word *phage* comes from the Greek word for devour. Other viruses are just identified by their host group, such as animal or plant viruses. Once a cell is infected, the effects of the virus can vary depending on the type of virus. Viruses may cause abnormal growth of the cell or cell death, alter the cell’s genome, or cause little noticeable effect in the cell.

Viral Structures

In general, virions (viral particles) are small and cannot be observed using a regular light microscope. They are much smaller than prokaryotic and eukaryotic cells; this is an adaptation allowing viruses to infect these larger cells (see [link]). The size of a virion can range from 20 nm for small viruses up to 900 nm for typical, large viruses (see [link]). Recent discoveries, however, have identified new giant viral species, such as *Pandoravirus salinus* and *Pithovirus sibericum*, with sizes approaching that of a bacterial cell.[footnote]

N. *Philippe et al. “Pandoraviruses: Amoeba Viruses with Genomes up to 2.5 Mb Reaching that of Parasitic Eukaryotes.” Science 341, no. 6143 (2013): 281–286.*

Classification and Taxonomy of Viruses

Although viruses are not classified in the three domains of life, their numbers are great enough to require classification. Since 1971, the International Union of Microbiological Societies Virology Division has given the task of developing, refining, and maintaining a universal virus taxonomy to the International Committee on Taxonomy of Viruses (ICTV). Since viruses can mutate so quickly, it can be difficult to classify them into a genus and a species epithet using the binomial nomenclature system. Thus, the ICTV’s viral nomenclature system classifies viruses into families and genera based on viral genetics, chemistry, morphology, and mechanism of multiplication. To date, the ICTV has classified known viruses in seven orders, 96 families, and 350 genera. Viral family names end in -*viridae* (e.g, *Parvoviridae*) and genus names end in *−virus* (e.g., *Parvovirus*). The names of viral orders, families, and genera are all italicized. When referring to a viral species, we often use a genus and species epithet such as *Pandoravirus dulcis* or *Pandoravirus salinus.*

The Viral Life Cycle

The Life Cycle of Viruses with Prokaryote Hosts

The life cycle of bacteriophages has been a good model for understanding how viruses affect the cells they infect, since similar processes have been observed for eukaryotic viruses, which can cause immediate death of the cell or establish a latent or chronic infection. Virulent phages typically lead to the death of the cell through cell lysis. Temperate phages, on the other hand, can become part of a host chromosome and are replicated with the cell genome until such time as they are induced to make newly assembled viruses, or progeny virus**es**.

Transduction

Transduction occurs when a bacteriophage transfers bacterial DNA from one bacterium to another during sequential infections. There are two types of transduction: generalized and specialized transduction. During the lytic cycle of viral replication, the virus hijacks the host cell, degrades the host chromosome, and makes more viral genomes. As it assembles and packages DNA into the phage head, packaging occasionally makes a mistake. Instead of packaging viral DNA, it takes a random piece of host DNA and inserts it into the capsid. Once released, this virion will then inject the former host’s DNA into a newly infected host. The asexual transfer of genetic information can allow for DNA recombination to occur, thus providing the new host with new genes (e.g., an antibiotic-resistance gene, or a sugar-metabolizing gene). Generalized transduction occurs when a random piece of bacterial chromosomal DNA is transferred by the phage during the lytic cycle. Specialized transduction occurs at the end of the lysogenic cycle, when the prophage is excised and the bacteriophage enters the lytic cycle. Since the phage is integrated into the host genome, the prophage can replicate as part of the host. However, some conditions (e.g., ultraviolet light exposure or chemical exposure) stimulate the prophage to undergo induction, causing the phage to excise from the genome, enter the lytic cycle, and produce new phages to leave host cells. During the process of excision from the host chromosome, a phage may occasionally remove some bacterial DNA near the site of viral integration. The phage and host DNA from one end or both ends of the integration site are packaged within the capsid and are transferred to the new, infected host. Since the DNA transferred by the phage is not randomly packaged but is instead a specific piece of DNA near the site of integration, this mechanism of gene transfer is referred to as specialized transduction (see [link]). The DNA can then recombine with host chromosome, giving the latter new characteristics. Transduction seems to play an important role in the evolutionary process of bacteria, giving them a mechanism for asexual exchange of genetic information.

Life Cycle of Viruses with Animal Hosts

Lytic animal viruses follow similar infection stages to bacteriophages: attachment, penetration, biosynthesis, maturation, and release (see [link]). However, the mechanisms of penetration, nucleic-acid biosynthesis, and release differ between bacterial and animal viruses. After binding to host receptors, animal viruses enter through endocytosis (engulfment by the host cell) or through membrane fusion (viral envelope with the host cell membrane). Many viruses are host specific, meaning they only infect a certain type of host; and most viruses only infect certain types of cells within tissues. This specificity is called a tissue tropism. Examples of this are demonstrated by the poliovirus, which exhibits tropism for the tissues of the brain and spinal cord, or the influenza virus, which has a primary tropism for the respiratory tract.

Persistent Infections

Persistent infection occurs when a virus is not completely cleared from the system of the host but stays in certain tissues or organs of the infected person. The virus may remain silent or undergo productive infection without seriously harming or killing the host. Mechanisms of persistent infection may involve the regulation of the viral or host gene expressions or the alteration of the host immune response. The two primary categories of persistent infections are latent infection and chronic infection. Examples of viruses that cause latent infections include herpes simplex virus (oral and genital herpes), varicella-zoster virus (chickenpox and shingles), and Epstein-Barr virus (mononucleosis). Hepatitis C virus and HIV are two examples of viruses that cause long-term chronic infections.

Life Cycle of Viruses with Plant Hosts

Plant viruses are more similar to animal viruses than they are to bacteriophages. Plant viruses may be enveloped or non-enveloped. Like many animal viruses, plant viruses can have either a DNA or RNA genome and be single stranded or double stranded. However, most plant viruses do not have a DNA genome; the majority have a +ssRNA genome, which acts like messenger RNA (mRNA). Only a minority of plant viruses have other types of genomes.

Viral Growth Curve

Unlike the growth curve for a bacterial population, the growth curve for a virus population over its life cycle does not follow a sigmoidal curve. During the initial stage, an inoculum of virus causes infection. In the eclipse phase, viruses bind and penetrate the cells with no virions detected in the medium. The chief difference that next appears in the viral growth curve compared to a bacterial growth curve occurs when virions are released from the lysed host cell at the same time. Such an occurrence is called a burst, and the number of virions per bacterium released is described as the burst size. In a one-step multiplication curve for bacteriophage, the host cells lyse, releasing many viral particles to the medium, which leads to a very steep rise in viral titer (the number of virions per unit volume). If no viable host cells remain, the viral particles begin to degrade during the decline of the culture (see [link]).

Isolation, Culture, and Identification of Viruses

Isolation of Viruses

Unlike bacteria, many of which can be grown on an artificial nutrient medium, viruses require a living host cell for replication. Infected host cells (eukaryotic or prokaryotic) can be cultured and grown, and then the growth medium can be harvested as a source of virus. Virions in the liquid medium can be separated from the host cells by either centrifugation or filtration. Filters can physically remove anything present in the solution that is larger than the virions; the viruses can then be collected in the filtrate (see [link]).

Cultivation of Viruses

Viruses can be grown in vivo (within a whole living organism, plant, or animal) or in vitro (outside a living organism in cells in an artificial environment. Flat horizontal cell culture flasks (see [link]**(a)**) are a common vessel used for in vitro work. Bacteriophages can be grown in the presence of a dense layer of bacteria (also called a bacterial lawn) grown in a 0.7 % soft agar in a Petri dish or flat (horizontal) flask (see [link]**(b)**). As the phage kills the bacteria, many plaques are observed among the cloudy bacterial lawn.

Detection of a Virus

Regardless of the method of cultivation, once a virus has been introduced into a whole host organism, embryo, or tissue-culture cell, a sample can be prepared from the infected host, embryo, or cell line for further analysis under a brightfield, electron, or fluorescent microscope. Cytopathic effects (CPEs) are distinct observable cell abnormalities due to viral infection. CPEs can include loss of adherence to the surface of the container, changes in cell shape from flat to round, shrinkage of the nucleus, vacuoles in the cytoplasm, fusion of cytoplasmic membranes and the formation of multinucleated syncytia, inclusion bodies in the nucleus or cytoplasm, and complete cell lysis (see [link]).

Viroids, Virusoids, and Prions

Viroids

In 1971, Theodor Diener, a pathologist working at the Agriculture Research Service, discovered an acellular particle that he named a viroid, meaning “virus-like.” Viroids consist only of a short strand of circular RNA capable of self-replication. The first viroid discovered was found to cause potato tuber spindle disease, which causes slower sprouting and various deformities in potato plants (see [link]). Like viruses, potato spindle tuber viroids (PSTVs) take control of the host machinery to replicate their RNA genome. Unlike viruses, viroids do not have a protein coat to protect their genetic information.

Virusoids

A second type of pathogenic RNA that can infect commercially important agricultural crops are the virusoid**s**, which are subviral particles best described as non–self-replicating ssRNAs. RNA replication of virusoids is similar to that of viroids but, unlike viroids, virusoids require that the cell also be infected with a specific “helper” virus. There are currently only five described types of virusoids and their associated helper viruses. The helper viruses are all from the family of Sobemoviruses. An example of a helper virus is the subterranean clover mottle virus, which has an associated virusoid packaged inside the viral capsid. Once the helper virus enters the host cell, the virusoids are released and can be found free in plant cell cytoplasm, where they possess ribozyme activity. The helper virus undergoes typical viral replication independent of the activity of the virusoid. The virusoid genomes are small, only 220 to 388 nucleotides long. A virusoid genome does not code for any proteins, but instead serves only to replicate virusoid RNA.

Prions

At one time, scientists believed that any infectious particle must contain DNA or RNA. Then, in 1982, Stanley Prusiner, a medical doctor studying scrapie (a fatal, degenerative disease in sheep) discovered that the disease was caused by proteinaceous infectious particles, or prion**s**. Because proteins are acellular and do not contain DNA or RNA, Prusiner’s findings were originally met with resistance and skepticism; however, his research was eventually validated, and he received the Nobel Prize in Physiology or Medicine in 1997.

Microbial Biochemistry

Introduction

Organic Molecules

Elements in Living Cells

The most abundant element in cells is hydrogen (H), followed by carbon (C), oxygen (O), nitrogen (N), phosphorous (P), and sulfur (S). We call these elements macronutrient**s**, and they account for about 99% of the dry weight of cells. Some elements, such as sodium (Na), potassium (K), magnesium (Mg), zinc (Zn), iron (Fe), calcium (Ca), molybdenum (Mo), copper (Cu), cobalt (Co), manganese (Mn), or vanadium (V), are required by some cells in very small amounts and are called micronutrient**s** or trace element**s**. All of these elements are essential to the function of many biochemical reactions, and, therefore, are essential to life.

Organic Molecules and Isomerism

Organic molecules in organisms are generally larger and more complex than inorganic molecules. Their carbon skeletons are held together by covalent bonds. They form the cells of an organism and perform the chemical reactions that facilitate life. All of these molecules, called biomolecule**s** because they are part of living matter, contain carbon, which is the building block of life. Carbon is a very unique element in that it has four valence electrons in its outer orbitals and can form four single covalent bonds with up to four other atoms at the same time (see Appendix A). These atoms are usually oxygen, hydrogen, nitrogen, sulfur, phosphorous, and carbon itself; the simplest organic compound is methane, in which carbon binds only to hydrogen ([link]).

Biologically Significant Functional Groups

In addition to containing carbon atoms, biomolecules also contain functional groups—groups of atoms within molecules that are categorized by their specific chemical composition and the chemical reactions they perform, regardless of the molecule in which the group is found. Some of the most common functional groups are listed in [link]. In the formulas, the symbol R stands for “residue” and represents the remainder of the molecule. R might symbolize just a single hydrogen atom or it may represent a group of many atoms. Notice that some functional groups are relatively simple, consisting of just one or two atoms, while some comprise two of these simpler functional groups. For example, a carbonyl group is a functional group composed of a carbon atom double bonded to an oxygen atom: C=O. It is present in several classes of organic compounds as part of larger functional groups such as ketones, aldehydes, carboxylic acids, and amides. In ketones, the carbonyl is present as an internal group, whereas in aldehydes it is a terminal group.

Macromolecules

Carbon chains form the skeletons of most organic molecules. Functional groups combine with the chain to form biomolecules. Because these biomolecules are typically large, we call them macromolecules. Many biologically relevant macromolecules are formed by linking together a great number of identical, or very similar, smaller organic molecules. The smaller molecules act as building blocks and are called monomer**s**, and the macromolecules that result from their linkage are called polymer**s**. Cells and cell structures include four main groups of carbon-containing macromolecules: polysaccharides, proteins, lipids, and nucleic acids. The first three groups of molecules will be studied throughout this chapter. The biochemistry of nucleic acids will be discussed in Biochemistry of the Genome.

Carbohydrates

Monosaccharides: The Sweet Ones

In biochemistry, carbohydrates are often called saccharide**s**, from the Greek *sakcharon*, meaning sugar, although not all the saccharides are sweet. The simplest carbohydrates are called monosaccharide**s**, or simple sugars. They are the building blocks (monomers) for the synthesis of polymers or complex carbohydrates, as will be discussed further in this section. Monosaccharides are classified based on the number of carbons in the molecule. General categories are identified using a prefix that indicates the number of carbons and the suffix –*ose*, which indicates a saccharide; for example, triose (three carbons), tetrose (four carbons), pentose (five carbons), and hexose (six carbons) ([link]). The hexose D-glucose is the most abundant monosaccharide in nature. Other very common and abundant hexose monosaccharides are galactose, used to make the disaccharide milk sugar lactose, and the fruit sugar fructose.

Disaccharides

Two monosaccharide molecules may chemically bond to form a disaccharide. The name given to the covalent bond between the two monosaccharides is a glycosidic bond. Glycosidic bonds form between hydroxyl groups of the two saccharide molecules, an example of the dehydration synthesis described in the previous section of this chapter:

Polysaccharides

Polysaccharides, also called glycans, are large polymers composed of hundreds of monosaccharide monomers. Unlike mono- and disaccharides, polysaccharides are not sweet and, in general, they are not soluble in water. Like disaccharides, the monomeric units of polysaccharides are linked together by glycosidic bonds.

Lipids

Fatty Acids and Triacylglycerides

The fatty acids are lipids that contain long-chain hydrocarbons terminated with a carboxylic acid functional group. Because the long hydrocarbon chain, fatty acids are hydrophobic (“water fearing”) or nonpolar. Fatty acids with hydrocarbon chains that contain only single bonds are called saturated fatty acids because they have the greatest number of hydrogen atoms possible and are, therefore, “saturated” with hydrogen. Fatty acids with hydrocarbon chains containing at least one double bond are called unsaturated fatty acids because they have fewer hydrogen atoms. Saturated fatty acids have a straight, flexible carbon backbone, whereas unsaturated fatty acids have “kinks” in their carbon skeleton because each double bond causes a rigid bend of the carbon skeleton. These differences in saturated versus unsaturated fatty acid structure result in different properties for the corresponding lipids in which the fatty acids are incorporated. For example, lipids containing saturated fatty acids are solids at room temperature, whereas lipids containing unsaturated fatty acids are liquids.

Phospholipids and Biological Membranes

Triglycerides are classified as simple lipids because they are formed from just two types of compounds: glycerol and fatty acids. In contrast, complex lipids contain at least one additional component, for example, a phosphate group (phospholipid**s**) or a carbohydrate moiety (glycolipid**s**). [link] depicts a typical phospholipid composed of two fatty acids linked to glycerol (a diglyceride). The two fatty acid carbon chains may be both saturated, both unsaturated, or one of each. Instead of another fatty acid molecule (as for triglycerides), the third binding position on the glycerol molecule is occupied by a modified phosphate group.

Isoprenoids and Sterols

The isoprenoids are branched lipids, also referred to as terpenoids, that are formed by chemical modifications of the isoprene molecule ([link]). These lipids play a wide variety of physiological roles in plants and animals, with many technological uses as pharmaceuticals (capsaicin), pigments (e.g., orange beta carotene, xanthophylls), and fragrances (e.g., menthol, camphor, limonene [lemon fragrance], and pinene [pine fragrance]). Long-chain isoprenoids are also found in hydrophobic oils and waxes. Waxes are typically water resistant and hard at room temperature, but they soften when heated and liquefy if warmed adequately. In humans, the main wax production occurs within the sebaceous glands of hair follicles in the skin, resulting in a secreted material called sebum, which consists mainly of triacylglycerol, wax esters, and the hydrocarbon squalene. There are many bacteria in the microbiota on the skin that feed on these lipids. One of the most prominent bacteria that feed on lipids is *Propionibacterium acnes*, which uses the skin’s lipids to generate short-chain fatty acids and is involved in the production of acne.

Proteins

Amino Acids and Peptide Bonds

An amino acid is an organic molecule in which a hydrogen atom, a carboxyl group (–COOH), and an amino group (–NH2) are all bonded to the same carbon atom, the so-called α carbon. The fourth group bonded to the α carbon varies among the different amino acids and is called a residue or a side chain, represented in structural formulas by the letter *R*. A residue is a monomer that results when two or more amino acids combine and remove water molecules. The primary structure of a protein, a peptide chain, is made of amino acid residues. The unique characteristics of the functional groups and *R* groups allow these components of the amino acids to form hydrogen, ionic, and disulfide bonds, along with polar/nonpolar interactions needed to form secondary, tertiary, and quaternary protein structures. These groups are composed primarily of carbon, hydrogen, oxygen, nitrogen, and sulfur, in the form of hydrocarbons, acids, amides, alcohols, and amines. A few examples illustrating these possibilities are provided in [link].

Protein Structure

The size (length) and specific amino acid sequence of a protein are major determinants of its shape, and the shape of a protein is critical to its function. For example, in the process of biological nitrogen fixation (see Biogeochemical Cycles), soil microorganisms collectively known as rhizobia symbiotically interact with roots of legume plants such as soybeans, peanuts, or beans to form a novel structure called a nodule on the plant roots. The plant then produces a carrier protein called leghemoglobin, a protein that carries nitrogen or oxygen. Leghemoglobin binds with a very high affinity to its substrate oxygen at a specific region of the protein where the shape and amino acid sequence are appropriate (the active site). If the shape or chemical environment of the active site is altered, even slightly, the substrate may not be able to bind as strongly, or it may not bind at all. Thus, for the protein to be fully active, it must have the appropriate shape for its function.

Using Biochemistry to Identify Microorganisms

Microbial Metabolism

Introduction

Energy, Matter, and Enzymes

Classification by Carbon and Energy Source

Organisms can be identified according to the source of carbon they use for metabolism as well as their energy source. The prefixes auto- (“self”) and hetero- (“other”) refer to the origins of the carbon sources various organisms can use. Organisms that convert inorganic carbon dioxide (CO2) into organic carbon compounds are autotroph**s**. Plants and cyanobacteria are well-known examples of autotrophs. Conversely, heterotroph**s** rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. Many organisms, ranging from humans to many prokaryotes, including the well-studied *Escherichia coli*, are heterotrophic.

Oxidation and Reduction in Metabolism

The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy incrementally; that is, in small packages rather than a single, destructive burst. Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reaction**s**; those that add electrons to acceptor molecules, leaving them reduced, are reduction reaction**s**. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions, or redox reaction**s**.

Energy Carriers: NAD+, NADP+, FAD, and ATP

The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carrier**s**, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides; they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide. These compounds can be easily reduced or oxidized. Nicotinamide adenine dinucleotide (NAD+/NADH) is the most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule. Nicotine adenine dinucleotide phosphate (NADP+), the oxidized form of an NAD+ variant that contains an extra phosphate group, is another important electron carrier; it forms NADPH when reduced. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2. Both NAD+/NADH and FAD/FADH2 are extensively used in energy extraction from sugars during catabolism in chemoheterotrophs, whereas NADP+/NADPH plays an important role in anabolic reactions and photosynthesis. Collectively, FADH2, NADH, and NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reactions.

Enzyme Structure and Function

A substance that helps speed up a chemical reaction is a catalyst. Catalysts are not used or changed during chemical reactions and, therefore, are reusable. Whereas inorganic molecules may serve as catalysts for a wide range of chemical reactions, proteins called enzymes serve as catalysts for biochemical reactions inside cells. Enzymes thus play an important role in controlling cellular metabolism.

Enzyme Inhibitors

Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so ([link]). A competitive inhibitor is a molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding. For a competitive inhibitor to be effective, the inhibitor concentration needs to be approximately equal to the substrate concentration. Sulfa drugs provide a good example of competitive competition. They are used to treat bacterial infections because they bind to the active site of an enzyme within the bacterial folic acid synthesis pathway. When present in a sufficient dose, a sulfa drug prevents folic acid synthesis, and bacteria are unable to grow because they cannot synthesize DNA, RNA, and proteins. Humans are unaffected because we obtain folic acid from our diets.

Catabolism of Carbohydrates

Glycolysis

For bacteria, eukaryotes, and most archaea, glycolysis is the most common pathway for the catabolism of glucose; it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism. Every living organism carries out some form of glycolysis, suggesting this mechanism is an ancient universal metabolic process. The process itself does not use oxygen; however, glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic. Glycolysis takes place in the cytoplasm of prokaryotic and eukaryotic cells. It begins with a single six-carbon glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Pyruvate may be broken down further after glycolysis to harness more energy through aerobic or anaerobic respiration, but many organisms, including many microbes, may be unable to respire; for these organisms, glycolysis may be their only source of generating ATP.

Other Glycolytic Pathways

When we refer to glycolysis, unless otherwise indicated, we are referring to the EMP pathway used by animals and many bacteria. However, some prokaryotes use alternative glycolytic pathways. One important alternative is the Entner-Doudoroff (ED) pathway, named after its discoverers Nathan Entner and Michael Doudoroff (1911–1975). Although some bacteria, including the opportunistic gram-negative pathogen *Pseudomonas aeruginosa*, contain only the ED pathway for glycolysis, other bacteria, like *E. coli*, have the ability to use either the ED pathway or the EMP pathway.

Transition Reaction, Coenzyme A, and the Krebs Cycle

Glycolysis produces pyruvate, which can be further oxidized to capture more energy. For pyruvate to enter the next oxidative pathway, it must first be decarboxylated by the enzyme complex pyruvate dehydrogenase to a two-carbon acetyl group in the transition reaction, also called the bridge reaction (see Appendix C and [link]). In the transition reaction, electrons are also transferred to NAD+ to form NADH. To proceed to the next phase of this metabolic process, the comparatively tiny two-carbon acetyl must be attached to a very large carrier compound called coenzyme A (CoA). The transition reaction occurs in the mitochondrial matrix of eukaryotes; in prokaryotes, it occurs in the cytoplasm because prokaryotes lack membrane-enclosed organelles.

Cellular Respiration

Electron Transport System

The electron transport system (ETS) is the last component involved in the process of cellular respiration; it comprises a series of membrane-associated protein complexes and associated mobile accessory electron carriers ([link]). Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons from NADH and FADH2 are passed rapidly from one ETS electron carrier to the next. These carriers can pass electrons along in the ETS because of their redox potential. For a protein or chemical to accept electrons, it must have a more positive redox potential than the electron donor. Therefore, electrons move from electron carriers with more negative redox potential to those with more positive redox potential. The four major classes of electron carriers involved in both eukaryotic and prokaryotic electron transport systems are the cytochromes, flavoproteins, iron-sulfur proteins, and the quinones.

Chemiosmosis, Proton Motive Force, and Oxidative Phosphorylation

In each transfer of an electron through the ETS, the electron loses energy, but with some transfers, the energy is stored as potential energy by using it to pump hydrogen ions (H+) across a membrane. In prokaryotic cells, H+ is pumped to the outside of the cytoplasmic membrane (called the periplasmic space in gram-negative and gram-positive bacteria), and in eukaryotic cells, they are pumped from the mitochondrial matrix across the inner mitochondrial membrane into the intermembrane space. There is an uneven distribution of H+ across the membrane that establishes an electrochemical gradient because H+ ions are positively charged (electrical) and there is a higher concentration (chemical) on one side of the membrane. This electrochemical gradient formed by the accumulation of H+ (also known as a proton) on one side of the membrane compared with the other is referred to as the proton motive force (PMF). Because the ions involved are H+, a pH gradient is also established, with the side of the membrane having the higher concentration of H+ being more acidic. Beyond the use of the PMF to make ATP, as discussed in this chapter, the PMF can also be used to drive other energetically unfavorable processes, including nutrient transport and flagella rotation for motility.

Fermentation

Catabolism of Lipids and Proteins

Lipid Catabolism

Triglycerides are a form of long-term energy storage in animals. They are made of glycerol and three fatty acids (see [link]). Phospholipids compose the cell and organelle membranes of all organisms except the archaea. Phospholipid structure is similar to triglycerides except that one of the fatty acids is replaced by a phosphorylated head group (see [link]). Triglycerides and phospholipids are broken down first by releasing fatty acid chains (and/or the phosphorylated head group, in the case of phospholipids) from the three-carbon glycerol backbone. The reactions breaking down triglycerides are catalyzed by lipases and those involving phospholipids are catalyzed by phospholipases. These enzymes contribute to the virulence of certain microbes, such as the bacterium *Staphylococcus aureus* and the fungus *Cryptococcus neoformans*. These microbes use phospholipases to destroy lipids and phospholipids in host cells and then use the catabolic products for energy (see Virulence Factors of Bacterial and Viral Pathogens).

Protein Catabolism

Proteins are degraded through the concerted action of a variety of microbial protease enzymes. Extracellular proteases cut proteins internally at specific amino acid sequences, breaking them down into smaller peptides that can then be taken up by cells. Some clinically important pathogens can be identified by their ability to produce a specific type of extracellular protease. For example, the production of the extracellular protease gelatinase by members of the genera *Proteus* and *Serratia* can be used to distinguish them from other gram-negative enteric bacteria. Following inoculation and growth of microbes in gelatin broth, degradation of the gelatin protein due to gelatinase production prevents solidification of gelatin when refrigerated. Other pathogens can be distinguished by their ability to degrade casein, the main protein found in milk. When grown on skim milk agar, production of the extracellular protease caseinase causes degradation of casein, which appears as a zone of clearing around the microbial growth. Caseinase production by the opportunist pathogen *Pseudomonas aeruginosa* can be used to distinguish it from other related gram-negative bacteria.

Photosynthesis

Photosynthetic Structures in Eukaryotes and Prokaryotes

In all phototrophic eukaryotes, photosynthesis takes place inside a chloroplast, an organelle that arose in eukaryotes by endosymbiosis of a photosynthetic bacterium (see Unique Characteristics of Eukaryotic Cells). These chloroplasts are enclosed by a double membrane with inner and outer layers. Within the chloroplast is a third membrane that forms stacked, disc-shaped photosynthetic structures called thylakoids ([link]). A stack of thylakoids is called a granum, and the space surrounding the granum within the chloroplast is called stroma.

Oxygenic and Anoxygenic Photosynthesis

For photosynthesis to continue, the electron lost from the reaction center pigment must be replaced. The source of this electron (H2A) differentiates the oxygenic photosynthesis of plants and cyanobacteria from anoxygenic photosynthesis carried out by other types of bacterial phototrophs ([link]). In oxygenic photosynthesis, H2O is split and supplies the electron to the reaction center. Because oxygen is generated as a byproduct and is released, this type of photosynthesis is referred to as oxygenic photosynthesis. However, when other reduced compounds serve as the electron donor, oxygen is not generated; these types of photosynthesis are called anoxygenic photosynthesis. Hydrogen sulfide (H2S) or thiosulfate $\left({\text{S}}_{2}{\text{O}}_{3}^{\text{2−}}\right)$ can serve as the electron donor, generating elemental sulfur and sulfate $\left({\text{SO}}_{4}^{\text{2−}}\right)$ ions, respectively, as a result.

Light-Independent Reactions

After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules (having lifespans of millionths of a second), photoautotrophs have the fuel needed to build multicarbon carbohydrate molecules, which can survive for hundreds of millions of years, for long-term energy storage. The carbon comes from CO2, the gas that is a waste product of cellular respiration.

Biogeochemical Cycles

Carbon Cycle

Carbon is one of the most important elements to living organisms, as shown by its abundance and presence in all organic molecules. The carbon cycle exemplifies the connection between organisms in various ecosystems. Carbon is exchanged between heterotrophs and autotrophs within and between ecosystems primarily by way of atmospheric CO2, a fully oxidized version of carbon that serves as the basic building block that autotrophs use to build multicarbon, high-energy organic molecules such as glucose. Photoautotrophs and chemoautotrophs harness energy from the sun and from inorganic chemical compounds, respectively, to covalently bond carbon atoms together into reduced organic compounds whose energy can be later accessed through the processes of respiration and fermentation ([link]).

Nitrogen Cycle

Many biological macromolecules, including proteins and nucleic acids, contain nitrogen; however, getting nitrogen into living organisms is difficult. Prokaryotes play essential roles in the nitrogen cycle ([link]), transforming nitrogen between various forms for their own needs, benefiting other organisms indirectly. Plants and phytoplankton cannot incorporate nitrogen from the atmosphere (where it exists as tightly bonded, triple covalent N2), even though this molecule composes approximately 78% of the atmosphere. Nitrogen enters the living world through free-living and symbiotic bacteria, which incorporate nitrogen into their macromolecules through specialized biochemical pathways called nitrogen fixation. Cyanobacteria in aquatic ecosystems fix inorganic nitrogen (from nitrogen gas) into ammonia (NH3) that can be easily incorporated into biological macromolecules. *Rhizobium* bacteria ([link]) also fix nitrogen and live symbiotically in the root nodules of legumes (such as beans, peanuts, and peas), providing them with needed organic nitrogen while receiving fixed carbon as sugar in exchange. Free-living bacteria, such as members of the genus *Azotobacter*, are also able to fix nitrogen.

Sulfur Cycle

Sulfur is an essential element for the macromolecules of living organisms. As part of the amino acids cysteine and methionine, it is involved in the formation of proteins. It is also found in several vitamins necessary for the synthesis of important biological molecules like coenzyme A. Several groups of microbes are responsible for carrying out processes involved in the sulfur cycle ([link]). Anoxygenic photosynthetic bacteria as well as chemoautotrophic archaea and bacteria use hydrogen sulfide as an electron donor, oxidizing it first to elemental sulfur (S0), then to sulfate $\left({{\text{SO}}_{4}}^{2-}\right).$ This leads to stratification of hydrogen sulfide in soil, with levels increasing at deeper, more anaerobic depths.

Other Biogeochemical Cycles

Beyond their involvement in the carbon, nitrogen, and sulfur cycles, prokaryotes are involved in other biogeochemical cycles as well. Like the carbon, nitrogen, and sulfur cycles, several of these additional biogeochemical cycles, such as the iron (Fe), manganese (Mn), and chromium (Cr) cycles, also involve redox chemistry, with prokaryotes playing roles in both oxidation and reduction. Several other elements undergo chemical cycles that do not involve redox chemistry. Examples of these are phosphorus (P), calcium (Ca), and silica (Si) cycles. The cycling of these elements is particularly important in oceans because large quantities of these elements are incorporated into the exoskeletons of marine organisms. These biogeochemical cycles do not involve redox chemistry but instead involve fluctuations in the solubility of compounds containing calcium, phosphorous, and silica. The overgrowth of naturally occurring microbial communities is typically limited by the availability of nitrogen (as previously mentioned), phosphorus, and iron. Human activities introducing excessive amounts of iron, nitrogen, or phosphorus (typically from detergents) may lead to eutrophication.

Bioremediation

Microbial bioremediation leverages microbial metabolism to remove xenobiotic**s** or other pollutants. Xenobiotics are compounds synthesized by humans and introduced into the environment in much higher concentrations than would naturally occur. Such environmental contamination may involve adhesives, dyes, flame retardants, lubricants, oil and petroleum products, organic solvents, pesticides, and products of the combustion of gasoline and oil. Many xenobiotics resist breakdown, and some accumulate in the food chain after being consumed or absorbed by fish and wildlife, which, in turn, may be eaten by humans. Of particular concern are contaminants like polycyclic aromatic hydrocarbon (PAH), a carcinogenic xenobiotic found in crude oil, and trichloroethylene (TCE), a common groundwater contaminant.

Microbial Growth

Introduction

How Microbes Grow

Binary Fission

The most common mechanism of cell replication in bacteria is a process called binary fission, which is depicted in [link]. Before dividing, the cell grows and increases its number of cellular components. Next, the replication of DNA starts at a location on the circular chromosome called the origin of replication, where the chromosome is attached to the inner cell membrane. Replication continues in opposite directions along the chromosome until the terminus is reached.

Generation Time

In eukaryotic organisms, the generation time is the time between the same points of the life cycle in two successive generations. For example, the typical generation time for the human population is 25 years. This definition is not practical for bacteria, which may reproduce rapidly or remain dormant for thousands of years. In prokaryotes (Bacteria and Archaea), the generation time is also called the doubling time and is defined as the time it takes for the population to double through one round of binary fission. Bacterial doubling times vary enormously. Whereas *Escherichia coli* can double in as little as 20 minutes under optimal growth conditions in the laboratory, bacteria of the same species may need several days to double in especially harsh environments. Most pathogens grow rapidly, like *E. coli*, but there are exceptions. For example, *Mycobacterium tuberculosis*, the causative agent of tuberculosis, has a generation time of between 15 and 20 hours. On the other hand, *M. leprae*, which causes Hansen’s disease (leprosy), grows much more slowly, with a doubling time of 14 days.

The Growth Curve

Microorganisms grown in closed culture (also known as a batch culture), in which no nutrients are added and most waste is not removed, follow a reproducible growth pattern referred to as the growth curve. An example of a batch culture in nature is a pond in which a small number of cells grow in a closed environment. The culture density is defined as the number of cells per unit volume. In a closed environment, the culture density is also a measure of the number of cells in the population. Infections of the body do not always follow the growth curve, but correlations can exist depending upon the site and type of infection. When the number of live cells is plotted against time, distinct phases can be observed in the curve ([link]).

Measurement of Bacterial Growth

Estimating the number of bacterial cells in a sample, known as a bacterial count, is a common task performed by microbiologists. The number of bacteria in a clinical sample serves as an indication of the extent of an infection. Quality control of drinking water, food, medication, and even cosmetics relies on estimates of bacterial counts to detect contamination and prevent the spread of disease. Two major approaches are used to measure cell number. The direct methods involve counting cells, whereas the indirect methods depend on the measurement of cell presence or activity without actually counting individual cells. Both direct and indirect methods have advantages and disadvantages for specific applications.

Plate Count

The viable plate count, or simply plate count, is a count of viable or live cells. It is based on the principle that viable cells replicate and give rise to visible colonies when incubated under suitable conditions for the specimen. The results are usually expressed as colony-forming units per milliliter (CFU/mL) rather than cells per milliliter because more than one cell may have landed on the same spot to give rise to a single colony. Furthermore, samples of bacteria that grow in clusters or chains are difficult to disperse and a single colony may represent several cells. Some cells are described as viable but nonculturable and will not form colonies on solid media. For all these reasons, the viable plate count is considered a low estimate of the actual number of live cells. These limitations do not detract from the usefulness of the method, which provides estimates of live bacterial numbers.

Indirect Cell Counts

Besides direct methods of counting cells, other methods, based on an indirect detection of cell density, are commonly used to estimate and compare cell densities in a culture. The foremost approach is to measure the turbidity (cloudiness) of a sample of bacteria in a liquid suspension. The laboratory instrument used to measure turbidity is called a spectrophotometer ([link]). In a spectrophotometer, a light beam is transmitted through a bacterial suspension, the light passing through the suspension is measured by a detector, and the amount of light passing through the sample and reaching the detector is converted to either percent transmission or a logarithmic value called absorbance (optical density). As the numbers of bacteria in a suspension increase, the turbidity also increases and causes less light to reach the detector. The decrease in light passing through the sample and reaching the detector is associated with a decrease in percent transmission and increase in absorbance measured by the spectrophotometer.

Alternative Patterns of Cell Division

Binary fission is the most common pattern of cell division in prokaryotes, but it is not the only one. Other mechanisms usually involve asymmetrical division (as in budding) or production of spores in aerial filaments.

Biofilms

In nature, microorganisms grow mainly in biofilms, complex and dynamic ecosystems that form on a variety of environmental surfaces, from industrial conduits and water treatment pipelines to rocks in river beds. Biofilms are not restricted to solid surface substrates, however. Almost any surface in a liquid environment containing some minimal nutrients will eventually develop a biofilm. Microbial mats that float on water, for example, are biofilms that contain large populations of photosynthetic microorganisms. Biofilms found in the human mouth may contain hundreds of bacterial species. Regardless of the environment where they occur, biofilms are not random collections of microorganisms; rather, they are highly structured communities that provide a selective advantage to their constituent microorganisms.

Oxygen Requirements for Microbial Growth

Oxygen Requirements of Microorganisms

Many ecosystems are still free of molecular oxygen. Some are found in extreme locations, such as deep in the ocean or in earth’s crust; others are part of our everyday landscape, such as marshes, bogs, and sewers. Within the bodies of humans and other animals, regions with little or no oxygen provide an anaerobic environment for microorganisms. ([link]).

Detoxification of Reactive Oxygen Species

Aerobic respiration constantly generates reactive oxygen species (ROS), byproducts that must be detoxified. Even organisms that do not use aerobic respiration need some way to break down some of the ROS that may form from atmospheric oxygen. Three main enzymes break down those toxic byproducts: superoxide dismutase, peroxidase, and catalase. Each one catalyzes a different reaction. Reactions of type seen in Reaction 1 are catalyzed by peroxidases.

The Effects of pH on Microbial Growth

Temperature and Microbial Growth

Other Environmental Conditions that Affect Growth

Osmotic and Barometric Pressure

Most natural environments tend to have lower solute concentrations than the cytoplasm of most microorganisms. Rigid cell walls protect the cells from bursting in a dilute environment. Not much protection is available against high osmotic pressure. In this case, water, following its concentration gradient, flows out of the cell. This results in plasmolysis (the shrinking of the protoplasm away from the intact cell wall) and cell death. This fact explains why brines and layering meat and fish in salt are time-honored methods of preserving food. Microorganisms called halophiles (“salt loving”) actually require high salt concentrations for growth. These organisms are found in marine environments where salt concentrations hover at 3.5%. Extreme halophilic microorganisms, such as the red alga *Dunaliella salina* and the archaeal species *Halobacterium* in [link], grow in hypersaline lakes such as the Great Salt Lake, which is 3.5–8 times saltier than the ocean, and the Dead Sea, which is 10 times saltier than the ocean.

Light

Photoautotrophs, such as cyanobacteria or green sulfur bacteria, and photoheterotrophs, such as purple nonsulfur bacteria, depend on sufficient light intensity at the wavelengths absorbed by their pigments to grow and multiply. Energy from light is captured by pigments and converted into chemical energy that drives carbon fixation and other metabolic processes. The portion of the electromagnetic spectrum that is absorbed by these organisms is defined as photosynthetically active radiation (PAR). It lies within the visible light spectrum ranging from 400 to 700 nanometers (nm) and extends in the near infrared for some photosynthetic bacteria. A number of accessory pigments, such as fucoxanthin in brown algae and phycobilins in cyanobacteria, widen the useful range of wavelengths for photosynthesis and compensate for the low light levels available at greater depths of water. Other microorganisms, such as the archaea of the class Halobacteria, use light energy to drive their proton and sodium pumps. The light is absorbed by a pigment protein complex called bacteriorhodopsin, which is similar to the eye pigment rhodopsin. Photosynthetic bacteria are present not only in aquatic environments but also in soil and in symbiosis with fungi in lichens. The peculiar watermelon snow is caused by a microalga *Chlamydomonas nivalis*, a green alga rich in a secondary red carotenoid pigment (astaxanthin) which gives the pink hue to the snow where the alga grows.

Media Used for Bacterial Growth

Nutritional Requirements

The number of available media to grow bacteria is considerable. Some media are considered general all-purpose media and support growth of a large variety of organisms. A prime example of an all-purpose medium is tryptic soy broth (TSB). Specialized media are used in the identification of bacteria and are supplemented with dyes, pH indicators, or antibiotics. One type, enriched media, contains growth factors, vitamins, and other essential nutrients to promote the growth of fastidious organisms, organisms that cannot make certain nutrients and require them to be added to the medium. When the complete chemical composition of a medium is known, it is called a chemically defined medium. For example, in EZ medium, all individual chemical components are identified and the exact amounts of each is known. In complex media, which contain extracts and digests of yeasts, meat, or plants, the precise chemical composition of the medium is not known. Amounts of individual components are undetermined and variable. Nutrient broth, tryptic soy broth, and brain heart infusion, are all examples of complex media.

Biochemistry of the Genome

Introduction

Using Microbiology to Discover the Secrets of Life

Discovery and Characterization of DNA

Modern understanding of DNA has evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher (1844–1895), a physician by profession, was the first person to isolate phosphorus-rich chemicals from leukocytes (white blood cells) from the pus on used bandages from a local surgical clinic. He named these chemicals (which would eventually be known as RNA and DNA) “nuclein” because they were isolated from the nuclei of the cells. His student Richard Altmann (1852–1900) subsequently termed it “nucleic acid” 20 years later when he discovered the acidic nature of nuclein. In the last two decades of the 19th century, German biochemist Albrecht Kossel (1853–1927) isolated and characterized the five different nucleotide bases composing nucleic acid. These are adenine, guanine, cytosine, thymine (in DNA), and uracil (in RNA). Kossell received the Nobel Prize in Physiology or Medicine in 1910 for his work on nucleic acids and for his considerable work on proteins, including the discovery of histidine.

Foundations of Genetics

Despite the discovery of DNA in the late 1800s, scientists did not make the association with heredity for many more decades. To make this connection, scientists, including a number of microbiologists, performed many experiments on plants, animals, and bacteria.

DNA as the Molecule Responsible for Heredity

By the beginning of the 20th century, a great deal of work had already been done on characterizing DNA and establishing the foundations of genetics, including attributing heredity to chromosomes found within the nucleus. Despite all of this research, it was not until well into the 20th century that these lines of research converged and scientists began to consider that DNA could be the genetic material that offspring inherited from their parents. DNA, containing only four different nucleotides, was thought to be structurally too simple to encode such complex genetic information. Instead, protein was thought to have the complexity required to serve as cellular genetic information because it is composed of 20 different amino acids that could be combined in a huge variety of combinations. Microbiologists played a pivotal role in the research that determined that DNA is the molecule responsible for heredity.

Structure and Function of DNA

DNA Nucleotides

The building blocks of nucleic acids are nucleotides. Nucleotides that compose DNA are called deoxyribonucleotides. The three components of a deoxyribonucleotide are a five-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base, a nitrogen-containing ring structure that is responsible for complementary base pairing between nucleic acid strands ([link]). The carbon atoms of the five-carbon deoxyribose are numbered 1ʹ, 2ʹ, 3ʹ, 4ʹ, and 5ʹ (1ʹ is read as “one prime”). A nucleoside comprises the five-carbon sugar and nitrogenous base.

Discovering the Double Helix

By the early 1950s, considerable evidence had accumulated indicating that DNA was the genetic material of cells, and now the race was on to discover its three-dimensional structure. Around this time, Austrian biochemist Erwin Chargaff[footnote] (1905–2002) examined the content of DNA in different species and discovered that adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine was very close to equaling the amount of thymine, and the amount of cytosine was very close to equaling the amount of guanine, or A = T and G = C. These relationships are also known as Chargaff’s rules.

N. Kresge et al. “Chargaff's Rules: The Work of Erwin Chargaff.” *Journal of Biological Chemistry* 280 (2005):e21.

DNA Structure

Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. The two DNA strands are antiparallel, such that the 3ʹ end of one strand faces the 5ʹ end of the other ([link]). The 3ʹ end of each strand has a free hydroxyl group, while the 5ʹ end of each strand has a free phosphate group. The sugar and phosphate of the polymerized nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. These nitrogenous bases on the interior of the molecule interact with each other, base pairing.

Structure and Function of RNA

RNA Structure

RNA is typically single stranded and is made of ribonucleotides that are linked by phosphodiester bonds. A ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. The subtle structural difference between the sugars gives DNA added stability, making DNA more suitable for storage of genetic information, whereas the relative instability of RNA makes it more suitable for its more short-term functions. The RNA-specific pyrimidine uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA. Even though RNA is single stranded, most types of RNA molecules show extensive intramolecular base pairing between complementary sequences within the RNA strand, creating a predictable three-dimensional structure essential for their function ([link] and [link]).

Functions of RNA in Protein Synthesis

Cells access the information stored in DNA by creating RNA to direct the synthesis of proteins through the process of translation. Proteins within a cell have many functions, including building cellular structures and serving as enzyme catalysts for cellular chemical reactions that give cells their specific characteristics. The three main types of RNA directly involved in protein synthesis are messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

RNA as Hereditary Information

Although RNA does not serve as the hereditary information in most cells, RNA does hold this function for many viruses that do not contain DNA. Thus, RNA clearly does have the additional capacity to serve as genetic information. Although RNA is typically single stranded within cells, there is significant diversity in viruses. Rhinoviruses, which cause the common cold; influenza viruses; and the Ebola virus are single-stranded RNA viruses. Rotaviruses, which cause severe gastroenteritis in children and other immunocompromised individuals, are examples of double-stranded RNA viruses. Because double-stranded RNA is uncommon in eukaryotic cells, its presence serves as an indicator of viral infection. The implications for a virus having an RNA genome instead of a DNA genome are discussed in more detail in Viruses.

Structure and Function of Cellular Genomes

Genotype versus Phenotype

All cellular activities are encoded within a cell’s DNA. The sequence of bases within a DNA molecule represents the genetic information of the cell. Segments of DNA molecules are called genes, and individual genes contain the instructional code necessary for synthesizing various proteins, enzymes, or stable RNA molecules.

Organization of Genetic Material

The vast majority of an organism’s genome is organized into the cell’s chromosomes, which are discrete DNA structures within cells that control cellular activity. Recall that while eukaryotic chromosomes are housed in the membrane-bound nucleus, most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid (see Unique Characteristics of Prokaryotic Cells). A chromosome may contain several thousand genes.

Noncoding DNA

In addition to genes, a genome also contains many regions of noncoding DNA that do not encode proteins or stable RNA products. Noncoding DNA is commonly found in areas prior to the start of coding sequences of genes as well as in intergenic regions (i.e., DNA sequences located between genes) ([link]).

Extrachromosomal DNA

Although most DNA is contained within a cell’s chromosomes, many cells have additional molecules of DNA outside the chromosomes, called extrachromosomal DNA, that are also part of its genome. The genomes of eukaryotic cells would also include the chromosomes from any organelles such as mitochondria and/or chloroplasts that these cells maintain ([link]). The maintenance of circular chromosomes in these organelles is a vestige of their prokaryotic origins and supports the endosymbiotic theory (see Foundations of Modern Cell Theory). In some cases, genomes of certain DNA viruses can also be maintained independently in host cells during latent viral infection. In these cases, these viruses are another form of extrachromosomal DNA. For example, the human papillomavirus (HPV) may be maintained in infected cells in this way.

Viral Genomes

Viral genomes exhibit significant diversity in structure. Some viruses have genomes that consist of DNA as their genetic material. This DNA may be single stranded, as exemplified by human parvoviruses, or double stranded, as seen in the herpesviruses and poxviruses. Additionally, although all cellular life uses DNA as its genetic material, some viral genomes are made of either single-stranded or double-stranded RNA molecules, as we have discussed. Viral genomes are typically smaller than most bacterial genomes, encoding only a few genes, because they rely on their hosts to carry out many of the functions required for their replication. The diversity of viral genome structures and their implications for viral replication life cycles are discussed in more detail in The Viral Life Cycle.

Mechanisms of Microbial Genetics

Introduction

The Functions of Genetic Material

DNA Replication

DNA Replication in Bacteria

DNA replication has been well studied in bacteria primarily because of the small size of the genome and the mutants that are available. *E. coli* has 4.6 million base pairs (Mbp) in a single circular chromosome and all of it is replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle bidirectionally (i.e., in both directions). This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs with few errors.

DNA Replication in Eukaryotes

Eukaryotic genomes are much more complex and larger than prokaryotic genomes and are typically composed of multiple linear chromosomes ([link]). The human genome, for example, has 3 billion base pairs per haploid set of chromosomes, and 6 billion base pairs are inserted during replication. There are multiple origins of replication on each eukaryotic chromosome ([link]); the human genome has 30,000 to 50,000 origins of replication. The rate of replication is approximately 100 nucleotides per second—10 times slower than prokaryotic replication.

DNA Replication of Extrachromosomal Elements: Plasmids and Viruses

To copy their nucleic acids, plasmids and viruses frequently use variations on the pattern of DNA replication described for prokaryote genomes. For more information on the wide range of viral replication strategies, see The Viral Life Cycle.

RNA Transcription

Transcription in Bacteria

Bacteria use the same RNA polymerase to transcribe all of their genes. Like DNA polymerase, RNA polymerase adds nucleotides one by one to the 3’-OH group of the growing nucleotide chain. One critical difference in activity between DNA polymerase and RNA polymerase is the requirement for a 3’-OH onto which to add nucleotides: DNA polymerase requires such a 3’-OH group, thus necessitating a primer, whereas RNA polymerase does not. During transcription, a ribonucleotide complementary to the DNA template strand is added to the growing RNA strand and a covalent phosphodiester bond is formed by dehydration synthesis between the new nucleotide and the last one added. In *E. coli*, RNA polymerase comprises six polypeptide subunits, five of which compose the polymerase core enzyme responsible for adding RNA nucleotides to a growing strand. The sixth subunit is known as sigma (σ). The σ factor enables RNA polymerase to bind to a specific promoter, thus allowing for the transcription of various genes. There are various σ factors that allow for transcription of various genes.

Transcription in Eukaryotes

Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few significant differences (see [link]). Eukaryotes use three different polymerases, RNA polymerases I, II, and III, all structurally distinct from the bacterial RNA polymerase. Each transcribes a different subset of genes. Interestingly, archaea contain a single RNA polymerase that is more closely related to eukaryotic RNA polymerase II than to its bacterial counterpart. Eukaryotic mRNAs are also usually monocistronic, meaning that they each encode only a single polypeptide, whereas prokaryotic mRNAs of bacteria and archaea are commonly polycistronic, meaning that they encode multiple polypeptides.

Protein Synthesis (Translation)

The Genetic Code

Translation of the mRNA template converts nucleotide-based genetic information into the “language” of amino acids to create a protein product. A protein sequence consists of 20 commonly occurring amino acids. Each amino acid is defined within the mRNA by a triplet of nucleotides called a codon. The relationship between an mRNA codon and its corresponding amino acid is called the genetic code.

The Protein Synthesis Machinery

In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component varies across taxa; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNAs) and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors.

The Mechanism of Protein Synthesis

Translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in *E. coli*, a representative prokaryote, and specify any differences between bacterial and eukaryotic translation.

Protein Targeting, Folding, and Modification

During and after translation, polypeptides may need to be modified before they are biologically active. Post-translational modifications include:

Mutations

Effects of Mutations on DNA Sequence

There are several types of mutations that are classified according to how the DNA molecule is altered. One type, called a point mutation, affects a single base and most commonly occurs when one base is substituted or replaced by another. Mutations also result from the addition of one or more bases, known as an insertion, or the removal of one or more bases, known as a deletion.

Effects of Mutations on Protein Structure and Function

Point mutations may have a wide range of effects on protein function ([link]). As a consequence of the degeneracy of the genetic code, a point mutation will commonly result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change. This change would have no effect on the protein’s structure, and is thus called a silent mutation. A missense mutation results in a different amino acid being incorporated into the resulting polypeptide. The effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid. The location of the changed amino acid within the protein also is important. For example, if the changed amino acid is part of the enzyme’s active site, then the effect of the missense mutation may be significant. Many missense mutations result in proteins that are still functional, at least to some degree. Sometimes the effects of missense mutations may be only apparent under certain environmental conditions; such missense mutations are called conditional mutations. Rarely, a missense mutation may be beneficial. Under the right environmental conditions, this type of mutation may give the organism that harbors it a selective advantage. Yet another type of point mutation, called a nonsense mutation, converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon). Nonsense mutations result in the synthesis of proteins that are shorter than the wild type and typically not functional.

Causes of Mutations

Mistakes in the process of DNA replication can cause spontaneous mutation**s** to occur. The error rate of DNA polymerase is one incorrect base per billion base pairs replicated. Exposure to mutagen**s** can cause induced mutation**s**, which are various types of chemical agents or radiation ([link]). Exposure to a mutagen can increase the rate of mutation more than 1000-fold. Mutagens are often also carcinogen**s**, agents that cause cancer. However, whereas nearly all carcinogens are mutagenic, not all mutagens are necessarily carcinogens.

DNA Repair

The process of DNA replication is highly accurate, but mistakes can occur spontaneously or be induced by mutagens. Uncorrected mistakes can lead to serious consequences for the phenotype. Cells have developed several repair mechanisms to minimize the number of mutations that persist.

Identifying Bacterial Mutants

One common technique used to identify bacterial mutants is called replica plating. This technique is used to detect nutritional mutants, called auxotrophs, which have a mutation in a gene encoding an enzyme in the biosynthesis pathway of a specific nutrient, such as an amino acid. As a result, whereas wild-type cells retain the ability to grow normally on a medium lacking the specific nutrient, auxotrophs are unable to grow on such a medium. During replica plating ([link]), a population of bacterial cells is mutagenized and then plated as individual cells on a complex nutritionally complete plate and allowed to grow into colonies. Cells from these colonies are removed from this master plate, often using sterile velvet. This velvet, containing cells, is then pressed in the same orientation onto plates of various media. At least one plate should also be nutritionally complete to ensure that cells are being properly transferred between the plates. The other plates lack specific nutrients, allowing the researcher to discover various auxotrophic mutants unable to produce specific nutrients. Cells from the corresponding colony on the nutritionally complete plate can be used to recover the mutant for further study.

The Ames Test

The Ames test, developed by Bruce Ames (1928–) in the 1970s, is a method that uses bacteria for rapid, inexpensive screening of the carcinogenic potential of new chemical compounds. The test measures the mutation rate associated with exposure to the compound, which, if elevated, may indicate that exposure to this compound is associated with greater cancer risk. The Ames test uses as the test organism a strain of *Salmonella typhimurium* that is a histidine auxotroph, unable to synthesize its own histidine because of a mutation in an essential gene required for its synthesis. After exposure to a potential mutagen, these bacteria are plated onto a medium lacking histidine, and the number of mutants regaining the ability to synthesize histidine is recorded and compared with the number of such mutants that arise in the absence of the potential mutagen ([link]). Chemicals that are more mutagenic will bring about more mutants with restored histidine synthesis in the Ames test. Because many chemicals are not directly mutagenic but are metabolized to mutagenic forms by liver enzymes, rat liver extract is commonly included at the start of this experiment to mimic liver metabolism. After the Ames test is conducted, compounds identified as mutagenic are further tested for their potential carcinogenic properties by using other models, including animal models like mice and rats.

How Asexual Prokaryotes Achieve Genetic Diversity

Transformation

Frederick Griffith was the first to demonstrate the process of transformation. In 1928, he showed that live, nonpathogenic *Streptococcus pneumoniae* bacteria could be transformed into pathogenic bacteria through exposure to a heat-killed pathogenic strain. He concluded that some sort of agent, which he called the “transforming principle,” had been passed from the dead pathogenic bacteria to the live, nonpathogenic bacteria. In 1944, Oswald Avery (1877–1955), Colin MacLeod (1909–1972), and Maclyn McCarty (1911–2005) demonstrated that the transforming principle was DNA (see Using Microorganisms to Discover the Secrets of Life).

Transduction

Viruses that infect bacteria (bacteriophages) may also move short pieces of chromosomal DNA from one bacterium to another in a process called transduction (see [link]). Recall that in generalized transduction, any piece of chromosomal DNA may be transferred to a new host cell by accidental packaging of chromosomal DNA into a phage head during phage assembly. By contrast, specialized transduction results from the imprecise excision of a lysogenic prophage from the bacterial chromosome such that it carries with it a piece of the bacterial chromosome from either side of the phage’s integration site to a new host cell. As a result, the host may acquire new properties. This process is called lysogenic conversion. Of medical significance, a lysogenic phage may carry with it a virulence gene to its new host. Once inserted into the new host’s chromosome, the new host may gain pathogenicity. Several pathogenic bacteria, including *Corynebacterium diphtheriae* (the causative agent of diphtheria) and *Clostridium botulinum* (the causative agent of botulism), are virulent because of the introduction of toxin-encoding genes by lysogenic bacteriophages, affirming the clinical relevance of transduction in the exchange of genes involved in infectious disease. Archaea have their own viruses that translocate genetic material from one individual to another.

Conjugation

In conjugation, DNA is directly transferred from one prokaryote to another by means of a conjugation pilus, which brings the organisms into contact with one another. In *E. coli*, the genes encoding the ability to conjugate are located on a bacterial plasmid called the F plasmid, also known as the fertility factor, and the conjugation pilus is called the F pilus. The F-plasmid genes encode both the proteins composing the F pilus and those involved in rolling circle replication of the plasmid. Cells containing the F plasmid, capable of forming an F pilus, are called F+ cells or donor cell**s**, and those lacking an F plasmid are called F− cells or recipient cell**s**.

Transposition

Genetic elements called transposons (transposable elements), or “jumping genes,” are molecules of DNA that include special inverted repeat sequences at their ends and a gene encoding the enzyme transposase ([link]). Transposons allow the entire sequence to independently excise from one location in a DNA molecule and integrate into the DNA elsewhere through a process called transposition. Transposons were originally discovered in maize (corn) by American geneticist Barbara McClintock (1902–1992) in the 1940s. Transposons have since been found in all types of organisms, both prokaryotes and eukaryotes. Thus, unlike the three previous mechanisms discussed, transposition is not prokaryote-specific. Most transposons are nonreplicative, meaning they move in a “cut-and-paste” fashion. Some may be replicative, however, retaining their location in the DNA while making a copy to be inserted elsewhere (“copy and paste”). Because transposons can move within a DNA molecule, from one DNA molecule to another, or even from one cell to another, they have the ability to introduce genetic diversity. Movement within the same DNA molecule can alter phenotype by inactivating or activating a gene.

Gene Regulation: Operon Theory

Prokaryotic Gene Regulation

In bacteria and archaea, structural proteins with related functions are usually encoded together within the genome in a block called an operon and are transcribed together under the control of a single promoter, resulting in the formation of a polycistronic transcript ([link]). In this way, regulation of the transcription of all of the structural genes encoding the enzymes that catalyze the many steps in a single biochemical pathway can be controlled simultaneously, because they will either all be needed at the same time, or none will be needed. For example, in *E. coli*, all of the structural genes that encode enzymes needed to use lactose as an energy source lie next to each other in the lactose (or *lac*) operon under the control of a single promoter, the *lac* promoter. French scientists François Jacob (1920–2013) and Jacques Monod at the Pasteur Institute were the first to show the organization of bacterial genes into operons, through their studies on the *lac* operon of *E. coli*. For this work, they won the Nobel Prize in Physiology or Medicine in 1965. Although eukaryotic genes are not organized into operons, prokaryotic operons are excellent models for learning about gene regulation generally. There are some gene clusters in eukaryotes that function similar to operons. Many of the principles can be applied to eukaryotic systems and contribute to our understanding of changes in gene expression in eukaryotes that can result pathological changes such as cancer.

Regulation by Repression

Prokaryotic operons are commonly controlled by the binding of repressors to operator regions, thereby preventing the transcription of the structural genes. Such operons are classified as either repressible operon**s** or inducible operons. Repressible operons, like the tryptophan (*trp*) operon, typically contain genes encoding enzymes required for a biosynthetic pathway. As long as the product of the pathway, like tryptophan, continues to be required by the cell, a repressible operon will continue to be expressed. However, when the product of the biosynthetic pathway begins to accumulate in the cell, removing the need for the cell to continue to make more, the expression of the operon is repressed. Conversely, inducible operon**s**, like the *lac* operon of *E. coli*, often contain genes encoding enzymes in a pathway involved in the metabolism of a specific substrate like lactose. These enzymes are only required when that substrate is available, thus expression of the operons is typically induced only in the presence of the substrate.

Global Responses of Prokaryotes

In prokaryotes, there are also several higher levels of gene regulation that have the ability to control the transcription of many related operons simultaneously in response to an environmental signal. A group of operons all controlled simultaneously is called a regulon.

Additional Methods of Regulation in Bacteria: Attenuation and Riboswitches

Although most gene expression is regulated at the level of transcription initiation in prokaryotes, there are also mechanisms to control both the completion of transcription as well as translation concurrently. Since their discovery, these mechanisms have been shown to control the completion of transcription and translation of many prokaryotic operons. Because these mechanisms link the regulation of transcription and translation directly, they are specific to prokaryotes, because these processes are physically separated in eukaryotes.

Other Factors Affecting Gene Expression in Prokaryotes and Eukaryotes

Although the focus on our discussion of transcriptional control used prokaryotic operons as examples, eukaryotic transcriptional control is similar in many ways. As in prokaryotes, eukaryotic transcription can be controlled through the binding of transcription factors including repressors and activators. Interestingly, eukaryotic transcription can be influenced by the binding of proteins to regions of DNA, called enhancers, rather far away from the gene, through DNA looping facilitated between the enhancer and the promoter ([link]). Overall, regulating transcription is a highly effective way to control gene expression in both prokaryotes and eukaryotes. However, the control of gene expression in eukaryotes in response to environmental and cellular stresses can be accomplished in additional ways without the binding of transcription factors to regulatory regions.

Modern Applications of Microbial Genetics

Introduction

Microbes and the Tools of Genetic Engineering

Molecular Cloning

Herbert Boyer and Stanley Cohen first demonstrated the complete molecular cloning process in 1973 when they successfully cloned genes from the African clawed frog (*Xenopus laevis*) into a bacterial plasmid that was then introduced into the bacterial host *Escherichia coli*. Molecular cloning is a set of methods used to construct recombinant DNA and incorporate it into a host organism; it makes use of a number of molecular tools that are derived from microorganisms.

Creating a Genomic Library

Molecular cloning may also be used to generate a genomic library. The library is a complete (or nearly complete) copy of an organism’s genome contained as recombinant DNA plasmids engineered into unique clones of bacteria. Having such a library allows a researcher to create large quantities of each fragment by growing the bacterial host for that fragment. These fragments can be used to determine the sequence of the DNA and the function of any genes present.

Introducing Recombinant Molecules into Eukaryotic Hosts

The use of bacterial hosts for genetic engineering laid the foundation for recombinant DNA technology; however, researchers have also had great interest in genetically engineering eukaryotic cells, particularly those of plants and animals. The introduction of recombinant DNA molecules into eukaryotic hosts is called transfection. Genetically engineered plants, called transgenic plants, are of significant interest for agricultural and pharmaceutical purposes. The first transgenic plant sold commercially was the Flavr Savr delayed-ripening tomato, which came to market in 1994. Genetically engineered livestock have also been successfully produced, resulting, for example, in pigs with increased nutritional value[footnote] and goats that secrete pharmaceutical products in their milk.[footnote]

Liangxue Lai, Jing X. Kang, Rongfeng Li, Jingdong Wang, William T. Witt, Hwan Yul Yong, Yanhong Hao et al. “Generation of Cloned Transgenic Pigs Rich in Omega-3 Fatty Acids.” *Nature Biotechnology 24* no. 4 (2006): 435–436.Raylene Ramos Moura, Luciana Magalhães Melo, and Vicente José de Figueirêdo Freitas. “Production of Recombinant Proteins in Milk of Transgenic and Non-Transgenic Goats.” *Brazilian Archives of Biology and Technology 54* no. 5 (2011): 927–938.

Visualizing and Characterizing DNA, RNA, and Protein

Molecular Analysis of DNA

In this subsection, we will outline some of the basic methods used for separating and visualizing specific fragments of DNA that are of interest to a scientist. Some of these methods do not require knowledge of the complete sequence of the DNA molecule. Before the advent of rapid DNA sequencing, these methods were the only ones available to work with DNA, but they still form the basic arsenal of tools used by molecular geneticists to study the body’s responses to microbial and other diseases.

Molecular Analysis of Proteins

In many cases it may not be desirable or possible to study DNA or RNA directly. Proteins can provide species-specific information for identification as well as important information about how and whether a cell or tissue is responding to the presence of a pathogenic microorganism. Various proteins require different methods for isolation and characterization.

Amplification-Based DNA Analysis Methods

Various methods can be used for obtaining sequences of DNA, which are useful for studying disease-causing organisms. With the advent of rapid sequencing technology, our knowledge base of the entire genomes of pathogenic organisms has grown phenomenally. We start with a description of the polymerase chain reaction, which is not a sequencing method but has allowed researchers and clinicians to obtain the large quantities of DNA needed for sequencing and other studies. The polymerase chain reaction eliminates the dependence we once had on cells to make multiple copies of DNA, achieving the same result through relatively simple reactions outside the cell.

Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering

Genomics, Transcriptomics, and Proteomics

The study and comparison of entire genomes, including the complete set of genes and their nucleotide sequence and organization, is called genomics. This field has great potential for future medical advances through the study of the human genome as well as the genomes of infectious organisms. Analysis of microbial genomes has contributed to the development of new antibiotics, diagnostic tools, vaccines, medical treatments, and environmental cleanup techniques.

Recombinant DNA Technology and Pharmaceutical Production

Genetic engineering has provided a way to create new pharmaceutical products called recombinant DNA pharmaceuticals. Such products include antibiotic drugs, vaccines, and hormones used to treat various diseases. [link] lists examples of recombinant DNA products and their uses.

RNA Interference Technology

In Structure and Function of RNA, we described the function of mRNA, rRNA, and tRNA. In addition to these types of RNA, cells also produce several types of small noncoding RNA molecules that are involved in the regulation of gene expression. These include antisense RNA molecules, which are complementary to regions of specific mRNA molecules found in both prokaryotes and eukaryotic cells. Non-coding RNA molecules play a major role in RNA interference (RNAi), a natural regulatory mechanism by which mRNA molecules are prevented from guiding the synthesis of proteins. RNA interference of specific genes results from the base pairing of short, single-stranded antisense RNA molecules to regions within complementary mRNA molecules, preventing protein synthesis. Cells use RNA interference to protect themselves from viral invasion, which may introduce double-stranded RNA molecules as part of the viral replication process ([link]).

Gene Therapy

Mechanisms and Risks of Gene Therapy

Human diseases that result from genetic mutations are often difficult to treat with drugs or other traditional forms of therapy because the signs and symptoms of disease result from abnormalities in a patient’s genome. For example, a patient may have a genetic mutation that prevents the expression of a specific protein required for the normal function of a particular cell type. This is the case in patients with Severe Combined Immunodeficiency (SCID), a genetic disease that impairs the function of certain white blood cells essential to the immune system.

Oversight of Gene Therapy

Presently, there is significant oversight of gene therapy clinical trials. At the federal level, three agencies regulate gene therapy in parallel: the Food and Drug Administration (FDA), the Office of Human Research Protection (OHRP), and the Recombinant DNA Advisory Committee (RAC) at the National Institutes of Health (NIH). Along with several local agencies, these federal agencies interact with the institutional review board to ensure that protocols are in place to protect patient safety during clinical trials. Compliance with these protocols is enforced mostly on the local level in cooperation with the federal agencies. Gene therapies are currently under the most extensive federal and local review compared to other types of therapies, which are more typically only under the review of the FDA. Some researchers believe that these extensive regulations actually inhibit progress in gene therapy research. In 2013, the Institute of Medicine (now the National Academy of Medicine) called upon the NIH to relax its review of gene therapy trials in most cases.[footnote] However, ensuring patient safety continues to be of utmost concern.

Kerry Grens. “Report: Ease Gene Therapy Reviews.” *The Scientist*, December 9, 2013. http://www.the-scientist.com/?articles.view/articleNo/38577/title/Report--Ease-Gene-Therapy-Reviews/. Accessed May 27, 2016.

Control of Microbial Growth

Introduction

Controlling Microbial Growth

Laboratory Biological Safety Levels

For researchers or laboratory personnel working with pathogens, the risks associated with specific pathogens determine the levels of cleanliness and control required. The Centers for Disease Control and Prevention (CDC) and the National Institutes of Health (NIH) have established four classification levels, called “biological safety levels” (BSLs). Various organizations around the world, including the World Health Organization (WHO) and the European Union (EU), use a similar classification scheme. According to the CDC, the BSL is determined by the agent’s infectivity, ease of transmission, and potential disease severity, as well as the type of work being done with the agent.[footnote]

US Centers for Disease Control and Prevention. “Recognizing the Biosafety Levels.” http://www.cdc.gov/training/quicklearns/biosafety/. Accessed June 7, 2016.

Sterilization

The most extreme protocols for microbial control aim to achieve sterilization: the complete removal or killing of all vegetative cells, endospores, and viruses from the targeted item or environment. Sterilization protocols are generally reserved for laboratory, medical, manufacturing, and food industry settings, where it may be imperative for certain items to be completely free of potentially infectious agents. Sterilization can be accomplished through either physical means, such as exposure to high heat, pressure, or filtration through an appropriate filter, or by chemical means. Chemicals that can be used to achieve sterilization are called sterilant**s**. Sterilants effectively kill all microbes and viruses, and, with appropriate exposure time, can also kill endospores.

Other Methods of Control

Sterilization protocols require procedures that are not practical, or necessary, in many settings. Various other methods are used in clinical and nonclinical settings to reduce the microbial load on items. Although the terms for these methods are often used interchangeably, there are important distinctions ([link]).

Measuring Microbial Control

Physical and chemical methods of microbial control that kill the targeted microorganism are identified by the suffix *-cide* (or *-cidal*). The prefix indicates the type of microbe or infectious agent killed by the treatment method: bactericide**s** kill bacteria, viricide**s** kill or inactivate viruses, and fungicide**s** kill fungi. Other methods do not kill organisms but, instead, stop their growth, making their population static; such methods are identified by the suffix *-stat* (or *-static*). For example, bacteriostatic treatments inhibit the growth of bacteria, whereas fungistatic treatments inhibit the growth of fungi. Factors that determine whether a particular treatment is *-cidal* or *-static* include the types of microorganisms targeted, the concentration of the chemical used, and the nature of the treatment applied.

Using Physical Methods to Control Microorganisms

Heat

Heating is one of the most common—and oldest—forms of microbial control. It is used in simple techniques like cooking and canning. Heat can kill microbes by altering their membranes and denaturing proteins. The thermal death point (TDP) of a microorganism is the lowest temperature at which all microbes are killed in a 10-minute exposure. Different microorganisms will respond differently to high temperatures, with some (e.g., endospore-formers such as *C. botulinum*) being more heat tolerant. A similar parameter, the thermal death time (TDT), is the length of time needed to kill all microorganisms in a sample at a given temperature. These parameters are often used to describe sterilization procedures that use high heat, such as autoclaving. Boiling is one of the oldest methods of moist-heat control of microbes, and it is typically quite effective at killing vegetative cells and some viruses. However, boiling is less effective at killing endospores; some endospores are able to survive up to 20 hours of boiling. Additionally, boiling may be less effective at higher altitudes, where the boiling point of water is lower and the boiling time needed to kill microbes is therefore longer. For these reasons, boiling is not considered a useful sterilization technique in the laboratory or clinical setting.

Refrigeration and Freezing

Just as high temperatures are effective for controlling microbial growth, exposing microbes to low temperatures can also be an easy and effective method of microbial control, with the exception of psychrophiles, which prefer cold temperatures (see Temperature and Microbial Growth). Refrigerators used in home kitchens or in the laboratory maintain temperatures between 0 °C and 7 °C. This temperature range inhibits microbial metabolism, slowing the growth of microorganisms significantly and helping preserve refrigerated products such as foods or medical supplies. Certain types of laboratory cultures can be preserved by refrigeration for later use.

Pressure

Exposure to high pressure kills many microbes. In the food industry, high-pressure processing (also called pascalization) is used to kill bacteria, yeast, molds, parasites, and viruses in foods while maintaining food quality and extending shelf life. The application of high pressure between 100 and 800 MPa (sea level atmospheric pressure is about 0.1 MPa) is sufficient to kill vegetative cells by protein denaturation, but endospores may survive these pressures.[footnote][footnote]

C. Ferstl. “High Pressure Processing: Insights on Technology and Regulatory Requirements.” Food for Thought/White Paper. Series Volume 10. Livermore, CA: The National Food Lab; July 2013.US Food and Drug Administration. “Kinetics of Microbial Inactivation for Alternative Food Processing Technologies: High Pressure Processing.” 2000. http://www.fda.gov/Food/FoodScienceResearch/SafePracticesforFoodProcesses/ucm101456.htm. Accessed July 19, 2106.

Desiccation

Drying, also known as desiccation or dehydration, is a method that has been used for millennia to preserve foods such as raisins, prunes, and jerky. It works because all cells, including microbes, require water for their metabolism and survival. Although drying controls microbial growth, it might not kill all microbes or their endospores, which may start to regrow when conditions are more favorable and water content is restored.

Radiation

Radiation in various forms, from high-energy radiation to sunlight, can be used to kill microbes or inhibit their growth. **Ionizing radiation** includes X-rays, gamma rays, and high-energy electron beams. Ionizing radiation is strong enough to pass into the cell, where it alters molecular structures and damages cell components. For example, ionizing radiation introduces double-strand breaks in DNA molecules. This may directly cause DNA mutations to occur, or mutations may be introduced when the cell attempts to repair the DNA damage. As these mutations accumulate, they eventually lead to cell death.

Sonication

The use of high-frequency ultrasound waves to disrupt cell structures is called sonication. Application of ultrasound waves causes rapid changes in pressure within the intracellular liquid; this leads to cavitation, the formation of bubbles inside the cell, which can disrupt cell structures and eventually cause the cell to lyse or collapse. Sonication is useful in the laboratory for efficiently lysing cells to release their contents for further research; outside the laboratory, sonication is used for cleaning surgical instruments, lenses, and a variety of other objects such as coins, tools, and musical instruments.

Filtration

Filtration is a method of physically separating microbes from samples. Air is commonly filtered through high-efficiency particulate air (HEPA) filters ([link]). HEPA filters have effective pore sizes of 0.3 µm, small enough to capture bacterial cells, endospores, and many viruses, as air passes through these filters, nearly sterilizing the air on the other side of the filter. HEPA filters have a variety of applications and are used widely in clinical settings, in cars and airplanes, and even in the home. For example, they may be found in vacuum cleaners, heating and air-conditioning systems, and air purifiers.

Using Chemicals to Control Microorganisms

Phenolics

In the 1800s, scientists began experimenting with a variety of chemicals for disinfection. In the 1860s, British surgeon Joseph Lister (1827–1912) began using carbolic acid, known as phenol, as a disinfectant for the treatment of surgical wounds (see Foundations of Modern Cell Theory). In 1879, Lister’s work inspired the American chemist Joseph Lawrence (1836–1909) to develop Listerine, an alcohol-based mixture of several related compounds that is still used today as an oral antiseptic. Today, carbolic acid is no longer used as a surgical disinfectant because it is a skin irritant, but the chemical compounds found in antiseptic mouthwashes and throat lozenges are called phenolics.

Heavy Metals

Some of the first chemical disinfectants and antiseptics to be used were heavy metals. Heavy metals kill microbes by binding to proteins, thus inhibiting enzymatic activity ([link]). Heavy metals are oligodynamic, meaning that very small concentrations show significant antimicrobial activity. Ions of heavy metals bind to sulfur-containing amino acids strongly and bioaccumulate within cells, allowing these metals to reach high localized concentrations. This causes proteins to denature.

Halogens

Other chemicals commonly used for disinfection are the halogens iodine, chlorine, and fluorine. Iodine works by oxidizing cellular components, including sulfur-containing amino acids, nucleotides, and fatty acids, and destabilizing the macromolecules that contain these molecules. It is often used as a topical tincture, but it may cause staining or skin irritation. An iodophor is a compound of iodine complexed with an organic molecule, thereby increasing iodine’s stability and, in turn, its efficacy. One common iodophor is povidone-iodine, which includes a wetting agent that releases iodine relatively slowly. Betadine is a brand of povidone-iodine commonly used as a hand scrub by medical personnel before surgery and for topical antisepsis of a patient’s skin before incision ([link]).

Alcohols

Alcohols make up another group of chemicals commonly used as disinfectants and antiseptics. They work by rapidly denaturing proteins, which inhibits cell metabolism, and by disrupting membranes, which leads to cell lysis. Once denatured, the proteins may potentially refold if enough water is present in the solution. Alcohols are typically used at concentrations of about 70% aqueous solution and, in fact, work better in aqueous solutions than 100% alcohol solutions. This is because alcohols coagulate proteins. In higher alcohol concentrations, rapid coagulation of surface proteins prevents effective penetration of cells. The most commonly used alcohols for disinfection are ethyl alcohol (ethanol) and isopropyl alcohol (isopropanol, rubbing alcohol) ([link]).

Surfactants

Surface-active agents, or surfactants, are a group of chemical compounds that lower the surface tension of water. Surfactants are the major ingredients in soaps and detergents. Soaps are salts of long-chain fatty acids and have both polar and nonpolar regions, allowing them to interact with polar and nonpolar regions in other molecules ([link]). They can interact with nonpolar oils and grease to create emulsions in water, loosening and lifting away dirt and microbes from surfaces and skin. Soaps do not kill or inhibit microbial growth and so are not considered antiseptics or disinfectants. However, proper use of soaps mechanically carries away microorganisms, effectively degerming a surface. Some soaps contain added bacteriostatic agents such as triclocarban or cloflucarban, compounds structurally related to triclosan, that introduce antiseptic or disinfectant properties to the soaps.

Bisbiguanides

Bisbiguanides were first synthesized in the 20th century and are cationic (positively charged) molecules known for their antiseptic properties ([link]). One important bisbiguanide antiseptic is chlorhexidine. It has broad-spectrum activity against yeasts, gram-positive bacteria, and gram-negative bacteria, with the exception of *Pseudomonas aeruginosa*, which may develop resistance on repeated exposure.[footnote] Chlorhexidine disrupts cell membranes and is bacteriostatic at lower concentrations or bactericidal at higher concentrations, in which it actually causes the cells’ cytoplasmic contents to congeal. It also has activity against enveloped viruses. However, chlorhexidine is poorly effective against *Mycobacterium tuberculosis* and nonenveloped viruses, and it is not sporicidal. Chlorhexidine is typically used in the clinical setting as a surgical scrub and for other handwashing needs for medical personnel, as well as for topical antisepsis for patients before surgery or needle injection. It is more persistent than iodophors, providing long-lasting antimicrobial activity. Chlorhexidine solutions may also be used as oral rinses after oral procedures or to treat gingivitis. Another bisbiguanide, alexidine, is gaining popularity as a surgical scrub and an oral rinse because it acts faster than chlorhexidine.

L. Thomas et al. “Development of Resistance to Chlorhexidine Diacetate in *Pseudomonas aeruginosa* and the Effect of a ‘Residual’ Concentration.” *Journal of Hospital Infection* 46 no. 4 (2000):297–303.

Alkylating Agents

The alkylating agents are a group of strong disinfecting chemicals that act by replacing a hydrogen atom within a molecule with an alkyl group (CnH2n+1), thereby inactivating enzymes and nucleic acids ([link]). The alkylating agent formaldehyde (CH2O) is commonly used in solution at a concentration of 37% (known as formalin) or as a gaseous disinfectant and biocide. It is a strong, broad-spectrum disinfectant and biocide that has the ability to kill bacteria, viruses, fungi, and endospores, leading to sterilization at low temperatures, which is sometimes a convenient alternative to the more labor-intensive heat sterilization methods. It also cross-links proteins and has been widely used as a chemical fixative. Because of this, it is used for the storage of tissue specimens and as an embalming fluid. It also has been used to inactivate infectious agents in vaccine preparation. Formaldehyde is very irritating to living tissues and is also carcinogenic; therefore, it is not used as an antiseptic.

Peroxygens

Peroxygens are strong oxidizing agents that can be used as disinfectants or antiseptics. The most widely used peroxygen is hydrogen peroxide (H2O2), which is often used in solution to disinfect surfaces and may also be used as a gaseous agent. Hydrogen peroxide solutions are inexpensive skin antiseptics that break down into water and oxygen gas, both of which are environmentally safe. This decomposition is accelerated in the presence of light, so hydrogen peroxide solutions typically are sold in brown or opaque bottles. One disadvantage of using hydrogen peroxide as an antiseptic is that it also causes damage to skin that may delay healing or lead to scarring. Contact lens cleaners often include hydrogen peroxide as a disinfectant.

Supercritical Fluids

Within the last 15 years, the use of supercritical fluids, especially supercritical carbon dioxide (scCO2), has gained popularity for certain sterilizing applications. When carbon dioxide is brought to approximately 10 times atmospheric pressure, it reaches a supercritical state that has physical properties between those of liquids and gases. Materials put into a chamber in which carbon dioxide is pressurized in this way can be sterilized because of the ability of scCO2 to penetrate surfaces.

Chemical Food Preservatives

Chemical preservatives are used to inhibit microbial growth and minimize spoilage in some foods. Commonly used chemical preservatives include sorbic acid, benzoic acid, and propionic acid, and their more soluble salts potassium sorbate, sodium benzoate, and calcium propionate, all of which are used to control the growth of molds in acidic foods. Each of these preservatives is nontoxic and readily metabolized by humans. They are also flavorless, so they do not compromise the flavor of the foods they preserve.

Testing the Effectiveness of Antiseptics and Disinfectants

Phenol Coefficient

The effectiveness of a disinfectant or antiseptic can be determined in a number of ways. Historically, a chemical agent’s effectiveness was often compared with that of phenol, the first chemical agent used by Joseph Lister. In 1903, British chemists Samuel Rideal (1863–1929) and J. T. Ainslie Walker (1868–1930) established a protocol to compare the effectiveness of a variety of chemicals with that of phenol, using as their test organisms *Staphylococcus aureus* (a gram-positive bacterium) and *Salmonella enterica* serovar Typhi (a gram-negative bacterium). They exposed the test bacteria to the antimicrobial chemical solutions diluted in water for 7.5 minutes. They then calculated a phenol coefficient for each chemical for each of the two bacteria tested. A phenol coefficient of 1.0 means that the chemical agent has about the same level of effectiveness as phenol. A chemical agent with a phenol coefficient of less than 1.0 is less effective than phenol. An example is formalin, with phenol coefficients of 0.3 (*S. aureus*) and 0.7 (*S. enterica* serovar Typhi). A chemical agent with a phenol coefficient greater than 1.0 is more effective than phenol, such as chloramine, with phenol coefficients of 133 and 100, respectively. Although the phenol coefficient was once a useful measure of effectiveness, it is no longer commonly used because the conditions and organisms used were arbitrarily chosen.

Disk-Diffusion Method

The disk-diffusion method involves applying different chemicals to separate, sterile filter paper disks ([link]). The disks are then placed on an agar plate that has been inoculated with the targeted bacterium and the chemicals diffuse out of the disks into the agar where the bacteria have been inoculated. As the “lawn” of bacteria grows, zones of inhibition of microbial growth are observed as clear areas around the disks. Although there are other factors that contribute to the sizes of zones of inhibition (e.g., whether the agent is water soluble and able to diffuse in the agar), larger zones typically correlate to increased inhibition effectiveness of the chemical agent. The diameter across each zone is measured in millimeters.

Use-Dilution Test

Other methods are also used for measuring the effectiveness of a chemical agent in clinical settings. The use-dilution test is commonly used to determine a chemical’s disinfection effectiveness on an inanimate surface. For this test, a cylinder of stainless steel is dipped in a culture of the targeted microorganism and then dried. The cylinder is then dipped in solutions of disinfectant at various concentrations for a specified amount of time. Finally, the cylinder is transferred to a new test tube containing fresh sterile medium that does not contain disinfectant, and this test tube is incubated. Bacterial survival is demonstrated by the presence of turbidity in the medium, whereas killing of the target organism on the cylinder by the disinfectant will produce no turbidity.

In-Use Test

An in-use test can determine whether an actively used solution of disinfectant in a clinical setting is microbially contaminated ([link]). A 1-mL sample of the used disinfectant is diluted into 9 mL of sterile broth medium that also contains a compound to inactivate the disinfectant. Ten drops, totaling approximately 0.2 mL of this mixture, are then inoculated onto each of two agar plates. One plate is incubated at 37 °C for 3 days and the other is incubated at room temperature for 7 days. The plates are monitored for growth of microbial colonies. Growth of five or more colonies on either plate suggests that viable microbial cells existed in the disinfectant solution and that it is contaminated. Such in-use tests monitor the effectiveness of disinfectants in the clinical setting.

Antimicrobial Drugs

Introduction

History of Chemotherapy and Antimicrobial Discovery

Use of Antimicrobials in Ancient Societies

Although the discovery of antimicrobials and their subsequent widespread use is commonly associated with modern medicine, there is evidence that humans have been exposed to antimicrobial compounds for millennia. Chemical analyses of the skeletal remains of people from Nubia[footnote] (now found in present-day Sudan) dating from between 350 and 550 AD have shown residue of the antimicrobial agent tetracycline in high enough quantities to suggest the purposeful fermentation of tetracycline-producing *Streptomyces* during the beer-making process. The resulting beer, which was thick and gruel-like, was used to treat a variety of ailments in both adults and children, including gum disease and wounds. The antimicrobial properties of certain plants may also have been recognized by various cultures around the world, including Indian and Chinese herbalists ([link]) who have long used plants for a wide variety of medical purposes. More contemporary researchers have utilized practices and even texts from these traditional sources. For example, Chinese researcher Tu Youyou, who in the 1970s was selected to lead a government effort to find a cure for malaria, utilized *Artemisia*, a plant she identified by consulting 4th Century physician Ge Hong's *Handbook of Prescription's for Emergencies*. After initial efforts were unsuccessful, Youyou and her team more carefully followed the 1650-year-old text's method of extracting the plant's chemicals, and within a year had conducted a trial that successfully cured malaria patients.[footnote]Youyou was awarded the Nobel Prize in Physiology or Medicine in 2015. Healers of many cultures understood the antimicrobial properties of fungi and their use of moldy bread or other mold-containing products to treat wounds has been well documented for centuries.[footnote] Today, while about 80% of the world’s population still relies on plant-derived medicines,[footnote] scientists are now discovering the active compounds conferring the medicinal benefits contained in many of these traditionally used plants.

M.L. Nelson et al. “Brief Communication: Mass Spectroscopic Characterization of Tetracycline in the Skeletal Remains of an Ancient Population from Sudanese Nubia 350–550 CE.” *American Journal of Physical Anthropology* 143 no. 1 (2010):151–154. E. Hsu. "The history of *qing hao* in the Chinese *materia medica*." Transactions of The Royal Society of Tropical Medicine and Hygiene, Volume 100, Issue 6. (2006.) 505–508.M. Wainwright. “Moulds in Ancient and More Recent Medicine.” *Mycologist* 3 no. 1 (1989):21–23.S. Verma, S.P. Singh. “Current and Future Status of Herbal Medicines.” *Veterinary World* 1 no. 11 (2008):347–350.

The First Antimicrobial Drugs

Societies relied on traditional medicine for thousands of years; however, the first half of the 20th century brought an era of strategic drug discovery. In the early 1900s, the German physician and scientist Paul Ehrlich (1854–1915) set out to discover or synthesize chemical compounds capable of killing infectious microbes without harming the patient. In 1909, after screening more than 600 arsenic-containing compounds, Ehrlich’s assistant Sahachiro Hata (1873–1938) found one such “magic bullet.” Compound 606 targeted the bacterium *Treponema pallidum*, the causative agent of syphilis. Compound 606 was found to successfully cure syphilis in rabbits and soon after was marketed under the name Salvarsan as a remedy for the disease in humans ([link]). Ehrlich’s innovative approach of systematically screening a wide variety of compounds remains a common strategy for the discovery of new antimicrobial agents even today.

Fundamentals of Antimicrobial Chemotherapy

Bacteriostatic Versus Bactericidal

Antibacterial drugs can be either bacteriostatic or bactericidal in their interactions with target bacteria. Bacteriostatic drugs cause a reversible inhibition of growth, with bacterial growth restarting after elimination of the drug. By contrast, bactericidal drugs kill their target bacteria. The decision of whether to use a bacteriostatic or bactericidal drugs depends on the type of infection and the immune status of the patient. In a patient with strong immune defenses, bacteriostatic and bactericidal drugs can be effective in achieving clinical cure. However, when a patient is immunocompromised, a bactericidal drug is essential for the successful treatment of infections. Regardless of the immune status of the patient, life-threatening infections such as acute endocarditis require the use of a bactericidal drug.

Spectrum of Activity

The spectrum of activity of an antibacterial drug relates to diversity of targeted bacteria. A narrow-spectrum antimicrobial targets only specific subsets of bacterial pathogens. For example, some narrow-spectrum drugs only target gram-positive bacteria, whereas others target only gram-negative bacteria. If the pathogen causing an infection has been identified, it is best to use a narrow-spectrum antimicrobial and minimize collateral damage to the normal microbiota. A broad-spectrum antimicrobial targets a wide variety of bacterial pathogens, including both gram-positive and gram-negative species, and is frequently used as empiric therapy to cover a wide range of potential pathogens while waiting on the laboratory identification of the infecting pathogen. Broad-spectrum antimicrobials are also used for polymicrobic infections (mixed infection with multiple bacterial species), or as prophylactic prevention of infections with surgery/invasive procedures. Finally, broad-spectrum antimicrobials may be selected to treat an infection when a narrow-spectrum drug fails because of development of drug resistance by the target pathogen.

Dosage and Route of Administration

The amount of medication given during a certain time interval is the dosage, and it must be determined carefully to ensure that optimum therapeutic drug levels are achieved at the site of infection without causing significant toxicity (side effects) to the patient. Each drug class is associated with a variety of potential side effects, and some of these are described for specific drugs later in this chapter. Despite best efforts to optimize dosing, allergic reactions and other potentially serious side effects do occur. Therefore, the goal is to select the optimum dosage that will minimize the risk of side effects while still achieving clinical cure, and there are important factors to consider when selecting the best dose and dosage interval. For example, in children, dose is based upon the patient’s mass. However, the same is not true for adults and children 12 years of age and older, for which there is typically a single standard dose regardless of the patient’s mass. With the great variability in adult body mass, some experts have argued that mass should be considered for all patients when determining appropriate dosage.[footnote] An additional consideration is how drugs are metabolized and eliminated from the body. In general, patients with a history of liver or kidney dysfunction may experience reduced drug metabolism or clearance from the body, resulting in increased drug levels that may lead to toxicity and make them more prone to side effects.

M.E. Falagas, D.E. Karageorgopoulos. “Adjustment of Dosing of Antimicrobial Agents for Bodyweight in Adults.” *The Lancet* 375 no. 9710 (2010):248–251.

Drug Interactions

For the optimum treatment of some infections, two antibacterial drugs may be administered together to provide a synergistic interaction that is better than the efficacy of either drug alone. A classic example of synergistic combinations is trimethoprim and sulfamethoxazole (Bactrim). Individually, these two drugs provide only bacteriostatic inhibition of bacterial growth, but combined, the drugs are bactericidal.

Mechanisms of Antibacterial Drugs

Inhibitors of Cell Wall Biosynthesis

Several different classes of antibacterials block steps in the biosynthesis of peptidoglycan, making cells more susceptible to osmotic lysis ([link]). Therefore, antibacterials that target cell wall biosynthesis are bactericidal in their action. Because human cells do not make peptidoglycan, this mode of action is an excellent example of selective toxicity.

Inhibitors of Protein Biosynthesis

The cytoplasmic ribosomes found in animal cells (80S) are structurally distinct from those found in bacterial cells (70S), making protein biosynthesis a good selective target for antibacterial drugs. Several types of protein biosynthesis inhibitors are discussed in this section and are summarized in [link].

Inhibitors of Membrane Function

A small group of antibacterials target the bacterial membrane as their mode of action ([link]). The polymyxins are natural polypeptide antibiotics that were first discovered in 1947 as products of *Bacillus polymyxa*; only polymyxin B and polymyxin E (colistin) have been used clinically. They are lipophilic with detergent-like properties and interact with the lipopolysaccharide component of the outer membrane of gram-negative bacteria, ultimately disrupting both their outer and inner membranes and killing the bacterial cells. Unfortunately, the membrane-targeting mechanism is not a selective toxicity, and these drugs also target and damage the membrane of cells in the kidney and nervous system when administered systemically. Because of these serious side effects and their poor absorption from the digestive tract, polymyxin B is used in over-the-counter topical antibiotic ointments (e.g., Neosporin), and oral colistin was historically used only for bowel decontamination to prevent infections originating from bowel microbes in immunocompromised patients or for those undergoing certain abdominal surgeries. However, the emergence and spread of multidrug-resistant pathogens has led to increased use of intravenous colistin in hospitals, often as a drug of last resort to treat serious infections. The antibacterial daptomycin is a cyclic lipopeptide produced by *Streptomyces roseosporus* that seems to work like the polymyxins, inserting in the bacterial cell membrane and disrupting it. However, in contrast to polymyxin B and colistin, which target only gram-negative bacteria, daptomycin specifically targets gram-positive bacteria. It is typically administered intravenously and seems to be well tolerated, showing reversible toxicity in skeletal muscles.

Inhibitors of Nucleic Acid Synthesis

Some antibacterial drugs work by inhibiting nucleic acid synthesis ([link]). For example, metronidazole is a semisynthetic member of the nitroimidazole family that is also an antiprotozoan. It interferes with DNA replication in target cells. The drug rifampin is a semisynthetic member of the rifamycin family and functions by blocking RNA polymerase activity in bacteria. The RNA polymerase enzymes in bacteria are structurally different from those in eukaryotes, providing for selective toxicity against bacterial cells. It is used for the treatment of a variety of infections, but its primary use, often in a cocktail with other antibacterial drugs, is against mycobacteria that cause tuberculosis. Despite the selectivity of its mechanism, rifampin can induce liver enzymes to increase metabolism of other drugs being administered (antagonism), leading to hepatotoxicity (liver toxicity) and negatively influencing the bioavailability and therapeutic effect of the companion drugs.

Inhibitors of Metabolic Pathways

Some synthetic drugs control bacterial infections by functioning as antimetabolites, competitive inhibitors for bacterial metabolic enzymes ([link]). The sulfonamides (sulfa drugs) are the oldest synthetic antibacterial agents and are structural analogues of *para*-aminobenzoic acid (PABA), an early intermediate in folic acid synthesis ([link]). By inhibiting the enzyme involved in the production of dihydrofolic acid, sulfonamides block bacterial biosynthesis of folic acid and, subsequently, pyrimidines and purines required for nucleic acid synthesis. This mechanism of action provides bacteriostatic inhibition of growth against a wide spectrum of gram-positive and gram-negative pathogens. Because humans obtain folic acid from food instead of synthesizing it intracellularly, sulfonamides are selectively toxic for bacteria. However, allergic reactions to sulfa drugs are common. The sulfones are structurally similar to sulfonamides but are not commonly used today except for the treatment of Hansen’s disease (leprosy).

Inhibitor of ATP Synthase

Bedaquiline, representing the synthetic antibacterial class of compounds called the diarylquinolines, uses a novel mode of action that specifically inhibits mycobacterial growth. Although the specific mechanism has yet to be elucidated, this compound appears to interfere with the function of ATP synthases, perhaps by interfering with the use of the hydrogen ion gradient for ATP synthesis by oxidative phosphorylation, leading to reduced ATP production. Due to its side effects, including hepatotoxicity and potentially lethal heart arrhythmia, its use is reserved for serious, otherwise untreatable cases of tuberculosis.

Mechanisms of Other Antimicrobial Drugs

Antifungal Drugs

The most common mode of action for antifungal drugs is the disruption of the cell membrane. Antifungals take advantage of small differences between fungi and humans in the biochemical pathways that synthesize sterols. The sterols are important in maintaining proper membrane fluidity and, hence, proper function of the cell membrane. For most fungi, the predominant membrane sterol is ergosterol. Because human cell membranes use cholesterol, instead of ergosterol, antifungal drugs that target ergosterol synthesis are selectively toxic ([link]).

Antiprotozoan Drugs

There are a few mechanisms by which antiprotozoan drugs target infectious protozoans ([link]). Some are antimetabolites, such as atovaquone, proguanil, and artemisinins. Atovaquone, in addition to being antifungal, blocks electron transport in protozoans and is used for the treatment of protozoan infections including malaria, babesiosis, and toxoplasmosis. Proguanil is another synthetic antimetabolite that is processed in parasitic cells into its active form, which inhibits protozoan folic acid synthesis. It is often used in combination with atovaquone, and the combination is marketed as Malarone for both malaria treatment and prevention.

Antihelminthic Drugs

Because helminths are multicellular eukaryotes like humans, developing drugs with selective toxicity against them is extremely challenging. Despite this, several effective classes have been developed ([link]). Synthetic benzimidazoles, like mebendazole and albendazole, bind to helminthic β-tubulin, preventing microtubule formation. Microtubules in the intestinal cells of the worms seem to be particularly affected, leading to a reduction in glucose uptake. Besides their activity against a broad range of helminths, benzimidazoles are also active against many protozoans, fungi, and viruses, and their use for inhibiting mitosis and cell cycle progression in cancer cells is under study.[footnote] Possible side effects of their use include liver damage and bone marrow suppression.

B. Chu et al. “A Benzimidazole Derivative Exhibiting Antitumor Activity Blocks EGFR and HER2 Activity and Upregulates DR5 in Breast Cancer Cells.” *Cell Death and Disease* 6 (2015):e1686

Antiviral Drugs

Unlike the complex structure of fungi, protozoa, and helminths, viral structure is simple, consisting of nucleic acid, a protein coat, viral enzymes, and, sometimes, a lipid envelope. Furthermore, viruses are obligate intracellular pathogens that use the host’s cellular machinery to replicate. These characteristics make it difficult to develop drugs with selective toxicity against viruses.

Drug Resistance

Mechanisms for Drug Resistance

There are several common mechanisms for drug resistance, which are summarized in [link]. These mechanisms include enzymatic modification of the drug, modification of the antimicrobial target, and prevention of drug penetration or accumulation.

Multidrug-Resistant Microbes and Cross Resistance

From a clinical perspective, our greatest concerns are multidrug-resistant microbes (MDRs) and cross resistance. MDRs are colloquially known as “superbugs” and carry one or more resistance mechanism(s), making them resistant to multiple antimicrobials. In cross-resistance, a single resistance mechanism confers resistance to multiple antimicrobial drugs. For example, having an efflux pump that can export multiple antimicrobial drugs is a common way for microbes to be resistant to multiple drugs by using a single resistance mechanism. In recent years, several clinically important superbugs have emerged, and the CDC reports that superbugs are responsible for more than 2 million infections in the US annually, resulting in at least 23,000 fatalities.[footnote] Several of the superbugs discussed in the following sections have been dubbed the ESKAPE pathogens. This acronym refers to the names of the pathogens (*Enterococcus faecium*, *Staphylococcus aureus*, *Klebsiella pneumoniae*, *Acinetobacter baumannii*, *Pseudomonas aeruginosa* and *Enterobacter* spp.) but it is also fitting in that these pathogens are able to “escape” many conventional forms of antimicrobial therapy. As such, infections by ESKAPE pathogens can be difficult to treat and they cause a large number of nosocomial infections.

Centers for Disease Control and Prevention. “Antibiotic/Antimicrobial Resistance.” http://www.cdc.gov/drugresistance/index.html. Accessed June 2, 2016.

Methicillin-Resistant *Staphylococcus aureus* (MRSA)

Methicillin, a semisynthetic penicillin, was designed to resist inactivation by β-lactamases. Unfortunately, soon after the introduction of methicillin to clinical practice, methicillin-resistant strains of *S. aureus* appeared and started to spread. The mechanism of resistance, acquisition of a new low-affinity PBP, provided *S. aureus* with resistance to all available β-lactams. Strains of methicillin-resistant *S. aureus* (MRSA) are widespread opportunistic pathogens and a particular concern for skin and other wound infections, but may also cause pneumonia and septicemia. Although originally a problem in health-care settings (hospital-acquired MRSA [HA-MRSA]), MRSA infections are now also acquired through contact with contaminated members of the general public, called community-associated MRSA (CA-MRSA). Approximately one-third of the population carries *S. aureus* as a member of their normal nasal microbiota without illness, and about 6% of these strains are methicillin resistant.[footnote][footnote]

A.S. Kalokhe et al. “Multidrug-Resistant Tuberculosis Drug Susceptibility and Molecular Diagnostic Testing: A Review of the Literature. *American Journal of the Medical Sciences* 345 no. 2 (2013):143–148.Centers for Disease Control and Prevention. “Methicillin-Resistant *Staphylococcus aureus* (MRSA): General Information About MRSA in the Community.” http://www.cdc.gov/mrsa/community/index.html. Accessed June 2, 2016

Vancomycin-Resistant Enterococci and *Staphylococcus aureus*

Vancomycin is only effective against gram-positive organisms, and it is used to treat wound infections, septic infections, endocarditis, and meningitis that are caused by pathogens resistant to other antibiotics. It is considered one of the last lines of defense against such resistant infections, including MRSA. With the rise of antibiotic resistance in the 1970s and 1980s, vancomycin use increased, and it is not surprising that we saw the emergence and spread of vancomycin-resistant enterococci (VRE), vancomycin-resistant *S. aureus* (VRSA), and vancomycin-intermediate *S. aureus* (VISA). The mechanism of vancomycin resistance among enterococci is target modification involving a structural change to the peptide component of the peptidoglycan subunits, preventing vancomycin from binding. These strains are typically spread among patients in clinical settings by contact with health-care workers and contaminated surfaces and medical equipment.

Extended-Spectrum β-Lactamase–Producing Gram-Negative Pathogens

Gram-negative pathogens that produce extended-spectrum β-lactamases (ESBLs) show resistance well beyond just penicillins. The spectrum of β-lactams inactivated by ESBLs provides for resistance to all penicillins, cephalosporins, monobactams, and the β-lactamase-inhibitor combinations, but not the carbapenems. An even greater concern is that the genes encoding for ESBLs are usually found on mobile plasmids that also contain genes for resistance to other drug classes (e.g., fluoroquinolones, aminoglycosides, tetracyclines), and may be readily spread to other bacteria by horizontal gene transfer. These multidrug-resistant bacteria are members of the intestinal microbiota of some individuals, but they are also important causes of opportunistic infections in hospitalized patients, from whom they can be spread to other people.

Carbapenem-Resistant Gram-Negative Bacteria

The occurrence of carbapenem-resistant Enterobacteriaceae (CRE) and carbapenem resistance among other gram-negative bacteria (e.g., *P. aeruginosa*, *Acinetobacter baumannii*, *Stenotrophomonas maltophila*) is a growing health-care concern. These pathogens develop resistance to carbapenems through a variety of mechanisms, including production of carbapenemases (broad-spectrum β-lactamases that inactivate all β-lactams, including carbapenems), active efflux of carbapenems out of the cell, and/or prevention of carbapenem entry through porin channels. Similar to concerns with ESBLs, carbapenem-resistant, gram-negative pathogens are usually resistant to multiple classes of antibacterials, and some have even developed pan-resistance (resistance to all available antibacterials). Infections with carbapenem-resistant, gram-negative pathogens commonly occur in health-care settings through interaction with contaminated individuals or medical devices, or as a result of surgery.

Multidrug-Resistant *Mycobacterium tuberculosis*

The emergence of multidrug-resistant *Mycobacterium tuberculosis* (MDR-TB) and extensively drug-resistant *Mycobacterium tuberculosis* (XDR-TB) is also of significant global concern. MDR-TB strains are resistant to both rifampin and isoniazid, the drug combination typically prescribed for treatment of tuberculosis. XDR-TB strains are additionally resistant to any fluoroquinolone and at least one of three other drugs (amikacin, kanamycin, or capreomycin) used as a second line of treatment, leaving these patients very few treatment options. Both types of pathogens are particularly problematic in immunocompromised persons, including those suffering from HIV infection. The development of resistance in these strains often results from the incorrect use of antimicrobials for tuberculosis treatment, selecting for resistance.

Testing the Effectiveness of Antimicrobials

The Kirby-Bauer Disk Diffusion Test

The Kirby-Bauer disk diffusion test has long been used as a starting point for determining the susceptibility of specific microbes to various antimicrobial drugs. The Kirby-Bauer assay starts with a Mueller-Hinton agar plate on which a confluent lawn is inoculated with a patient’s isolated bacterial pathogen. Filter paper disks impregnated with known amounts of antibacterial drugs to be tested are then placed on the agar plate. As the bacterial inoculum grows, antibiotic diffuses from the circular disk into the agar and interacts with the growing bacteria. Antibacterial activity is observed as a clear circular zone of inhibition around the drug-impregnated disk, similar to the disk-diffusion assay depicted in [link]. The diameter of the zone of inhibition, measured in millimeters and compared to a standardized chart, determines the susceptibility or resistance of the bacterial pathogen to the drug.

Dilution Tests

As discussed, the limitations of the Kirby-Bauer disk diffusion test do not allow for a direct comparison of antibacterial potencies to guide selection of the best therapeutic choice. However, antibacterial dilution tests can be used to determine a particular drug’s minimal inhibitory concentration (MIC), the lowest concentration of drug that inhibits visible bacterial growth, and minimal bactericidal concentration (MBC), the lowest drug concentration that kills ≥99.9% of the starting inoculum. Determining these concentrations helps identify the correct drug for a particular pathogen. For the macrobroth dilution assay, a dilution series of the drug in broth is made in test tubes and the same number of cells of a test bacterial strain is added to each tube ([link]). The MIC is determined by examining the tubes to find the lowest drug concentration that inhibits visible growth; this is observed as turbidity (cloudiness) in the broth. Tubes with no visible growth are then inoculated onto agar media without antibiotic to determine the MBC. Generally, serum levels of an antibacterial should be at least three to five times above the MIC for treatment of an infection.

Current Strategies for Antimicrobial Discovery

Microbial Mechanisms of Pathogenicity

Introduction

Characteristics of Infectious Disease

Signs and Symptoms of Disease

An infection is the successful colonization of a host by a microorganism. Infections can lead to disease, which causes signs and symptoms resulting in a deviation from the normal structure or functioning of the host. Microorganisms that can cause disease are known as pathogens.

Classifications of Disease

The World Health Organization’s (WHO) International Classification of Diseases (ICD) is used in clinical fields to classify diseases and monitor morbidity (the number of cases of a disease) and mortality (the number of deaths due to a disease). In this section, we will introduce terminology used by the ICD (and in health-care professions in general) to describe and categorize various types of disease.

Periods of Disease

The five periods of disease (sometimes referred to as stages or phases) include the incubation, prodromal, illness, decline, and convalescence periods ([link]). The incubation period occurs in an acute disease after the initial entry of the pathogen into the host (patient). It is during this time the pathogen begins multiplying in the host. However, there are insufficient numbers of pathogen particles (cells or viruses) present to cause signs and symptoms of disease. Incubation periods can vary from a day or two in acute disease to months or years in chronic disease, depending upon the pathogen. Factors involved in determining the length of the incubation period are diverse, and can include strength of the pathogen, strength of the host immune defenses, site of infection, type of infection, and the size infectious dose received. During this incubation period, the patient is unaware that a disease is beginning to develop.

Acute and Chronic Diseases

The duration of the period of illness can vary greatly, depending on the pathogen, effectiveness of the immune response in the host, and any medical treatment received. For an acute disease, pathologic changes occur over a relatively short time (e.g., hours, days, or a few weeks) and involve a rapid onset of disease conditions. For example, influenza (caused by Influenzavirus) is considered an acute disease because the incubation period is approximately 1–2 days. Infected individuals can spread influenza to others for approximately 5 days after becoming ill. After approximately 1 week, individuals enter the period of decline.

How Pathogens Cause Disease

Koch’s Postulates

In 1884, Koch published four postulates ([link]) that summarized his method for determining whether a particular microorganism was the cause of a particular disease. Each of Koch’s postulates represents a criterion that must be met before a disease can be positively linked with a pathogen. In order to determine whether the criteria are met, tests are performed on laboratory animals and cultures from healthy and diseased animals are compared ([link]).

Molecular Koch’s Postulates

In 1988, Stanley Falkow (1934–) proposed a revised form of Koch’s postulates known as molecular Koch’s postulates. These are listed in the left column of [link]. The premise for molecular Koch’s postulates is not in the ability to isolate a particular pathogen but rather to identify a gene that may cause the organism to be pathogenic.

Pathogenicity and Virulence

The ability of a microbial agent to cause disease is called pathogenicity, and the degree to which an organism is pathogenic is called virulence. Virulence is a continuum. On one end of the spectrum are organisms that are avirulent (not harmful) and on the other are organisms that are highly virulent. Highly virulent pathogens will almost always lead to a disease state when introduced to the body, and some may even cause multi-organ and body system failure in healthy individuals. Less virulent pathogens may cause an initial infection, but may not always cause severe illness. Pathogens with low virulence would more likely result in mild signs and symptoms of disease, such as low-grade fever, headache, or muscle aches. Some individuals might even be asymptomatic.

Primary Pathogens versus Opportunistic Pathogens

Pathogens can be classified as either primary pathogens or opportunistic pathogens. A primary pathogen can cause disease in a host regardless of the host’s resident microbiota or immune system. An opportunistic pathogen, by contrast, can only cause disease in situations that compromise the host’s defenses, such as the body’s protective barriers, immune system, or normal microbiota. Individuals susceptible to opportunistic infections include the very young, the elderly, people who are pregnant, patients undergoing chemotherapy, people with immunodeficiencies (such as acquired immunodeficiency syndrome [AIDS]), patients who are recovering from surgery, and those who have had a breach of protective barriers (such as a severe wound or burn).

Stages of Pathogenesis

To cause disease, a pathogen must successfully achieve four steps or stages of pathogenesis: exposure (contact), adhesion (colonization), invasion, and infection. The pathogen must be able to gain entry to the host, travel to the location where it can establish an infection, evade or overcome the host’s immune response, and cause damage (i.e., disease) to the host. In many cases, the cycle is completed when the pathogen exits the host and is transmitted to a new host.

Transmission of Disease

For a pathogen to persist, it must put itself in a position to be transmitted to a new host, leaving the infected host through a portal of exit ([link]). As with portals of entry, many pathogens are adapted to use a particular portal of exit. Similar to portals of entry, the most common portals of exit include the skin and the respiratory, urogenital, and gastrointestinal tracts. Coughing and sneezing can expel pathogens from the respiratory tract. A single sneeze can send thousands of virus particles into the air. Secretions and excretions can transport pathogens out of other portals of exit. Feces, urine, semen, vaginal secretions, tears, sweat, and shed skin cells can all serve as vehicles for a pathogen to leave the body. Pathogens that rely on insect vectors for transmission exit the body in the blood extracted by a biting insect. Similarly, some pathogens exit the body in blood extracted by needles.

Virulence Factors of Bacterial and Viral Pathogens

Virulence Factors for Adhesion

As discussed in the previous section, the first two steps in pathogenesis are exposure and adhesion. Recall that an adhesin is a protein or glycoprotein found on the surface of a pathogen that attaches to receptors on the host cell. Adhesins are found on bacterial, viral, fungal, and protozoan pathogens. One example of a bacterial adhesin is type 1 fimbrial adhesin, a molecule found on the tips of fimbriae of enterotoxigenic *E. coli* (ETEC). Recall that fimbriae are hairlike protein bristles on the cell surface. Type 1 fimbrial adhesin allows the fimbriae of ETEC cells to attach to the mannose glycans expressed on intestinal epithelial cells. [link] lists common adhesins found in some of the pathogens we have discussed or will be seeing later in this chapter.

Bacterial Exoenzymes and Toxins as Virulence Factors

After exposure and adhesion, the next step in pathogenesis is invasion, which can involve enzymes and toxins. Many pathogens achieve invasion by entering the bloodstream, an effective means of dissemination because blood vessels pass close to every cell in the body. The downside of this mechanism of dispersal is that the blood also includes numerous elements of the immune system. Various terms ending in –emia are used to describe the presence of pathogens in the bloodstream. The presence of bacteria in blood is called bacteremia. Bacteremia involving pyogens (pus-forming bacteria) is called pyemia. When viruses are found in the blood, it is called viremia. The term toxemia describes the condition when toxins are found in the blood. If bacteria are both present and multiplying in the blood, this condition is called septicemia.

Virulence Factors for Survival in the Host and Immune Evasion

Evading the immune system is also important to invasiveness. Bacteria use a variety of virulence factors to evade phagocytosis by cells of the immune system. For example, many bacteria produce capsules, which are used in adhesion but also aid in immune evasion by preventing ingestion by phagocytes. The composition of the capsule prevents immune cells from being able to adhere and then phagocytose the cell. In addition, the capsule makes the bacterial cell much larger, making it harder for immune cells to engulf the pathogen ([link]). A notable capsule-producing bacterium is the gram-positive pathogen *Streptococcus pneumoniae*, which causes pneumococcal pneumonia, meningitis, septicemia, and other respiratory tract infections. Encapsulated strains of *S. pneumoniae* are more virulent than nonencapsulated strains and are more likely to invade the bloodstream and cause septicemia and meningitis.

Viral Virulence

Although viral pathogens are not similar to bacterial pathogens in terms of structure, some of the properties that contribute to their virulence are similar. Viruses use adhesins to facilitate adhesion to host cells, and certain enveloped viruses rely on antigenic variation to avoid the host immune defenses. These virulence factors are discussed in more detail in the following sections.

Virulence Factors of Eukaryotic Pathogens

Fungal Virulence

Pathogenic fungi can produce virulence factors that are similar to the bacterial virulence factors that have been discussed earlier in this chapter. In this section, we will look at the virulence factors associated with species of *Candida*, *Cryptococcus, Claviceps,* and *Aspergillus*.

Protozoan Virulence

Protozoan pathogens are unicellular eukaryotic parasites that have virulence factors and pathogenic mechanisms analogous to prokaryotic and viral pathogens, including adhesins, toxins, antigenic variation, and the ability to survive inside phagocytic vesicles.

Helminth Virulence

Helminths, or parasitic worms, are multicellular eukaryotic parasites that depend heavily on virulence factors that allow them to gain entry to host tissues. For example, the aquatic larval form of *Schistosoma mansoni*, which causes schistosomiasis, penetrates intact skin with the aid of proteases that degrade skin proteins, including elastin.

Disease and Epidemiology

Introduction

The Language of Epidemiologists

Analyzing Disease in a Population

Epidemiological analyses are always carried out with reference to a population, which is the group of individuals that are at risk for the disease or condition. The population can be defined geographically, but if only a portion of the individuals in that area are susceptible, additional criteria may be required. Susceptible individuals may be defined by particular behaviors, such as intravenous drug use, owning particular pets, or membership in an institution, such as a college. Being able to define the population is important because most measures of interest in epidemiology are made with reference to the size of the population.

Patterns of Incidence

Diseases that are seen only occasionally, and usually without geographic concentration, are called sporadic disease**s**. Examples of sporadic diseases include tetanus, rabies, and plague. In the United States, *Clostridium tetani*, the bacterium that causes tetanus, is ubiquitous in the soil environment, but incidences of infection occur only rarely and in scattered locations because most individuals are vaccinated, clean wounds appropriately, or are only rarely in a situation that would cause infection.[footnote] Likewise in the United States there are a few scattered cases of plague each year, usually contracted from rodents in rural areas in the western states.[footnote]

Centers for Disease Control and Prevention. “Tetanus Surveillance—United States, 2001–2008.” *Morbidity and Mortality Weekly Report* 60, no. 12 (2011): 365.Centers for Disease Control and Prevention. “Plague in the United States.” 2015. http://www.cdc.gov/plague/maps. Accessed June 1, 2016.

Etiology

When studying an epidemic, an epidemiologist’s first task is to determinate the cause of the disease, called the etiologic agent or causative agent. Connecting a disease to a specific pathogen can be challenging because of the extra effort typically required to demonstrate direct causation as opposed to a simple association. It is not enough to observe an association between a disease and a suspected pathogen; controlled experiments are needed to eliminate other possible causes. In addition, pathogens are typically difficult to detect when there is no immediate clue as to what is causing the outbreak. Signs and symptoms of disease are also commonly nonspecific, meaning that many different agents can give rise to the same set of signs and symptoms. This complicates diagnosis even when a causative agent is familiar to scientists.

The Role of Public Health Organizations

The main national public health agency in the United States is the Centers for Disease Control and Prevention (CDC), an agency of the Department of Health and Human Services. The CDC is charged with protecting the public from disease and injury. One way that the CDC carries out this mission is by overseeing the National Notifiable Disease Surveillance System (NNDSS) in cooperation with regional, state, and territorial public health departments. The NNDSS monitors diseases considered to be of public health importance on a national scale. Such diseases are called notifiable disease**s** or reportable disease**s** because all cases must be reported to the CDC. A physician treating a patient with a notifiable disease is legally required to submit a report on the case. Notifiable diseases include HIV infection, measles, West Nile virus infections, and many others. Some states have their own lists of notifiable diseases that include diseases beyond those on the CDC’s list.

Tracking Infectious Diseases

Pioneers of Epidemiology

John Snow ([link]) was a British physician known as the father of epidemiology for determining the source of the 1854 Broad Street cholera epidemic in London. Based on observations he had made during an earlier cholera outbreak (1848–1849), Snow proposed that cholera was spread through a fecal-oral route of transmission and that a microbe was the infectious agent. He investigated the 1854 cholera epidemic in two ways. First, suspecting that contaminated water was the source of the epidemic, Snow identified the source of water for those infected. He found a high frequency of cholera cases among individuals who obtained their water from the River Thames downstream from London. This water contained the refuse and sewage from London and settlements upstream. He also noted that brewery workers did not contract cholera and on investigation found the owners provided the workers with beer to drink and stated that they likely did not drink water.[footnote] Second, he also painstakingly mapped the incidence of cholera and found a high frequency among those individuals using a particular water pump located on Broad Street. In response to Snow’s advice, local officials removed the pump’s handle,[footnote] resulting in the containment of the Broad Street cholera epidemic.

John Snow. *On the Mode of Communication of Cholera. Second edition, Much Enlarged*. John Churchill, 1855.John Snow. “The Cholera near Golden-Wquare, and at Deptford.” *Medical Times and Gazette* 9 (1854): 321–322. http://www.ph.ucla.edu/epi/snow/choleragoldensquare.html.

Types of Epidemiological Studies

Today, epidemiologists make use of study designs, the manner in which data are gathered to test a hypothesis, similar to those of researchers studying other phenomena that occur in populations. These approaches can be divided into observational studies (in which subjects are not manipulated) and experimental studies (in which subjects are manipulated). Collectively, these studies give modern-day epidemiologists multiple tools for exploring the connections between infectious diseases and the populations of susceptible individuals they might infect.

Modes of Disease Transmission

Reservoirs and Carriers

For pathogens to persist over long periods of time they require reservoir**s** where they normally reside. Reservoirs can be living organisms or nonliving sites. Nonliving reservoirs can include soil and water in the environment. These may naturally harbor the organism because it may grow in that environment. These environments may also become contaminated with pathogens in human feces, pathogens shed by intermediate hosts, or pathogens contained in the remains of intermediate hosts.

Transmission

Regardless of the reservoir, transmission must occur for an infection to spread. First, transmission from the reservoir to the individual must occur. Then, the individual must transmit the infectious agent to other susceptible individuals, either directly or indirectly. Pathogenic microorganisms employ diverse transmission mechanisms.

Quarantining

Individuals suspected or known to have been exposed to certain contagious pathogens may be quarantined, or isolated to prevent transmission of the disease to others. Hospitals and other health-care facilities generally set up special wards to isolate patients with particularly hazardous diseases such as tuberculosis or Ebola ([link]). Depending on the setting, these wards may be equipped with special air-handling methods, and personnel may implement special protocols to limit the risk of transmission, such as personal protective equipment or the use of chemical disinfectant sprays upon entry and exit of medical personnel.

Healthcare-Associated (Nosocomial) Infections

Hospitals, retirement homes, and prisons attract the attention of epidemiologists because these settings are associated with increased incidence of certain diseases. Higher rates of transmission may be caused by characteristics of the environment itself, characteristics of the population, or both. Consequently, special efforts must be taken to limit the risks of infection in these settings.

Global Public Health

The World Health Organization (WHO)

International public health issues are coordinated by the World Health Organization (WHO), an agency of the United Nations. Of its roughly \$4 billion budget for 2015–16[footnote], about \$1 billion was funded by member states and the remaining \$3 billion by voluntary contributions. In addition to monitoring and reporting on infectious disease, WHO also develops and implements strategies for their control and prevention. WHO has had a number of successful international public health campaigns. For example, its vaccination program against smallpox, begun in the mid-1960s, resulted in the global eradication of the disease by 1980. WHO continues to be involved in infectious disease control, primarily in the developing world, with programs targeting malaria, HIV/AIDS, and tuberculosis, among others. It also runs programs to reduce illness and mortality that occur as a result of violence, accidents, lifestyle-associated illnesses such as diabetes, and poor health-care infrastructure.

World Health Organization. “Programme Budget 2014–2015.” http://www.who.int/about/finances-accountability/budget/en.

Emerging and Reemerging Infectious Diseases

Both WHO and some national public health agencies such as the CDC monitor and prepare for emerging infectious diseases. An emerging infectious disease is either new to the human population or has shown an increase in prevalence in the previous twenty years. Whether the disease is new or conditions have changed to cause an increase in frequency, its status as emerging implies the need to apply resources to understand and control its growing impact.

Innate Nonspecific Host Defenses

Introduction

Physical Defenses

Physical Barriers

Physical barriers play an important role in preventing microbes from reaching tissues that are susceptible to infection. At the cellular level, barriers consist of cells that are tightly joined to prevent invaders from crossing through to deeper tissue. For example, the endothelial cells that line blood vessels have very tight cell-to-cell junctions, blocking microbes from gaining access to the bloodstream. Cell junctions are generally composed of cell membrane proteins that may connect with the extracellular matrix or with complementary proteins from neighboring cells. Tissues in various parts of the body have different types of cell junctions. These include tight junctions, desmosomes, and gap junctions, as illustrated in [link]. Invading microorganisms may attempt to break down these substances chemically, using enzymes such as proteases that can cause structural damage to create a point of entry for pathogens.

Mechanical Defenses

In addition to physical barriers that keep microbes out, the body has a number of mechanical defenses that physically remove pathogens from the body, preventing them from taking up residence. We have already discussed several examples of mechanical defenses, including the shedding of skin cells, the expulsion of mucus via the mucociliary escalator, and the excretion of feces through intestinal peristalsis. Other important examples of mechanical defenses include the flushing action of urine and tears, which both serve to carry microbes away from the body. The flushing action of urine is largely responsible for the normally sterile environment of the urinary tract, which includes the kidneys, ureters, and urinary bladder. Urine passing out of the body washes out transient microorganisms, preventing them from taking up residence. The eyes also have physical barriers and mechanical mechanisms for preventing infections. The eyelashes and eyelids prevent dust and airborne microorganisms from reaching the surface of the eye. Any microbes or debris that make it past these physical barriers may be flushed out by the mechanical action of blinking, which bathes the eye in tears, washing debris away ([link]).

Microbiome

In various regions of the body, resident microbiota serve as an important first-line defense against invading pathogens. Through their occupation of cellular binding sites and competition for available nutrients, the resident microbiota prevent the critical early steps of pathogen attachment and proliferation required for the establishment of an infection. For example, in the vagina, members of the resident microbiota compete with opportunistic pathogens like the yeast *Candida*. This competition prevents infections by limiting the availability of nutrients, thus inhibiting the growth of *Candida**,* keeping its population in check. Similar competitions occur between the microbiota and potential pathogens on the skin, in the upper respiratory tract, and in the gastrointestinal tract. As will be discussed later in this chapter, the resident microbiota also contribute to the chemical defenses of the innate nonspecific host defenses.

Chemical Defenses

Chemical and Enzymatic Mediators Found in Body Fluids

Fluids produced by the skin include examples of both endogenous and exogenous mediators. Sebaceous glands in the dermis secrete an oil called sebum that is released onto the skin surface through hair follicles. This sebum is an endogenous mediator, providing an additional layer of defense by helping seal off the pore of the hair follicle, preventing bacteria on the skin’s surface from invading sweat glands and surrounding tissue ([link]). Certain members of the microbiome, such as the bacterium *Propionibacterium acnes* and the fungus *Malassezia*, among others, can use lipase enzymes to degrade sebum, using it as a food source. This produces oleic acid, which creates a mildly acidic environment on the surface of the skin that is inhospitable to many pathogenic microbes. Oleic acid is an example of an exogenously produced mediator because it is produced by resident microbes and not directly by body cells.

Antimicrobial Peptides

The antimicrobial peptides (AMPs) are a special class of nonspecific cell-derived mediators with broad-spectrum antimicrobial properties. Some AMPs are produced routinely by the body, whereas others are primarily produced (or produced in greater quantities) in response to the presence of an invading pathogen. Research has begun exploring how AMPs can be used in the diagnosis and treatment of disease.

Plasma Protein Mediators

Many nonspecific innate immune factors are found in plasma, the fluid portion of blood. Plasma contains electrolytes, sugars, lipids, and proteins, each of which helps to maintain homeostasis (i.e., stable internal body functioning), and contains the proteins involved in the clotting of blood. Additional proteins found in blood plasma, such as acute-phase proteins, complement proteins, and cytokines, are involved in the nonspecific innate immune response.

Inflammation-Eliciting Mediators

Many of the chemical mediators discussed in this section contribute in some way to inflammation and fever, which are nonspecific immune responses discussed in more detail in Inflammation and Fever. Cytokines stimulate the production of acute-phase proteins such as C-reactive protein and mannose-binding lectin in the liver. These acute-phase proteins act as opsonins, activating complement cascades through the lectin pathway.

Cellular Defenses

Hematopoiesis

All of the formed elements of blood are derived from pluripotent hematopoietic stem cells (HSCs) in the bone marrow. As the HSCs make copies of themselves in the bone marrow, individual cells receive different cues from the body that control how they develop and mature. As a result, the HSCs differentiate into different types of blood cells that, once mature, circulate in peripheral blood. This process of differentiation, called hematopoiesis, is shown in more detail in [link].

Granulocytes

The various types of granulocytes can be distinguished from one another in a blood smear by the appearance of their nuclei and the contents of their granules, which confer different traits, functions, and staining properties. The neutrophils, also called polymorphonuclear neutrophils (PMNs), have a nucleus with three to five lobes and small, numerous, lilac-colored granules. Each lobe of the nucleus is connected by a thin strand of material to the other lobes. The eosinophils have fewer lobes in the nucleus (typically 2–3) and larger granules that stain reddish-orange. The basophils have a two-lobed nucleus and large granules that stain dark blue or purple ([link]).

Agranulocytes

As their name suggests, agranulocytes lack visible granules in the cytoplasm. Agranulocytes can be categorized as lymphocytes or monocytes ([link]). Among the lymphocytes are natural killer cells, which play an important role in nonspecific innate immune defenses. Lymphocytes also include the B cells and T cells, which are discussed in the next chapter because they are central players in the specific adaptive immune defenses. The monocytes differentiate into macrophages and dendritic cells, which are collectively referred to as the mononuclear phagocyte system.

Pathogen Recognition and Phagocytosis

Extravasation (Diapedesis) of Leukocytes

Some phagocytes are leukocytes (WBCs) that normally circulate in the bloodstream. To reach pathogens located in infected tissue, leukocytes must pass through the walls of small capillary blood vessels within tissues. This process, called extravasation, or diapedesis, is initiated by complement factor C5a, as well as cytokines released into the immediate vicinity by resident macrophages and tissue cells responding to the presence of the infectious agent ([link]). Similar to C5a, many of these cytokines are proinflammatory and chemotactic, and they bind to cells of small capillary blood vessels, initiating a response in the endothelial cells lining the inside of the blood vessel walls. This response involves the upregulation and expression of various cellular adhesion molecules and receptors. Leukocytes passing through will stick slightly to the adhesion molecules, slowing down and rolling along the blood vessel walls near the infected area. When they reach a cellular junction, they will bind to even more of these adhesion molecules, flattening out and squeezing through the cellular junction in a process known as transendothelial migration. This mechanism of “rolling adhesion” allows leukocytes to exit the bloodstream and enter the infected areas, where they can begin phagocytosing the invading pathogens.

Pathogen Recognition

As described in the previous section, opsonization of pathogens by antibody; complement factors C1q, C3b, and C4b; and lectins can assist phagocytic cells in recognition of pathogens and attachment to initiate phagocytosis. However, not all pathogen recognition is opsonin dependent. Phagocytes can also recognize molecular structures that are common to many groups of pathogenic microbes. Such structures are called pathogen-associated molecular patterns (PAMPs). Common PAMPs include the following:

Pathogen Degradation

Once pathogen recognition and attachment occurs, the pathogen is engulfed in a vesicle and brought into the internal compartment of the phagocyte in a process called phagocytosis ([link]). PRRs can aid in phagocytosis by first binding to the pathogen’s surface, but phagocytes are also capable of engulfing nearby items even if they are not bound to specific receptors. To engulf the pathogen, the phagocyte forms a pseudopod that wraps around the pathogen and then pinches it off into a membrane vesicle called a phagosome. Acidification of the phagosome (pH decreases to the range of 4–5) provides an important early antibacterial mechanism. The phagosome containing the pathogen fuses with one or more lysosomes, forming a phagolysosome. Formation of the phagolysosome enhances the acidification, which is essential for activation of pH-dependent digestive lysosomal enzymes and production of hydrogen peroxide and toxic reactive oxygen species. Lysosomal enzymes such as lysozyme, phospholipase, and proteases digest the pathogen. Other enzymes are involved in a respiratory burst. During the respiratory burst, phagocytes will increase their uptake and consumption of oxygen, but not for energy production. The increased oxygen consumption is focused on the production of superoxide anion, hydrogen peroxide, hydroxyl radicals, and other reactive oxygen species that are antibacterial.

Inflammation and Fever

Acute Inflammation

An early, if not immediate, response to tissue injury is acute inflammation. Immediately following an injury, vasoconstriction of blood vessels will occur to minimize blood loss. The amount of vasoconstriction is related to the amount of vascular injury, but it is usually brief. Vasoconstriction is followed by vasodilation and increased vascular permeability, as a direct result of the release of histamine from resident mast cells. Increased blood flow and vascular permeability can dilute toxins and bacterial products at the site of injury or infection. They also contribute to the five observable signs associated with the inflammatory response: erythema (redness), edema (swelling), heat, pain, and altered function. Vasodilation and increased vascular permeability are also associated with an influx of phagocytes at the site of injury and/or infection. This can enhance the inflammatory response because phagocytes may release proinflammatory chemicals when they are activated by cellular distress signals released from damaged cells, by PAMPs, or by opsonins on the surface of pathogens. Activation of the complement system can further enhance the inflammatory response through the production of the anaphylatoxin C5a. [link] illustrates a typical case of acute inflammation at the site of a skin wound.

Chronic Inflammation

When acute inflammation is unable to clear an infectious pathogen, chronic inflammation may occur. This often results in an ongoing (and sometimes futile) lower-level battle between the host organism and the pathogen. The wounded area may heal at a superficial level, but pathogens may still be present in deeper tissues, stimulating ongoing inflammation. Additionally, chronic inflammation may be involved in the progression of degenerative neurological diseases such as Alzheimer’s and Parkinson’s, heart disease, and metastatic cancer.

Fever

A fever is an inflammatory response that extends beyond the site of infection and affects the entire body, resulting in an overall increase in body temperature. Body temperature is normally regulated and maintained by the hypothalamus, an anatomical section of the brain that functions to maintain homeostasis in the body. However, certain bacterial or viral infections can result in the production of pyrogens, chemicals that effectively alter the “thermostat setting” of the hypothalamus to elevate body temperature and cause fever. Pyrogens may be exogenous or endogenous. For example, the endotoxin lipopolysaccharide (LPS), produced by gram-negative bacteria, is an exogenous pyrogen that may induce the leukocytes to release endogenous pyrogens such as interleukin-1 (IL-1), IL-6, interferon-γ (IFN-γ), and tumor necrosis factor (TNF). In a cascading effect, these molecules can then lead to the release of prostaglandin E2 (PGE2) from other cells, resetting the hypothalamus to initiate fever ([link]).

Adaptive Specific Host Defenses

Introduction

Overview of Specific Adaptive Immunity

Antigens

Activation of the adaptive immune defenses is triggered by pathogen-specific molecular structures called antigens. Antigens are similar to the pathogen-associated molecular patterns (PAMPs) discussed in Pathogen Recognition and Phagocytosis; however, whereas PAMPs are molecular structures found on numerous pathogens, antigens are unique to a specific pathogen. The antigens that stimulate adaptive immunity to chickenpox, for example, are unique to the varicella-zoster virus but significantly different from the antigens associated with other viral pathogens.

Antibodies

Antibodies (also called immunoglobulins) are glycoproteins that are present in both the blood and tissue fluids. The basic structure of an antibody monomer consists of four protein chains held together by disulfide bonds ([link]). A disulfide bond is a covalent bond between the sulfhydryl *R* groups found on two cysteine amino acids. The two largest chains are identical to each other and are called the heavy chains. The two smaller chains are also identical to each other and are called the light chains. Joined together, the heavy and light chains form a basic Y-shaped structure.

Antigen-Antibody Interactions

Different classes of antibody play important roles in the body’s defense against pathogens. These functions include neutralization of pathogens, opsonization for phagocytosis, agglutination, complement activation, and antibody-dependent cell-mediated cytotoxicity. For most of these functions, antibodies also provide an important link between adaptive specific immunity and innate nonspecific immunity.

Major Histocompatibility Complexes and Antigen-Presenting Cells

Major Histocompatibility Complex Molecules

The major histocompatibility complex (MHC) is a collection of genes coding for MHC molecules found on the surface of all nucleated cells of the body. In humans, the MHC genes are also referred to as human leukocyte antigen (HLA) genes. Mature red blood cells, which lack a nucleus, are the only cells that do not express MHC molecules on their surface.

Antigen-Presenting Cells (APCs)

All nucleated cells in the body have mechanisms for processing and presenting antigens in association with MHC molecules. This signals the immune system, indicating whether the cell is normal and healthy or infected with an intracellular pathogen. However, only macrophages, dendritic cells, and B cells have the ability to present antigens specifically for the purpose of activating T cells; for this reason, these types of cells are sometimes referred to as antigen-presenting cells (APCs).

T Lymphocytes and Cellular Immunity

T Cell Production and Maturation

T cells, like all other white blood cells involved in innate and adaptive immunity, are formed from multipotent hematopoietic stem cells (HSCs) in the bone marrow (see [link]). However, unlike the white blood cells of innate immunity, eventual T cells differentiate first into lymphoid stem cells that then become small, immature lymphocytes, sometimes called lymphoblasts. The first steps of differentiation occur in the red marrow of bones ([link]), after which immature T lymphocytes enter the bloodstream and travel to the thymus for the final steps of maturation ([link]). Once in the thymus, the immature T lymphocytes are referred to as thymocytes.

Classes of T Cells

T cells can be categorized into three distinct classes: helper T cells, regulatory T cells, and cytotoxic T cells. These classes are differentiated based on their expression of certain surface molecules, their mode of activation, and their functional roles in adaptive immunity ([link]).

T-Cell Receptors

For both helper T cells and cytotoxic T cells, activation is a complex process that requires the interactions of multiple molecules and exposure to cytokines. The T-cell receptor (TCR) is involved in the first step of pathogen epitope recognition during the activation process.

Activation and Differentiation of Helper T Cells

Helper T cells can only be activated by APCs presenting processed foreign epitopes in association with MHC II. The first step in the activation process is TCR recognition of the specific foreign epitope presented within the MHC II antigen-binding cleft. The second step involves the interaction of CD4 on the helper T cell with a region of the MHC II molecule separate from the antigen-binding cleft. This second interaction anchors the MHC II-TCR complex and ensures that the helper T cell is recognizing both the foreign (“nonself”) epitope and “self” antigen of the APC; both recognitions are required for activation of the cell. In the third step, the APC and T cell secrete cytokines that activate the helper T cell. The activated helper T cell then proliferates, dividing by mitosis to produce clonal naïve helper T cells that differentiate into subtypes with different functions ([link]).

Activation and Differentiation of Cytotoxic T Cells

Cytotoxic T cells (also referred to as cytotoxic T lymphocytes, or CTLs) are activated by APCs in a three-step process similar to that of helper T cells. The key difference is that the activation of cytotoxic T cells involves recognition of an antigen presented with MHC I (as opposed to MHC II) and interaction of CD8 (as opposed to CD4) with the receptor complex. After the successful co-recognition of foreign epitope and self-antigen, the production of cytokines by the APC and the cytotoxic T cell activate clonal proliferation and differentiation. Activated cytotoxic T cells can differentiate into effector cytotoxic T cells that target pathogens for destruction or memory cells that are ready to respond to subsequent exposures.

Superantigens and Unregulated Activation of T Cells

When T cell activation is controlled and regulated, the result is a protective response that is effective in combating infections. However, if T cell activation is unregulated and excessive, the result can be life-threatening. Certain bacterial and viral pathogens produce toxins known as superantigens (see Virulence Factors of Bacterial and Viral Pathogens) that can trigger such an unregulated response. Known bacterial superantigens include toxic shock syndrome toxin (TSST), staphylococcal enterotoxins, streptococcal pyrogenic toxins, streptococcal superantigen, and the streptococcal mitogenic exotoxin. Viruses known to produce superantigens include Epstein-Barr virus (human herpesvirus 4), cytomegalovirus (human herpesvirus 5), and others.

B Lymphocytes and Humoral Immunity

B Cell Production and Maturation

Like T cells, B cells are formed from multipotent hematopoietic stem cells (HSCs) in the bone marrow and follow a pathway through lymphoid stem cell and lymphoblast (see [link]). Unlike T cells, however, lymphoblasts destined to become B cells do not leave the bone marrow and travel to the thymus for maturation. Rather, eventual B cells continue to mature in the bone marrow.

B-Cell Receptors

Like T cells, B cells possess antigen-specific receptors with diverse specificities. Although they rely on T cells for optimum function, B cells can be activated without help from T cells. B-cell receptors (BCRs) for naïve mature B cells are membrane-bound monomeric forms of IgD and IgM. They have two identical heavy chains and two identical light chains connected by disulfide bonds into a basic “Y” shape ([link]). The trunk of the Y-shaped molecule, the constant region of the two heavy chains, spans the B cell membrane. The two antigen-binding sites exposed to the exterior of the B cell are involved in the binding of specific pathogen epitopes to initiate the activation process. It is estimated that each naïve mature B cell has upwards of 100,000 BCRs on its membrane, and each of these BCRs has an identical epitope-binding specificity.

Primary and Secondary Responses

T cell-dependent activation of B cells plays an important role in both the primary and secondary responses associated with adaptive immunity. With the first exposure to a protein antigen, a T cell-dependent primary antibody response occurs. The initial stage of the primary response is a lag period, or latent period, of approximately 10 days, during which no antibody can be detected in serum. This lag period is the time required for all of the steps of the primary response, including naïve mature B cell binding of antigen with BCRs, antigen processing and presentation, helper T cell activation, B cell activation, and clonal proliferation. The end of the lag period is characterized by a rise in IgM levels in the serum, as TH2 cells stimulate B cell differentiation into plasma cells. IgM levels reach their peak around 14 days after primary antigen exposure; at about this same time, TH2 stimulates antibody class switching, and IgM levels in serum begin to decline. Meanwhile, levels of IgG increase until they reach a peak about three weeks into the primary response ([link]).

Vaccines

Classifications of Adaptive Immunity

All forms of adaptive immunity can be described as either active or passive. Active immunity refers to the activation of an individual’s own adaptive immune defenses, whereas passive immunity refers to the transfer of adaptive immune defenses from another individual or animal. Active and passive immunity can be further subdivided based on whether the protection is acquired naturally or artificially.

Variolation and Vaccination

Thousands of years ago, it was first recognized that individuals who survived a smallpox infection were immune to subsequent infections. The practice of inoculating individuals to actively protect them from smallpox appears to have originated in the 10th century in China, when the practice of variolation was described ([link]). Variolation refers to the deliberate inoculation of individuals with infectious material from scabs or pustules of smallpox victims. Infectious materials were either injected into the skin or introduced through the nasal route. The infection that developed was usually milder than naturally acquired smallpox, and recovery from the milder infection provided protection against the more serious disease.

Classes of Vaccines

For a vaccine to provide protection against a disease, it must expose an individual to pathogen-specific antigens that will stimulate a protective adaptive immune response. By its very nature, this entails some risk. As with any pharmaceutical drug, vaccines have the potential to cause adverse effects. However, the ideal vaccine causes no severe adverse effects and poses no risk of contracting the disease that it is intended to prevent. Various types of vaccines have been developed with these goals in mind. These different classes of vaccines are described in the next section and summarized in [link].

Diseases of the Immune System

Introduction

Hypersensitivities

Type I Hypersensitivities

When a presensitized individual is exposed to an allergen, it can lead to a rapid immune response that occurs almost immediately. Such a response is called an allergy and is classified as a type I hypersensitivity. Allergens may be seemingly harmless substances such as animal dander, molds, or pollen. Allergens may also be substances considered innately more hazardous, such as insect venom or therapeutic drugs. Food intolerances can also yield allergic reactions as individuals become sensitized to foods such as peanuts or shellfish ([link]). Regardless of the allergen, the first exposure activates a primary IgE antibody response that sensitizes an individual to type I hypersensitivity reaction upon subsequent exposure.

Type II (Cytotoxic) Hypersensitivities

Immune reactions categorized as type II hypersensitivities, or cytotoxic hypersensitivities, are mediated by IgG and IgM antibodies binding to cell-surface antigens or matrix-associated antigens on basement membranes. These antibodies can either activate complement, resulting in an inflammatory response and lysis of the targeted cells, or they can be involved in antibody-dependent cell-mediated cytotoxicity (ADCC) with cytotoxic T cells.

Type III Hypersensitivities

Type III hypersensitivities are immune-complex reactions that were first characterized by Nicolas Maurice Arthus (1862–1945) in 1903. To produce antibodies for experimental procedures, Arthus immunized rabbits by injecting them with serum from horses. However, while immunizing rabbits repeatedly with horse serum, Arthus noticed a previously unreported and unexpected localized subcutaneous hemorrhage with edema at the site of injection. This reaction developed within 3 to10 hours after injection. This localized reaction to non-self serum proteins was called an Arthus reaction. An Arthus reaction occurs when soluble antigens bind with IgG in a ratio that results in the accumulation of antigen-antibody aggregates called immune complexes.

Type IV Hypersensitivities

Type IV hypersensitivities are not mediated by antibodies like the other three types of hypersensitivities. Rather, type IV hypersensitivities are regulated by T cells and involve the action of effector cells. These types of hypersensitivities can be organized into three subcategories based on T-cell subtype, type of antigen, and the resulting effector mechanism ([link]).

Hypersensitivity Pneumonitis

Some disease caused by hypersensitivities are not caused exclusively by one type. For example, hypersensitivity pneumonitis (HP), which is often an occupational or environmental disease, occurs when the lungs become inflamed due to an allergic reaction to inhaled dust, endospores, bird feathers, bird droppings, molds, or chemicals. HP goes by many different names associated with various forms of exposure ([link]). HP associated with bird droppings is sometimes called pigeon fancier’s lung or poultry worker’s lung—both common in bird breeders and handlers. Cheese handler’s disease, farmer’s lung, sauna takers' disease, and hot-tub lung are other names for HP associated with exposure to molds in various environments.

Diagnosis of Hypersensitivities

Diagnosis of type I hypersensitivities is a complex process requiring several diagnostic tests in addition to a well-documented patient history. Serum IgE levels can be measured, but elevated IgE alone does not confirm allergic disease. As part of the process to identify the antigens responsible for a type I reaction allergy, testing through a prick puncture skin test (PPST) or an intradermal test can be performed. PPST is carried out with the introduction of allergens in a series of superficial skin pricks on the patient’s back or arms ([link]). PPSTs are considered to be the most convenient and least expensive way to diagnose allergies, according to the US Joint Council of Allergy and the European Academy of Allergy and Immunology. The second type of testing, the intradermal test, requires injection into the dermis with a small needle. This needle, also known as a tuberculin needle, is attached to a syringe containing a small amount of allergen. Both the PPST and the intradermal tests are observed for 15–20 minutes for a wheal-flare reaction to the allergens. Measurement of any wheal (a raised, itchy bump) and flare (redness) within minutes indicates a type I hypersensitivity, and the larger the wheal-flare reaction, the greater the patient’s sensitivity to the allergen.

Treatments of Hypersensitivities

Allergic reactions can be treated in various ways. Prevention of allergic reactions can be achieved by desensitization (hyposensitization) therapy, which can be used to reduce the hypersensitivity reaction through repeated injections of allergens. Extremely dilute concentrations of known allergens (determined from the allergen tests) are injected into the patient at prescribed intervals (e.g., weekly). The quantity of allergen delivered by the shots is slowly increased over a buildup period until an effective dose is determined and that dose is maintained for the duration of treatment, which can last years. Patients are usually encouraged to remain in the doctor’s office for 30 minutes after receiving the injection in case the allergens administered cause a severe systemic reaction. Doctors’ offices that administer desensitization therapy must be prepared to provide resuscitation and drug treatment in the case of such an event.

Autoimmune Disorders

Organ-Specific Autoimmune Diseases

Some autoimmune diseases are considered organ specific, meaning that the immune system targets specific organs or tissues. Examples of organ-specific autoimmune diseases include celiac disease, Graves disease, Hashimoto thyroiditis, type I diabetes mellitus, and Addison disease.

Systemic Autoimmune Diseases

Whereas organ-specific autoimmune diseases target specific organs or tissues, systemic autoimmune diseases are more generalized, targeting multiple organs or tissues throughout the body. Examples of systemic autoimmune diseases include multiple sclerosis, myasthenia gravis, psoriasis, rheumatoid arthritis, and systemic lupus erythematosus.

Organ Transplantation and Rejection

Transplant Rejection

The different types of grafts described above have varying risks for rejection ([link]). Rejection occurs when the recipient’s immune system recognizes the donor tissue as foreign (non-self), triggering an immune response. The major histocompatibility complex markers MHC I and MHC II, more specifically identified as human leukocyte antigens (HLAs), play a role in transplant rejection. The HLAs expressed in tissue transplanted from a genetically different individual or species may be recognized as non-self molecules by the host’s dendritic cells. If this occurs, the dendritic cells will process and present the foreign HLAs to the host’s helper T cells and cytotoxic T cells, thereby activating them. Cytotoxic T cells then target and kill the grafted cells through the same mechanism they use to kill virus-infected cells; helper T cells may also release cytokines that activate macrophages to kill graft cells.

Graft-versus-Host Disease

A form of rejection called graft-versus-host disease (GVHD) primarily occurs in recipients of bone marrow transplants and peripheral blood stem cells. GHVD presents a unique situation because the transplanted tissue is capable of producing immune cells; APCs in the donated bone marrow may recognize the host cells as non-self, leading to activation of the donor cytotoxic T cells. Once activated, the donor’s T cells attack the recipient cells, causing acute GVHD.

The Future of Transplantation

Historically speaking, the practice of transplanting tissues—and the complications that can accompany such procedures—is a relatively recent development. It was not until 1954 that the first successful organ transplantation between two humans was achieved. Yet the field of organ transplantation has progressed rapidly since that time.

Immunodeficiency

Primary Immunodeficiency

Primary immunodeficiencies, which number more than 250, are caused by inherited defects of either nonspecific innate or specific adaptive immune defenses. In general, patients born with primary immunodeficiency (PI) commonly have an increased susceptibility to infection. This susceptibility can become apparent shortly after birth or in early childhood for some individuals, whereas other patients develop symptoms later in life. Some primary immunodeficiencies are due to a defect of a single cellular or humoral component of the immune system; others may result from defects of more than one component. Examples of primary immunodeficiencies include chronic granulomatous disease, X-linked agammaglobulinemia, selective IgA deficiency, and severe combined immunodeficiency disease.

Secondary Immunodeficiency

A secondary immunodeficiency occurs as a result an acquired impairment of function of B cells, T cells, or both. Secondary immunodeficiencies can be caused by:

Cancer Immunobiology and Immunotherapy

Cell-Mediated Response to Tumors

Cell-mediated immune responses can be directed against cancer cells, many of which do not have the normal complement of self-proteins, making them a target for elimination. Abnormal cancer cells may also present tumor antigens. These tumor antigens are not a part of the screening process used to eliminate lymphocytes during development; thus, even though they are self-antigens, they can stimulate and drive adaptive immune responses against abnormal cells.

Cancer Vaccines

There are two types of cancer vaccines: preventive and therapeutic. Preventive vaccines are used to prevent cancer from occurring, whereas therapeutic vaccines are used to treat patients with cancer. Most preventive cancer vaccines target viral infections that are known to lead to cancer. These include vaccines against human papillomavirus (HPV) and hepatitis B, which help prevent cervical and liver cancer, respectively.

Laboratory Analysis of the Immune Response

Introduction

Polyclonal and Monoclonal Antibody Production

Producing Polyclonal Antibodies

Antibodies used for research and diagnostic purposes are often obtained by injecting a lab animal such as a rabbit or a goat with a specific antigen. Within a few weeks, the animal’s immune system will produce high levels of antibodies specific for the antigen. These antibodies can be harvested in an antiserum, which is whole serum collected from an animal following exposure to an antigen. Because most antigens are complex structures with multiple epitopes, they result in the production of multiple antibodies in the lab animal. This so-called polyclonal antibody response is also typical of the response to infection by the human immune system. Antiserum drawn from an animal will thus contain antibodies from multiple clones of B cells, with each B cell responding to a specific epitope on the antigen ([link]).

Clinical Uses of Polyclonal Antisera

Polyclonal antisera are used in many clinical tests that are designed to determine whether a patient is producing antibodies in response to a particular pathogen. While these tests are certainly powerful diagnostic tools, they have their limitations, because they are an indirect means of determining whether a particular pathogen is present. Tests based on a polyclonal response can sometimes lead to a false-positive result—in other words, a test that confirms the presence of an antigen that is, in fact, not present. Antibody-based tests can also result in a false-negative result, which occurs when the test fails to detect an antibody that is, in fact, present.

Producing Monoclonal Antibodies

Some types of assays require better antibody specificity and affinity than can be obtained using a polyclonal antiserum. To attain this high specificity, all of the antibodies must bind with high affinity to a single epitope. This high specificity can be provided by monoclonal antibodies (mAbs). [link] compares some of the important characteristics of monoclonal and polyclonal antibodies.

Clinical Uses of Monoclonal Antibodies

Since the most common methods for producing monoclonal antibodies use mouse cells, it is necessary to create humanized monoclonal antibodies for human clinical use. Mouse antibodies cannot be injected repeatedly into humans, because the immune system will recognize them as being foreign and will respond to them with neutralizing antibodies. This problem can be minimized by genetically engineering the antibody in the mouse B cell. The variable regions of the mouse light and heavy chain genes are ligated to human constant regions, and the chimeric gene is then transferred into a host cell. This allows production of a mAb that is mostly “human” with only the antigen-binding site being of mouse origin.

Detecting Antigen-Antibody Complexes

Precipitin Reactions

A visible antigen-antibody complex is called a precipitin, and *in vitro* assays that produce a precipitin are called precipitin reactions. A precipitin reaction typically involves adding soluble antigens to a test tube containing a solution of antibodies. Each antibody has two arms, each of which can bind to an epitope. When an antibody binds to two antigens, the two antigens become bound together by the antibody. A lattice can form as antibodies bind more and more antigens together, resulting in a precipitin ([link]). Most precipitin tests use a polyclonal antiserum rather than monoclonal antibodies because polyclonal antibodies can bind to multiple epitopes, making lattice formation more likely. Although mAbs may bind some antigens, the binding will occur less often, making it much less likely that a visible precipitin will form.

Neutralization Assay

To cause infection, viruses must bind to receptors on host cells. Antiviral antibodies can neutralize viral infections by coating the virions, blocking the binding ([link]). This activity neutralizes virions and can result in the formation of large antibody-virus complexes (which are readily removed by phagocytosis) or by antibody binding to the virus and blocking its binding to host cell receptors. This neutralization activity is the basis of neutralization assays, sensitive assays used for diagnoses of viral infections.

Immunoelectrophoresis

When a patient has elevated protein levels in the blood or is losing protein in the urine, a clinician will often order a polyacrylamide gel electrophoresis (PAGE) assay (see Visualizing and Characterizing DNA, RNA, and Protein). This assay compares the relative abundance of the various types of serum proteins. Abnormal protein electrophoresis patterns can be further studied using immunoelectrophoresis (IEP). The IEP begins by running a PAGE. Antisera against selected serum proteins are added to troughs running parallel to the electrophoresis track, forming precipitin arcs similar to those seen in an Ouchterlony assay ([link]). This allows the identification of abnormal immunoglobulin proteins in the sample.

Immunoblot Assay: The Western Blot

After performing protein gel electrophoresis, specific proteins can be identified in the gel using antibodies. This technique is known as the western blot. Following separation of proteins by PAGE, the protein antigens in the gel are transferred to and immobilized on a nitrocellulose membrane. This membrane can then be exposed to a primary antibody produced to specifically bind to the protein of interest. A second antibody equipped with a molecular beacon will then bind to the first. These secondary antibodies are coupled to another molecule such as an enzyme or a fluorophore (a molecule that fluoresces when excited by light). When using antibodies coupled to enzymes, a chromogenic substrate for the enzyme is added. This substrate is usually colorless but will develop color in the presence of the antibody. The fluorescence or substrate coloring identifies the location of the specific protein in the membrane to which the antibodies are bound ([link]).

Complement-Mediated Immunoassay

One of the key functions of antibodies is the activation (fixation) of complement. When antibody binds to bacteria, for example, certain complement proteins recognize the bound antibody and activate the complement cascade. In response, other complement proteins bind to the bacteria where some serve as opsonins to increase the efficiency of phagocytosis and others create holes in gram-negative bacterial cell membranes, causing lysis. This lytic activity can be used to detect the presence of antibodies against specific antigens in the serum.

Agglutination Assays

Agglutination of Bacteria and Viruses

The use of agglutination tests to identify streptococcal bacteria was developed in the 1920s by Rebecca Lancefield working with her colleagues A.R. Dochez and Oswald Avery.[footnote] She used antibodies to identify M protein, a virulence factor on streptococci that is necessary for the bacteria’s ability to cause strep throat. Production of antibodies against M protein is crucial in mounting a protective response against the bacteria.

Lancefield, Rebecca C., “The Antigenic Complex of *Streptococcus haemoliticus*. I. Demonstration of a Type-Specific Substance in Extracts of *Streptococcus haemolyticus*,” *The Journal of Experimental Medicine* 47, no. 1 (1928): 91-103.

Blood Typing and Cross-Matching

In addition to antibodies against bacteria and viruses to which they have previously been exposed, most individuals also carry antibodies against blood types other than their own. There are presently 33 immunologically important blood-type systems, many of which are restricted within various ethnic groups or rarely result in the production of antibodies. The most important and perhaps best known are the ABO and Rh blood groups (see [link]).

EIAs and ELISAs

Immunostaining

One powerful use of EIA is immunostaining, in which antibody-enzyme conjugates enhance microscopy. Immunohistochemistry (IHC) is used for examining whole tissues. As seen in [link], a section of tissue can be stained to visualize the various cell types. In this example, a mAb against CD8 was used to stain CD8 cells in a section of tonsil tissue. It is now possible to count the number of CD8 cells, determine their relative numbers versus the other cell types present, and determine the location of these cells within this tissue. Such data would be useful for studying diseases such as AIDS, in which the normal function of CD8 cells is crucial for slowing disease progression.

Enzyme-linked Immunosorbent Assays (ELISAs)

The enzyme-linked immunosorbent assays (ELISAs) are widely used EIAs. In the direct ELISA, antigens are immobilized in the well of a microtiter plate. An antibody that is specific for a particular antigen and is conjugated to an enzyme is added to each well. If the antigen is present, then the antibody will bind. After washing to remove any unbound antibodies, a colorless substrate (chromogen) is added. The presence of the enzyme converts the substrate into a colored end product ([link]). While this technique is faster because it only requires the use of one antibody, it has the disadvantage that the signal from a direct ELISA is lower (lower sensitivity).

Immunofiltration and Immunochromatographic Assays

For some situations, it may be necessary to detect or quantify antigens or antibodies that are present at very low concentration in solution. Immunofiltration techniques have been developed to make this possible. In immunofiltration, a large volume of fluid is passed through a porous membrane into an absorbent pad. An antigen attached to the porous membrane will capture antibody as it passes; alternatively, we can also attach an antibody to the membrane to capture antigen.

Fluorescent Antibody Techniques

Direct Fluorescent Antibody Techniques

Direct fluorescent antibody (DFA) tests use a fluorescently labeled mAb to bind and illuminate a target antigen. DFA tests are particularly useful for the rapid diagnosis of bacterial diseases. For example, fluorescence-labeled antibodies against *Streptococcus pyogenes* (group A strep) can be used to obtain a diagnosis of strep throat from a throat swab. The diagnosis is ready in a matter of minutes, and the patient can be started on antibiotics before even leaving the clinic. DFA techniques may also be used to diagnose pneumonia caused by *Mycoplasma pneumoniae* or *Legionella pneumophila* from sputum samples ([link]). The fluorescent antibodies bind to the bacteria on a microscope slide, allowing ready detection of the bacteria using a fluorescence microscope. Thus, the DFA technique is valuable for visualizing certain bacteria that are difficult to isolate or culture from patient samples.

Indirect Fluorescent Antibody Techniques

Indirect fluorescent antibody (IFA) tests ([link]) are used to look for antibodies in patient serum. For example, an IFA test for the diagnosis of syphilis uses *T. pallidum* cells isolated from a lab animal (the bacteria cannot be grown on lab media) and a smear prepared on a glass slide. Patient serum is spread over the smear and anti-treponemal antibodies, if present, are allowed to bind. The serum is washed off and a secondary antibody added. The secondary antibody is an antihuman immunoglobulin conjugated to a fluorogen. On examination, the *T. pallidum* bacteria will only be visible if they have been bound by the antibodies from the patient’s serum.

Flow Cytometry

Fluorescently labeled antibodies can be used to quantify cells of a specific type in a complex mixture using flow cytometry ([link]), an automated, cell-counting system that detects fluorescing cells as they pass through a narrow tube one cell at a time. For example, in HIV infections, it is important to know the level of CD4 T cells in the patient’s blood; if the numbers fall below 500 per μL of blood, the patient becomes more likely to acquire opportunistic infections; below 200 per μL, the patient can no longer mount a useful adaptive immune response at all. The analysis begins by incubating a mixed-cell population (e.g., white blood cells from a donor) with a fluorescently labeled mAb specific for a subpopulation of cells (e.g., anti-CD4). Some experiments look at two cell markers simultaneously by adding a different fluorogen to the appropriate mAb. The cells are then introduced to the flow cytometer through a narrow capillary that forces the cells to pass in single file. A laser is used to activate the fluorogen. The fluorescent light radiates out in all directions, so the fluorescence detector can be positioned at an angle from the incident laser light.

Cell Sorting Using Immunofluorescence

The flow cytometer and immunofluorescence can also be modified to sort cells from a single sample into purified subpopulations of cells for research purposes. This modification of the flow cytometer is called a fluorescence-activated cell sorter (FACS). In a FACS, fluorescence by a cell induces the device to put a charge on a droplet of the transporting fluid containing that cell. The charge is specific to the wavelength of the fluorescent light, which allows for differential sorting by those different charges. The sorting is accomplished by an electrostatic deflector that moves the charged droplet containing the cell into one collecting vessel or another. The process results in highly purified subpopulations of cells.

Skin and Eye Infections

Introduction

Anatomy and Normal Microbiota of the Skin and Eyes

Layers of the Skin

Human skin is made up of several layers and sublayers. The two main layers are the epidermis and the dermis. These layers cover a third layer of tissue called the hypodermis, which consists of fibrous and adipose connective tissue ([link]).

Normal Microbiota of the Skin

The skin is home to a wide variety of normal microbiota, consisting of commensal organisms that derive nutrition from skin cells and secretions such as sweat and sebum. The normal microbiota of skin tends to inhibit transient-microbe colonization by producing antimicrobial substances and outcompeting other microbes that land on the surface of the skin. This helps to protect the skin from pathogenic infection.

Infections of the Skin

While the microbiota of the skin can play a protective role, it can also cause harm in certain cases. Often, an opportunistic pathogen residing in the skin microbiota of one individual may be transmitted to another individual more susceptible to an infection. For example, methicillin-resistant *Staphylococcus aureus* (MRSA) can often take up residence in the nares of health care workers and hospital patients; though harmless on intact, healthy skin, MRSA can cause infections if introduced into other parts of the body, as might occur during surgery or via a post-surgical incision or wound. This is one reason why clean surgical sites are so important.

Anatomy and Microbiota of the Eye

Although the eye and skin have distinct anatomy, they are both in direct contact with the external environment. An important component of the eye is the nasolacrimal drainage system, which serves as a conduit for the fluid of the eye, called tears. Tears flow from the external eye to the nasal cavity by the lacrimal apparatus, which is composed of the structures involved in tear production ([link]). The lacrimal gland, above the eye, secretes tears to keep the eye moist. There are two small openings, one on the inside edge of the upper eyelid and one on the inside edge of the lower eyelid, near the nose. Each of these openings is called a lacrimal punctum. Together, these lacrimal puncta collect tears from the eye that are then conveyed through lacrimal ducts to a reservoir for tears called the lacrimal sac**,** also known as the dacrocyst or tear sac.

Infections of the Eye

The conjunctiva is a frequent site of infection of the eye; like other mucous membranes, it is also a common portal of entry for pathogens. Inflammation of the conjunctiva is called conjunctivitis, although it is commonly known as pinkeye because of the pink appearance in the eye. Infections of deeper structures, beneath the cornea, are less common ([link]). Conjunctivitis occurs in multiple forms. It may be acute or chronic. Acute purulent conjunctivitis is associated with pus formation, while acute hemorrhagic conjunctivitis is associated with bleeding in the conjunctiva. The term blepharitis refers to an inflammation of the eyelids, while keratitis refers to an inflammation of the cornea ([link]); keratoconjunctivitis is an inflammation of both the cornea and the conjunctiva, and dacryocystitis is an inflammation of the lacrimal sac that can often occur when a nasolacrimal duct is blocked.

Bacterial Infections of the Skin and Eyes

Staphylococcal Infections of the Skin

*Staphylococcus* species are commonly found on the skin, with *S. epidermidis* and *S. hominis* being prevalent in the normal microbiota. *S. aureus* is also commonly found in the nasal passages and on healthy skin, but pathogenic strains are often the cause of a broad range of infections of the skin and other body systems.

Streptococcal Infections of the Skin

*Streptococcus* are gram-positive cocci with a microscopic morphology that resembles chains of bacteria. Colonies are typically small (1–2 mm in diameter), translucent, entire edge, with a slightly raised elevation that can be either nonhemolytic, alpha-hemolytic, or beta-hemolytic when grown on blood agar ([link]). Additionally, they are facultative anaerobes that are catalase-negative.

*Pseudomonas* Infections of the Skin

Another important skin pathogen is *Pseudomonas aeruginosa*, a gram-negative, oxidase-positive, aerobic bacillus that is commonly found in water and soil as well as on human skin. *P. aeruginosa* is a common cause of opportunistic infections of wounds and burns. It can also cause hot tub rash, a condition characterized by folliculitis that frequently afflicts users of pools and hot tubs (recall the Clinical Focus case in Microbial Biochemistry). *P. aeruginosa* is also the cause of otitis externa (swimmer’s ear), an infection of the ear canal that causes itching, redness, and discomfort, and can progress to fever, pain, and swelling ([link]).

Acne

One of the most ubiquitous skin conditions is acne. Acne afflicts nearly 80% of teenagers and young adults, but it can be found in individuals of all ages. Higher incidence among adolescents is due to hormonal changes that can result in overproduction of sebum.

Anthrax

The zoonotic disease anthrax is caused by *Bacillus* *anthracis*, a gram-positive, endospore-forming, facultative anaerobe. Anthrax mainly affects animals such as sheep, goats, cattle, and deer, but can be found in humans as well. Sometimes called wool sorter’s disease, it is often transmitted to humans through contact with infected animals or animal products, such as wool or hides. However, exposure to *B.* *anthracis* can occur by other means, as the endospores are widespread in soils and can survive for long periods of time, sometimes for hundreds of years.

Bacterial Conjunctivitis

Like the skin, the surface of the eye comes in contact with the outside world and is somewhat prone to infection by bacteria in the environment. Bacterial conjunctivitis (pinkeye) is a condition characterized by inflammation of the conjunctiva, often accompanied by a discharge of sticky fluid (described as acute purulent conjunctivitis) ([link]). Conjunctivitis can affect one eye or both, and it usually does not affect vision permanently. Bacterial conjunctivitis is most commonly caused by *Haemophilus* *influenzae*, but can also be caused by other species such as *Moraxella catarrhalis*, *S. pneumoniae,* and *S. aureus*. The causative agent may be identified using bacterial cultures, Gram stain, and diagnostic biochemical, antigenic, or nucleic acid profile tests of the isolated pathogen. Bacterial conjunctivitis is very contagious, being transmitted via secretions from infected individuals, but it is also self-limiting. Bacterial conjunctivitis usually resolves in a few days, but topical antibiotics are sometimes prescribed. Because this condition is so contagious, medical attention is recommended whenever it is suspected. Individuals who use contact lenses should discontinue their use when conjunctivitis is suspected. Certain symptoms, such as blurred vision, eye pain, and light sensitivity, can be associated with serious conditions and require medical attention.

Trachoma

Trachoma, or granular conjunctivitis, is a common cause of preventable blindness that is rare in the United States but widespread in developing countries, especially in Africa and Asia. The condition is caused by the same species that causes neonatal inclusion conjunctivitis in infants, *Chlamydia trachomatis*. *C. trachomatis* can be transmitted easily through fomites such as contaminated towels, bed linens, and clothing and also by direct contact with infected individuals. *C. trachomatis* can also be spread by flies that transfer infected mucous containing *C. trachomatis* from one human to another.

Bacterial Keratitis

Keratitis can have many causes, but bacterial keratitis is most frequently caused by *Staphylococcus epidermidis* and/or *Pseudomonas aeruginosa*. Contact lens users are particularly at risk for such an infection because *S. epidermidis* and *P. aeruginosa* both adhere well to the surface of the lenses. Risk of infection can be greatly reduced by proper care of contact lenses and avoiding wearing lenses overnight. Because the infection can quickly lead to blindness, prompt and aggressive treatment with antibiotics is important. The causative agent may be identified using bacterial cultures, Gram stain, and diagnostic biochemical, antigenic, or nucleic acid profile tests of the isolated pathogen.

Biofilms and Infections of the Skin and Eyes

When treating bacterial infections of the skin and eyes, it is important to consider that few such infections can be attributed to a single pathogen. While biofilms may develop in other parts of the body, they are especially relevant to skin infections (such as those caused by *S. aureus* or *P. aeruginosa*) because of their prevalence in chronic skin wounds. Biofilms develop when bacteria (and sometimes fungi) attach to a surface and produce extracellular polymeric substances (EPS) in which cells of multiple organisms may be embedded. When a biofilm develops on a wound, it may interfere with the natural healing process as well as diagnosis and treatment.

Viral Infections of the Skin and Eyes

Papillomas

Papillomas (warts) are the expression of common skin infections by human papillomavirus (HPV) and are transmitted by direct contact. There are many types of HPV, and they lead to a variety of different presentations, such as common warts, plantar warts, flat warts, and filiform warts. HPV can also cause sexually-transmitted genital warts, which will be discussed in Urogenital System Infections. Vaccination is available for some strains of HPV.

Oral Herpes

Another common skin virus is herpes simplex virus (HSV). HSV has historically been divided into two types, HSV-1 and HSV-2. HSV-1 is typically transmitted by direct oral contact between individuals, and is usually associated with oral herpes. HSV-2 is usually transmitted sexually and is typically associated with genital herpes. However, both HSV-1 and HSV-2 are capable of infecting any mucous membrane, and the incidence of genital HSV-1 and oral HSV-2 infections has been increasing in recent years. In this chapter, we will limit our discussion to infections caused by HSV-1; HSV-2 and genital herpes will be discussed in Urogenital System Infections.

Roseola and Fifth Disease

The viral diseases roseola and fifth disease are somewhat similar in terms of their presentation, but they are caused by different viruses. Roseola, sometimes called roseola infantum or exanthem subitum (“sudden rash”), is a mild viral infection usually caused by human herpesvirus-6 (HHV-6) and occasionally by HHV-7. It is spread via direct contact with the saliva or respiratory secretions of an infected individual, often through droplet aerosols. Roseola is very common in children, with symptoms including a runny nose, a sore throat, and a cough, along with (or followed by) a high fever (39.4 ºC). About three to five days after the fever subsides, a rash may begin to appear on the chest and abdomen. The rash, which does not cause discomfort, initially forms characteristic macules that are flat or papules that are firm and slightly raised; some macules or papules may be surrounded by a white ring. The rash may eventually spread to the neck and arms, and sometimes continues to spread to the face and legs. The diagnosis is generally made based upon observation of the symptoms. However, it is possible to perform serological tests to confirm the diagnosis. While treatment may be recommended to control the fever, the disease usually resolves without treatment within a week after the fever develops. For individuals at particular risk, such as those who are immunocompromised, the antiviral medication ganciclovir may be used.

Viral Conjunctivitis

Like bacterial conjunctivitis viral infections of the eye can cause inflammation of the conjunctiva and discharge from the eye. However, viral conjunctivitis tends to produce a discharge that is more watery than the thick discharge associated with bacterial conjunctivitis. The infection is contagious and can easily spread from one eye to the other or to other individuals through contact with eye discharge.

Mycoses of the Skin

Tineas

A group of cutaneous mycoses called tineas are caused by dermatophytes, fungal molds that require keratin, a protein found in skin, hair, and nails, for growth. There are three genera of dermatophytes, all of which can cause cutaneous mycoses: *Trichophyton*, *Epidermophyton*, and *Microsporum*. Tineas on most areas of the body are generally called ringworm, but tineas in specific locations may have distinctive names and symptoms (see [link] and [link]). Keep in mind that these names—even though they are Latinized—refer to locations on the body, not causative organisms. Tineas can be caused by different dermatophytes in most areas of the body.

Cutaneous Aspergillosis

Another cause of cutaneous mycoses is *Aspergillus*, a genus consisting of molds of many different species, some of which cause a condition called aspergillosis. Primary cutaneous aspergillosis, in which the infection begins in the skin, is rare but does occur. More common is secondary cutaneous aspergillosis, in which the infection begins in the respiratory system and disseminates systemically. Both primary and secondary cutaneous aspergillosis result in distinctive eschars that form at the site or sites of infection ([link]). Pulmonary aspergillosis will be discussed more thoroughly in Respiratory Mycoses).

Candidiasis of the Skin and Nails

*Candida albicans* and other yeasts in the genus *Candida* can cause skin infections referred to as cutaneous candidiasis. *Candida* spp. are sometimes responsible for intertrigo, a general term for a rash that occurs in a skin fold, or other localized rashes on the skin. *Candida* can also infect the nails, causing them to become yellow and harden ([link]).

Sporotrichosis

Whereas cutaneous mycoses are superficial, subcutaneous mycoses can spread from the skin to deeper tissues. In temperate regions, the most common subcutaneous mycosis is a condition called sporotrichosis, caused by the fungus *Sporothrix* *schenkii* and commonly known as rose gardener’s disease or rose thorn disease (recall Case in Point: Every Rose Has Its Thorn). Sporotrichosis is often contracted after working with soil, plants, or timber, as the fungus can gain entry through a small wound such as a thorn-prick or splinter. Sporotrichosis can generally be avoided by wearing gloves and protective clothing while gardening and promptly cleaning and disinfecting any wounds sustained during outdoor activities.

Protozoan and Helminthic Infections of the Skin and Eyes

*Acanthamoeba* Infections

*Acanthamoeba* is a genus of free-living protozoan amoebae that are common in soils and unchlorinated bodies of fresh water. (This is one reason why some swimming pools are treated with chlorine.) The genus contains a few parasitic species, some of which can cause infections of the eyes, skin, and nervous system. Such infections can sometimes travel and affect other body systems. Skin infections may manifest as abscesses, ulcers, and nodules. When acanthamoebae infect the eye*,* causing inflammation of the cornea, the condition is called *Acanthamoeba* keratitis. [link] illustrates the *Acanthamoeba* life cycle and various modes of infection.

Loiasis

The helminth *Loa loa*, also known as the African eye worm, is a nematode that can cause loiasis, a disease endemic to West and Central Africa ([link]). The disease does not occur outside that region except when carried by travelers. There is evidence that individual genetic differences affect susceptibility to developing loiasis after infection by the *Loa loa* worm. Even in areas in which *Loa loa* worms are common, the disease is generally found in less than 30% of the population.[footnote] It has been suggested that travelers who spend time in the region may be somewhat more susceptible to developing symptoms than the native population, and the presentation of infection may differ.[footnote]

Garcia, A.. et al. “Genetic Epidemiology of Host Predisposition Microfilaraemia in Human Loiasis.” *Tropical Medicine and International Health* 4 (1999) 8:565–74. http://www.ncbi.nlm.nih.gov/pubmed/10499080. Accessed Sept 14, 2016.Spinello, A., et al. “Imported *Loa loa* Filariasis: Three Cases and a Review of Cases Reported in Non-Endemic Countries in the Past 25 Years.” *International Journal of Infectious Disease* 16 (2012) 9: e649–e662. DOI: http://dx.doi.org/10.1016/j.ijid.2012.05.1023.

Respiratory System Infections

Introduction

Anatomy and Normal Microbiota of the Respiratory Tract

Anatomy of the Upper Respiratory System

The respiratory system can be conceptually divided into upper and lower regions at the point of the epiglottis, the structure that seals off the lower respiratory system from the pharynx during swallowing ([link]). The upper respiratory system is in direct contact with the external environment. The nares (or nostrils) are the external openings of the nose that lead back into the nasal cavity, a large air-filled space behind the nares. These anatomical sites constitute the primary opening and first section of the respiratory tract, respectively. The nasal cavity is lined with hairs that trap large particles, like dust and pollen, and prevent their access to deeper tissues. The nasal cavity is also lined with a mucous membrane and Bowman’s glands that produce mucus to help trap particles and microorganisms for removal. The nasal cavity is connected to several other air-filled spaces. The sinuses, a set of four, paired small cavities in the skull, communicate with the nasal cavity through a series of small openings. The nasopharynx is part of the upper throat extending from the posterior nasal cavity. The nasopharynx carries air inhaled through the nose. The middle ear is connected to the nasopharynx through the eustachian tube. The middle ear is separated from the outer ear by the tympanic membrane, or ear drum. And finally, the lacrimal glands drain to the nasal cavity through the nasolacrimal ducts (tear ducts). The open connections between these sites allow microorganisms to move from the nasal cavity to the sinuses, middle ears (and back), and down into the lower respiratory tract from the nasopharynx.

Anatomy of the Lower Respiratory System

The lower respiratory system begins below the epiglottis in the larynx or voice box ([link]). The trachea, or windpipe, is a cartilaginous tube extending from the larynx that provides an unobstructed path for air to reach the lungs. The trachea bifurcates into the left and right bronchi as it reaches the lungs. These paths branch repeatedly to form smaller and more extensive networks of tubes, the bronchioles. The terminal bronchioles formed in this tree-like network end in cul-de-sacs called the alveoli. These structures are surrounded by capillary networks and are the site of gas exchange in the respiratory system. Human lungs contain on the order of 400,000,000 alveoli. The outer surface of the lungs is protected with a double-layered pleural membrane. This structure protects the lungs and provides lubrication to permit the lungs to move easily during respiration.

Defenses of the Respiratory System

The inner lining of the respiratory system consists of mucous membranes ([link]) and is protected by multiple immune defenses. The goblet cells within the respiratory epithelium secrete a layer of sticky mucus. The viscosity and acidity of this secretion inhibits microbial attachment to the underlying cells. In addition, the respiratory tract contains ciliated epithelial cells. The beating cilia dislodge and propel the mucus, and any trapped microbes, upward to the epiglottis, where they will be swallowed. Elimination of microbes in this manner is referred to as the mucociliary escalator effect and is an important mechanism that prevents inhaled microorganisms from migrating further into the lower respiratory tract.

Normal Microbiota of the Respiratory System

The upper respiratory tract contains an abundant and diverse microbiota. The nasal passages and sinuses are primarily colonized by members of the Firmicutes, Actinobacteria, and Proteobacteria. The most common bacteria identified include *Staphylococcus epidermidis*, viridans group streptococci (VGS), *Corynebacterium* spp. (diphtheroids), *Propionibacterium* spp., and *Haemophilus* spp. The oropharynx includes many of the same isolates as the nose and sinuses, with the addition of variable numbers of bacteria like species of *Prevotella*, *Fusobacterium*, *Moraxella*, and *Eikenella*, as well as some *Candida* fungal isolates. In addition, many healthy humans asymptomatically carry potential pathogens in the upper respiratory tract. As much as 20% of the population carry *Staphylococcus aureus* in their nostrils.[footnote] The pharynx, too, can be colonized with pathogenic strains of *Streptococcus*, *Haemophilus*, and *Neisseria*.

J. Kluytmans et al. “Nasal Carriage of *Staphylococcus aureus*: Epidemiology, Underlying Mechanisms, and Associated Risks.” *Clinical Microbiology Reviews* 10 no. 3 (1997):505–520.

Signs and Symptoms of Respiratory Infection

Microbial diseases of the respiratory system typically result in an acute inflammatory response. These infections can be grouped by the location affected and have names ending in “itis”, which literally means *inflammation of*. For instance, rhinitis is an inflammation of the nasal cavities, often characteristic of the common cold. Rhinitis may also be associated with hay fever allergies or other irritants. Inflammation of the sinuses is called sinusitis inflammation of the ear is called otitis. Otitis media is an inflammation of the middle ear. A variety of microbes can cause pharyngitis, commonly known as a sore throat. An inflammation of the larynx is called laryngitis. The resulting inflammation may interfere with vocal cord function, causing voice loss. When tonsils are inflamed, it is called tonsillitis. Chronic cases of tonsillitis may be treated surgically with tonsillectomy. More rarely, the epiglottis can be infected, a condition called epiglottitis. In the lower respiratory system, the inflammation of the bronchial tubes results in bronchitis. Most serious of all is pneumonia, in which the alveoli in the lungs are infected and become inflamed. Pus and edema accumulate and fill the alveoli with fluids (called consolidations). This reduces the lungs’ ability to exchange gases and often results in a productive cough expelling phlegm and mucus. Cases of pneumonia can range from mild to life-threatening, and remain an important cause of mortality in the very young and very old.

Bacterial Infections of the Respiratory Tract

Streptococcal Infections

A common upper respiratory infection, streptococcal pharyngitis (strep throat) is caused by *Streptococcus pyogenes*. This gram-positive bacterium appears as chains of cocci, as seen in [link]. Rebecca Lancefield serologically classified streptococci in the 1930s using carbohydrate antigens from the bacterial cell walls. *S. pyogenes* is the sole member of the Lancefield group A streptococci and is often referred to as GAS, or group A strep.

Acute Otitis Media

An infection of the middle ear is called acute otitis media (AOM), but often it is simply referred to as an earache. The condition is most common between ages 3 months and 3 years. In the United States, AOM is the second-leading cause of visits to pediatricians by children younger than age 5 years, and it is the leading indication for antibiotic prescription.[footnote]

G. Worrall. “Acute Otitis Media.” *Canadian Family Physician* 53 no. 12 (2007):2147–2148.

Diphtheria

The causative agent of diphtheria, *Corynebacterium diphtheriae*, is a club-shaped, gram-positive rod that belongs to the phylum Actinobacteria. Diphtheroids are common members of the normal nasopharyngeal microbiota. However, some strains of *C. diphtheriae* become pathogenic because of the presence of a temperate bacteriophage-encoded protein—the diphtheria toxin. Diphtheria is typically a respiratory infection of the oropharynx but can also cause impetigo-like lesions on the skin. Although the disease can affect people of all ages, it tends to be most severe in those younger than 5 years or older than 40 years. Like strep throat, diphtheria is commonly transmitted in the droplets and aerosols produced by coughing. After colonizing the throat, the bacterium remains in the oral cavity and begins producing the diphtheria toxin. This protein is an A-B toxin that blocks host-cell protein synthesis by inactivating elongation factor (EF)-2 (see Virulence Factors of Bacterial and Viral Pathogens). The toxin’s action leads to the death of the host cells and an inflammatory response. An accumulation of grayish exudate consisting of dead host cells, pus, red blood cells, fibrin, and infectious bacteria results in the formation of a pseudomembrane. The pseudomembrane can cover mucous membranes of the nasal cavity, tonsils, pharynx, and larynx ([link]). This is a classic sign of diphtheria. As the disease progresses, the pseudomembrane can enlarge to obstruct the fauces of the pharynx or trachea and can lead to suffocation and death. Sometimes, intubation, the placement of a breathing tube in the trachea, is required in advanced infections. If the diphtheria toxin spreads throughout the body, it can damage other tissues as well. This can include myocarditis (heart damage) and nerve damage that may impair breathing.

Bacterial Pneumonia

Pneumonia is a general term for infections of the lungs that lead to inflammation and accumulation of fluids and white blood cells in the alveoli. Pneumonia can be caused by bacteria, viruses, fungi, and other organisms, although the vast majority of pneumonias are bacterial in origin. Bacterial pneumonia is a prevalent, potentially serious infection; it caused more 50,000 deaths in the United States in 2014.[footnote] As the alveoli fill with fluids and white blood cells (consolidation), air exchange becomes impaired and patients experience respiratory distress ([link]). In addition, pneumonia can lead to pleurisy, an infection of the pleural membrane surrounding the lungs, which can make breathing very painful. Although many different bacteria can cause pneumonia under the right circumstances, three bacterial species cause most clinical cases: *Streptococcus pneumoniae*, *H*. *influenzae*, and *Mycoplasma pneumoniae*. In addition to these, we will also examine some of the less common causes of pneumonia.

KD Kochanek et al. “Deaths: Final Data for 2014.” *National Vital Statistics Reports* 65 no 4 (2016).

Tuberculosis

Tuberculosis (TB) is one of the deadliest infectious diseases in human history. Although tuberculosis infection rates in the United States are extremely low, the CDC estimates that about one-third of the world’s population is infected with *Mycobacterium tuberculosis*, the causal organism of TB, with 9.6 million new TB cases and 1.5 million deaths worldwide in 2014.[footnote]

Centers for Disease Control and Prevention. “Tuberculosis (TB). Data and Statistics.” http://www.cdc.gov/tb/statistics/default.htm

Pertussis (Whooping Cough)

The causative agent of pertussis, commonly called whooping cough, is *Bordetella pertussis*, a gram-negative coccobacillus. The disease is characterized by mucus accumulation in the lungs that leads to a long period of severe coughing. Sometimes, following a bout of coughing, a sound resembling a “whoop” is produced as air is inhaled through the inflamed and restricted airway—hence the name whooping cough. Although adults can be infected, the symptoms of this disease are most pronounced in infants and children. Pertussis is highly communicable through droplet transmission, so the uncontrollable coughing produced is an efficient means of transmitting the disease in a susceptible population.

Legionnaires Disease

An atypical pneumonia called Legionnaires disease (also known as legionellosis) is caused by an aerobic gram-negative bacillus, *Legionella pneumophila*. This bacterium infects free-living amoebae that inhabit moist environments, and infections typically occur from human-made reservoirs such as air-conditioning cooling towers, humidifiers, misting systems, and fountains. Aerosols from these reservoirs can lead to infections of susceptible individuals, especially those suffering from chronic heart or lung disease or other conditions that weaken the immune system.

Q Fever

The zoonotic disease Q fever is caused by a rickettsia, *Coxiella burnetii*. The primary reservoirs for this bacterium are domesticated livestock such as cattle, sheep, and goats. The bacterium may be transmitted by ticks or through exposure to the urine, feces, milk, or amniotic fluid of an infected animal. In humans, the primary route of infection is through inhalation of contaminated farmyard aerosols. It is, therefore, largely an occupational disease of farmers. Humans are acutely sensitive to *C. burnetii*—the infective dose is estimated to be just a few cells.[footnote] In addition, the organism is hardy and can survive in a dry environment for an extended time. Symptoms associated with acute Q fever include high fever, headache, coughing, pneumonia, and general malaise. In a small number of patients (less than 5%[footnote]), the condition may become chronic, often leading to endocarditis, which may be fatal.

WD Tigertt et al. “Airborne Q Fever.” *Bacteriological Reviews* 25 no. 3 (1961):285–293.Centers for Disease Control and Prevention. “Q fever. Symptoms, Diagnosis, and Treatment.” 2013. http://www.cdc.gov/qfever/symptoms/index.html. Accessed July 6, 2016.

Viral Infections of the Respiratory Tract

The Common Cold

The common cold is a generic term for a variety of mild viral infections of the nasal cavity. More than 200 different viruses are known to cause the common cold. The most common groups of cold viruses include rhinoviruses, coronaviruses, and adenoviruses. These infections are widely disseminated in the human population and are transmitted through direct contact and droplet transmission. Coughing and sneezing efficiently produce infectious aerosols, and rhinoviruses are known to persist on environmental surfaces for up to a week.[footnote]

AG L’Huillier et al. “Survival of Rhinoviruses on Human Fingers.” *Clinical Microbiology and Infection* 21, no. 4 (2015):381–385.

Influenza

Commonly known as the flu, influenza is a common viral disease caused by an orthomyxovirus that primarily affects the upper respiratory tract but can also extend into the lower respiratory tract. Influenza is pervasive worldwide and causes 3,000–50,000 deaths each year in the United States. The annual mortality rate can vary greatly depending on the virulence of the strain(s) responsible for seasonal epidemics. [footnote]

Centers for Disease Control and Prevention. “Estimating Seasonal Influenza-Associated Deaths in the United States: CDC Study Confirms Variability of Flu.” 2016. http://www.cdc.gov/flu/about/disease/us_flu-related_deaths.htm. Accessed July 6, 2016.

Viral Pneumonia

Viruses cause fewer cases of pneumonia than bacteria; however, several viruses can lead to pneumonia in children and the elderly. The most common sources of viral pneumonia are adenoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial viruses. The signs and symptoms produced by these viruses can range from mild cold-like symptoms to severe cases of pneumonia, depending on the virulence of the virus strain and the strength of the host defenses of the infected individual. Occasionally, infections can result in otitis media.

SARS and MERS

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) are two acute respiratory infections caused by coronaviruses. In both cases, these are thought to be zoonotic infections. Bats and civet cats are thought to have been the reservoirs for SARS; camels seem to be the reservoir for MERS.

Viral Respiratory Diseases Causing Skin Rashes

Measles, rubella (German measles), and chickenpox are three important viral diseases often associated with skin rashes. However, their symptoms are systemic, and because their portal of entry is the respiratory tract, they can be considered respiratory infections.

Respiratory Mycoses

Histoplasmosis

Histoplasmosis is a fungal disease of the respiratory system and most commonly occurs in the Mississippi Valley of the United States and in parts of Central and South America, Africa, Asia, and Australia. The causative agent, *Histoplasma capsulatum*, is a dimorphic fungus. This microbe grows as a filamentous mold in the environment but occurs as a budding yeast during human infections. The primary reservoir for this pathogen is soil, particularly in locations rich in bat or bird feces.

Coccidioidomycosis

Infection by the dimorphic fungus *Coccidioides immitis* causes coccidioidomycosis. Because the microbe is endemic to the San Joaquin Valley of California, the disease is sometimes referred to as Valley fever. A related species that causes similar infections is found in semi-arid and arid regions of the southwestern United States, Mexico, and Central and South America.[footnote]

DR Hospenthal. “Coccioidomycosis.” Medscape. 2015. http://emedicine.medscape.com/article/215978-overview. Accessed July 7, 2016.

Blastomycosis

Blastomycosis is a rare disease caused by another dimorphic fungus, *Blastomyces dermatitidis*. Like *Histoplasma* and *Coccidioides*, *Blastomyces* uses the soil as a reservoir, and fungal spores can be inhaled from disturbed soil. The pulmonary form of blastomycosis generally causes mild flu-like symptoms and is self-limiting. It can, however, become disseminated in immunocompromised people, leading to chronic cutaneous disease with subcutaneous lesions on the face and hands ([link]). These skin lesions eventually become crusty and discolored and can result in deforming scars. Systemic blastomycosis is rare, but if left untreated, it is always fatal.

Mucormycosis

A variety of fungi in the order Mucorales cause mucormycosis, a rare fungal disease. These include bread molds, like *Rhizopus* and *Mucor*; the most commonly associated species is *Rhizopus arrhizus (oryzae)* (see [link]). These fungi can colonize many different tissues in immunocompromised patients, but often infect the skin, sinuses, or the lungs.

Aspergillosis

*Aspergillus* is a common filamentous fungus found in soils and organic debris. Nearly everyone has been exposed to this mold, yet very few people become sick. In immunocompromised patients, however, *Aspergillus* may become established and cause aspergillosis. Inhalation of spores can lead to asthma-like allergic reactions. The symptoms commonly include shortness of breath, wheezing, coughing, runny nose, and headaches. Fungal balls, or aspergilloma, can form when hyphal colonies collect in the lungs ([link]). The fungal hyphae can invade the host tissues, leading to pulmonary hemorrhage and a bloody cough. In severe cases, the disease may progress to a disseminated form that is often fatal. Death most often results from pneumonia or brain hemorrhages.

*Pneumocystis* Pneumonia

A type of pneumonia called *Pneumocystis* pneumonia (PCP) is caused by *Pneumocystis jirovecii*. Once thought to be a protozoan, this organism was formerly named *P. carinii* but it has been reclassified as a fungus and renamed based on biochemical and genetic analyses. *Pneumocystis* is a leading cause of pneumonia in patients with acquired immunodeficiency syndrome (AIDS) and can be seen in other compromised patients and premature infants. Respiratory infection leads to fever, cough, and shortness of breath. Diagnosis of these infections can be difficult. The organism is typically identified by microscopic examination of tissue and fluid samples from the lungs ([link]). A PCR-based test is available to detect *P. jirovecii* in asymptomatic patients with AIDS. The best treatment for these infections is the combination drug trimethoprim-sulfamethoxazole (TMP/SMZ). These sulfa drugs often have adverse effects, but the benefits outweigh these risks. Left untreated, PCP infections are often fatal.

*Cryptococcosis*

Infection by the encapsulated yeast *Cryptococcus neoformans* causes cryptococcosis. This fungus is ubiquitous in the soil and can be isolated from bird feces. Immunocompromised people are infected by inhaling basidiospores found in aerosols. The thick polysaccharide capsule surrounding these microbes enables them to avoid clearance by the alveolar macrophage. Initial symptoms of infection include fever, fatigue, and a dry cough. In immunocompromised patients, pulmonary infections often disseminate to the brain. The resulting meningitis produces headaches, sensitivity to light, and confusion. Left untreated, such infections are often fatal.

Urogenital System Infections

Introduction

Anatomy and Normal Microbiota of the Urogenital Tract

Anatomy of the Urinary Tract

The basic structures of the urinary tract are common in males and females. However, there are unique locations for these structures in females and males, and there is a significant amount of overlap between the urinary and genital structures in males. [link] illustrates the urinary anatomy common to females and males.

Anatomy of the Reproductive System

The male reproductive system ([link]) is located in close proximity to the urinary system, and the urethra is part of both systems. The testes are responsible for the production of sperm. The epididymis is a coiled tube that collects sperm from the testes and passes it on to the vas deferens. The epididymis is also the site of sperm maturation after they leave the testes. The seminal vesicles and prostate are accessory glands that produce fluid that supports sperm. During ejaculation, the vas deferens releases this mixture of fluid and sperm, called semen, into the urethra, which extends to the end of the penis.

Normal Microbiota of the Urogenital System

The normal microbiota of different body sites provides an important nonspecific defense against infectious diseases (see Physical Defenses), and the urogenital tract is no exception. However, the kidneys are sterile. Although urine does contain some antibacterial components, bacteria will grow in urine left out at room temperature. Therefore, it is primarily the flushing action that keeps the ureters and bladder free of microbes.

General Signs and Symptoms of Urogenital Infections

Infections of the urinary tract most commonly cause inflammation of the bladder (cystitis) or of the urethra (urethritis). Urethritis can be associated with cystitis, but can also be caused by sexually transmitted infections. Symptoms of urethritis in males include burning sensation while urinating, discharge from the penis, and blood in the semen or the urine. In females, urethritis is associated with painful and frequent urination, vaginal discharge, fever, chills, and abdominal pain. The symptoms of cystitis are similar to those of urethritis. When urethritis is caused by a sexually transmitted pathogen, additional symptoms involving the genitalia can occur. These can include painful vesicles (blisters), warts, and ulcers. Ureteritis, a rare infection of the ureter, can also occur with cystitis. These infections can be acute or chronic.

General Causes and Modes of Transmission of Urogenital Infections

Hormonal changes, particularly shifts in estrogen due to pregnancy or menopause, can increase susceptibility to urogenital infections. As discussed earlier, estrogen plays an important role in regulating the availability of glycogen and subsequent production of lactic acid by *Lactobacillus* species. Low levels of estrogen are associated with an increased vaginal pH and an increased risk of bacterial vaginosis and yeast infections. Estrogen also plays a role in maintaining the elasticity, strength, and thickness of the vaginal wall, and keeps the vaginal wall lubricated, reducing dryness. Low levels of estrogen are associated with thinning of the vaginal wall. This thinning increases the risk of tears and abrasions, which compromise the protective barrier and increase susceptibility to pathogens.

Bacterial Infections of the Urinary System

Cystitis

Cystitis is most often caused by a bacterial infection of the bladder, but it can also occur as a reaction to certain treatments or irritants such as radiation treatment, hygiene sprays, or spermicides. Common symptoms of cystitis include dysuria (urination accompanied by burning, discomfort, or pain), pyuria (pus in the urine), hematuria (blood in the urine), and bladder pain.

Kidney Infections (Pyelonephritis and Glomerulonephritis)

Pyelonephritis, an inflammation of the kidney, can be caused by bacteria that have spread from other parts of the urinary tract (such as the bladder). In addition, pyelonephritis can develop from bacteria that travel through the bloodstream to the kidney. When the infection spreads from the lower urinary tract, the causative agents are typically fecal bacteria such as *E. coli*. Common signs and symptoms include back pain (due to the location of the kidneys), fever, and nausea or vomiting. Gross hematuria (visible blood in the urine) occurs in 30–40% of females but is rare in males.[footnote] The infection can become serious, potentially leading to bacteremia and systemic effects that can become life-threatening. Scarring of the kidney can occur and persist after the infection has cleared, which may lead to dysfunction.

Tibor Fulop. “Acute Pyelonephritis” *Medscape*, 2015. http://emedicine.medscape.com/article/245559-overview.

Nongonococcal Urethritis (NGU)

There are two main categories of bacterial urethritis: gonorrheal and nongonococcal. Gonorrheal urethritis is caused by *Neisseria gonorrhoeae* and is associated with gonorrhea, a common STI. This cause of urethritis will be discussed in Bacterial Infections of the Reproductive System. The term nongonococcal urethritis (NGU) refers to inflammation of the urethra that is unrelated to *N. gonorrhoeae*. In females, NGU is often asymptomatic. In males, NGU is typically a mild disease, but can lead to purulent discharge and dysuria. Because the symptoms are often mild or nonexistent, most infected individuals do not know that they are infected, yet they are carriers of the disease. Asymptomatic patients also have no reason to seek treatment, and although not common, untreated NGU can spread to the reproductive organs, causing pelvic inflammatory disease and salpingitis in females and epididymitis and prostatitis in males. Important bacterial pathogens that cause nongonococcal urethritis include *Chlamydia trachomatis*, *Mycoplasma genitalium*, *Ureaplasma urealyticum*, and *Mycoplasma hominis*.

Bacterial Infections of the Reproductive System

Bacterial Vaginitis and Vaginosis

Inflammation of the vagina is called vaginitis, often caused by a bacterial infection. It is also possible to have an imbalance in the normal vaginal microbiota without inflammation called bacterial vaginosis (BV). Vaginosis may be asymptomatic or may cause mild symptoms such as a thin, white-to-yellow, homogeneous vaginal discharge, burning, odor, and itching. The major causative agent is *Gardnerella vaginalis*, a gram-variable to gram-negative pleomorphic bacterium. Other causative agents include anaerobic species such as members of the genera *Bacteroides* and *Fusobacterium*. Additionally, ureaplasma and mycoplasma may be involved. The disease is usually self-limiting, although antibiotic treatment is recommended if symptoms develop.

Gonorrhea

Also known as the clap, gonorrhea is a common sexually transmitted disease of the reproductive system that is especially prevalent in individuals between the ages of 15 and 24. It is caused by *Neisseria gonorrhoeae*, often called gonococcus or GC, which have fimbriae that allow the cells to attach to epithelial cells. It also has a type of lipopolysaccharide endotoxin called lipooligosaccharide as part of the outer membrane structure that enhances its pathogenicity. In addition to causing urethritis, *N. gonorrhoeae* can infect other body tissues such as the skin, meninges, pharynx, and conjunctiva.

Chlamydia

*Chlamydia trachomatis* is the causative agent of the STI chlamydia ([link]). While many *Chlamydia* infections are asymptomatic, chlamydia is a major cause of nongonococcal urethritis (NGU) and may also cause epididymitis and orchitis in males. In females, chlamydia infections can cause urethritis, salpingitis, and PID. In addition, chlamydial infections may be associated with an increased risk of cervical cancer.

Syphilis

Syphilis is spread through direct physical (generally sexual) contact, and is caused by the gram-negative spirochete *Treponema pallidum*. *T. pallidum* has a relatively simple genome and lacks lipopolysaccharide endotoxin characteristic of gram-negative bacteria. However, it does contain lipoproteins that trigger an immune response in the host, causing tissue damage that may enhance the pathogen’s ability to disseminate while evading the host immune system.

Chancroid

The sexually transmitted infection chancroid is caused by the gram-negative rod *Haemophilus ducreyi*. It is characterized by soft chancres **(**[link]) on the genitals or other areas associated with sexual contact, such as the mouth and anus. Unlike the hard chancres associated with syphilis, soft chancres develop into painful, open sores that may bleed or produce fluid that is highly contagious. In addition to causing chancres, the bacteria can invade the lymph nodes, potentially leading to pus discharge through the skin from lymph nodes in the groin. Like other genital lesions, soft chancres are of particular concern because they compromise the protective barriers of the skin or mucous membranes, making individuals more susceptible to HIV and other sexually transmitted diseases.

Viral Infections of the Reproductive System

Genital Herpes

Genital herpes is a common condition caused by the herpes simplex virus ([link]), an enveloped, double-stranded DNA virus that is classified into two distinct types. Herpes simplex virus has several virulence factors, including infected cell protein (ICP) 34.5, which helps in replication and inhibits the maturation of dendritic cells as a mechanism of avoiding elimination by the immune system. In addition, surface glycoproteins on the viral envelope promote the coating of herpes simplex virus with antibodies and complement factors, allowing the virus to appear as “self” and prevent immune system activation and elimination.

Human Papillomas

Warts of all types are caused by a variety of strains of human papillomavirus (HPV) (see Viral Infections of the Skin and Eyes). Condylomata acuminata, more commonly called genital warts or venereal warts ([link]), are an extremely prevalent STI caused by certain strains of HPV. Condylomata are irregular, soft, pink growths that are found on external genitalia or the anus.

Fungal Infections of the Reproductive System

Protozoan Infections of the Urogenital System

Digestive System Infections

Introduction

Anatomy and Normal Microbiota of the Digestive System

Anatomy and Normal Microbiota of the Oral Cavity

Food enters the digestive tract through the mouth, where mechanical digestion (by chewing) and chemical digestion (by enzymes in saliva) begin. Within the mouth are the tongue, teeth, and salivary glands, including the parotid, sublingual, and submandibular glands ([link]). The salivary glands produce saliva, which lubricates food and contains digestive enzymes.

Anatomy and Normal Microbiota of the GI Tract

As food leaves the oral cavity, it travels through the pharynx, or the back of the throat, and moves into the esophagus, which carries the food from the pharynx to the stomach without adding any additional digestive enzymes. The stomach produces mucus to protect its lining, as well as digestive enzymes and acid to break down food. Partially digested food then leaves the stomach through the pyloric sphincter, reaching the first part of the small intestine called the duodenum. Pancreatic juice, which includes enzymes and bicarbonate ions, is released into the small intestine to neutralize the acidic material from the stomach and to assist in digestion. Bile, produced by the liver but stored in the gallbladder, is also released into the small intestine to emulsify fats so that they can travel in the watery environment of the small intestine. Digestion continues in the small intestine, where the majority of nutrients contained in the food are absorbed. Simple columnar epithelial cells called enterocytes line the lumen surface of the small intestinal folds called villi. Each enterocyte has smaller microvilli (cytoplasmic membrane extensions) on the cellular apical surface that increase the surface area to allow more absorption of nutrients to occur ([link]).

General Signs and Symptoms of Oral and GI Disease

Despite numerous defense mechanisms that protect against infection, all parts of the digestive tract can become sites of infection or intoxication. The term food poisoning is sometimes used as a catch-all for GI infections and intoxications, but not all forms of GI disease originate with foodborne pathogens or toxins.

Microbial Diseases of the Mouth and Oral Cavity

Dental Caries

Cavities of the teeth, known clinically as dental caries, are microbial lesions that cause damage to the teeth. Over time, the lesion can grow through the outer enamel layer to infect the underlying dentin or even the innermost pulp. If dental caries are not treated, the infection can become an abscess that spreads to the deeper tissues of the teeth, near the roots, or to the bloodstream.

Periodontal Disease

In addition to damage to the teeth themselves, the surrounding structures can be affected by microbes. Periodontal disease is the result of infections that lead to inflammation and tissue damage in the structures surrounding the teeth. The progression from mild to severe periodontal disease is generally reversible and preventable with good oral hygiene.

Oral Infections

As noted earlier, normal oral microbiota can cause dental and periodontal infections. However, there are number of other infections that can manifest in the oral cavity when other microbes are present.

Bacterial Infections of the Gastrointestinal Tract

Staphylococcal Food Poisoning

Staphylococcal food poisoning is one form of food intoxication. When *Staphylococcus aureus* grows in food, it may produce enterotoxins that, when ingested, can cause symptoms such as nausea, diarrhea, cramping, and vomiting within one to six hours. In some severe cases, it may cause headache, dehydration, and changes in blood pressure and heart rate. Signs and symptoms resolve within 24 to 48 hours. *S. aureus* is often associated with a variety of raw or undercooked and cooked foods including meat (e.g., canned meat, ham, and sausages) and dairy products (e.g., cheeses, milk, and butter). It is also commonly found on hands and can be transmitted to prepared foods through poor hygiene, including poor handwashing and the use of contaminated food preparation surfaces, such as cutting boards. The greatest risk is for food left at a temperature below 60 °C (140 °F), which allows the bacteria to grow. Cooked foods should generally be reheated to at least 60 °C (140 °F) for safety and most raw meats should be cooked to even higher internal temperatures ([link]).

Shigellosis (Bacillary Dysentery)

When gastrointestinal illness is associated with the rod-shaped, gram-negative bacterium *Shigella*, it is called bacillary dysentery, or shigellosis. Infections can be caused by *S. dysenteriae*, *S. flexneri*, *S. boydii*, and/or *S. sonnei* that colonize the GI tract. Shigellosis can be spread from hand to mouth or through contaminated food and water. Most commonly, it is transmitted through the fecal-oral route.

Salmonellosis

*Salmonella* gastroenteritis, also called salmonellosis, is caused by the rod-shaped, gram-negative bacterium *Salmonella*. Two species, *S. enterica* and *S. bongori*, cause disease in humans, but *S. enterica* is the most common. The most common serotypes of *S. enterica* are Enteritidis and Typhi. We will discuss typhoid fever caused by serotypes Typhi and Paratyphi A separately. Here, we will focus on salmonellosis caused by other serotypes.

Typhoid Fever

Certain serotypes of *S. enterica*, primarily serotype Typhi (*S. typhi*) but also Paratyphi, cause a more severe type of salmonellosis called typhoid fever. This serious illness, which has an untreated mortality rate of 10%, causes high fever, body aches, headache, nausea, lethargy, and a possible rash.

*E. coli* Infections

The gram-negative rod *Escherichia coli* is a common member of the normal microbiota of the colon. Although the vast majority of *E. coli* strains are helpful commensal bacteria, some can be pathogenic and may cause dangerous diarrheal disease. The pathogenic strains have additional virulence factors such as type 1 fimbriae that promote colonization of the colon or may produce toxins (see Virulence Factors of Bacterial and Viral Pathogens). These virulence factors are acquired through horizontal gene transfer.

Cholera and Other Vibrios

The gastrointestinal disease cholera is a serious infection often associated with poor sanitation, especially following natural disasters, because it is spread through contaminated water and food that has not been heated to temperatures high enough to kill the bacteria. It is caused by *Vibrio cholerae* serotype O1, a gram-negative, flagellated bacterium in the shape of a curved rod (vibrio). According to the CDC, cholera causes an estimated 3 to 5 million cases and 100,000 deaths each year.[footnote]

Centers for Disease Control and Prevention. *Cholera—Vibrio cholerae Infection*. Updated November 6, 2014. http://www.cdc.gov/cholera/general. Accessed Sept 14, 2016.

*Campylobacter jejuni* Gastroenteritis

*Campylobacter* is a genus of gram-negative, spiral or curved bacteria. They may have one or two flagella. *Campylobacter jejuni* gastroenteritis, a form of campylobacteriosis, is a widespread illness that is caused by *Campylobacter jejuni*. The primary route of transmission is through poultry that becomes contaminated during slaughter. Handling of the raw chicken in turn contaminates cooking surfaces, utensils, and other foods. Unpasteurized milk or contaminated water are also potential vehicles of transmission. In most cases, the illness is self-limiting and includes fever, diarrhea, cramps, vomiting, and sometimes dysentery. More serious signs and symptoms, such as bacteremia, meningitis, pancreatitis, cholecystitis, and hepatitis, sometimes occur. It has also been associated with autoimmune conditions such as Guillain-Barré syndrome, a neurological disease that occurs after some infections and results in temporary paralysis. HUS following infection can also occur. The virulence in many strains is the result of hemolysin production and the presence of *Campylobacter* cytolethal distending toxin (CDT), a powerful deoxyribonuclease (DNase) that irreversibly damages host cell DNA.

Peptic Ulcers

The gram-negative bacterium *Helicobacter pylori* is able to tolerate the acidic environment of the human stomach and has been shown to be a major cause of peptic ulcers, which are ulcers of the stomach or duodenum. The bacterium is also associated with increased risk of stomach cancer ([link]). According to the CDC, approximately two-thirds of the population is infected with *H. pylori,* but less than 20% have a risk of developing ulcers or stomach cancer. *H. pylori* is found in approximately 80% of stomach ulcers and in over 90% of duodenal ulcers.[footnote]

Centers for Disease Control and Prevention. “*Helicobacter pylori*: Fact Sheet for Health Care Providers.” Updated July 1998. http://www.cdc.gov/ulcer/files/hpfacts.pdf.

*Clostridium perfringens* Gastroenteritis

*Clostridium perfringens* gastroenteritis is a generally mild foodborne disease that is associated with undercooked meats and other foods. *C. perfringens* is a gram-positive, rod-shaped, endospore-forming anaerobic bacterium that is tolerant of high and low temperatures. At high temperatures, the bacteria can form endospores that will germinate rapidly in foods or within the intestine. Food poisoning by type A strains is common. This strain always produces an enterotoxin, sometimes also present in other strains, that causes the clinical symptoms of cramps and diarrhea. A more severe form of the illness, called pig-bel or enteritis necroticans, causes hemorrhaging, pain, vomiting, and bloating. Gangrene of the intestines may result. This form has a high mortality rate but is rare in the United States.

*Clostridium difficile*

*Clostridium difficile* is a gram-positive rod that can be a commensal bacterium as part of the normal microbiota of healthy individuals. When the normal microbiota is disrupted by long-term antibiotic use, it can allow the overgrowth of this bacterium, resulting in antibiotic-associated diarrhea caused by *C. difficile*. Antibiotic-associated diarrhea can also be considered a nosocomial disease. Patients at the greatest risk of *C. difficile* infection are those who are immunocompromised, have been in health-care settings for extended periods, are older, have recently taken antibiotics, have had gastrointestinal procedures done, or use proton pump inhibitors, which reduce stomach acidity and allow proliferation of *C. difficile*. Because this species can form endospores, it can survive for extended periods of time in the environment under harsh conditions and is a considerable concern in health-care settings.

Foodborne Illness Due to *Bacillus cereus*

*Bacillus cereus*, commonly found in soil, is a gram-positive endospore-forming bacterium that can sometimes cause foodborne illness. *B. cereus* endospores can survive cooking and produce enterotoxins in food after it has been heated; illnesses often occur after eating rice and other prepared foods left at room temperature for too long. The signs and symptoms appear within a few hours of ingestion and include nausea, pain, and abdominal cramps. *B. cereus* produces two toxins: one causing diarrhea, and the other causing vomiting. More severe signs and symptoms can sometimes develop.

Foodborne Illness Due to *Yersinia*

The genus *Yersinia* is best known for *Yersinia pestis*, a gram-negative rod that causes the plague. However, *Y. enterocolitica* and *Y. pseudotuberculosis* can cause gastroenteritis. The infection is generally transmitted through the fecal-oral route, with ingestion of food or water that has been contaminated by feces. Intoxication can also result because of the activity of its endotoxin and exotoxins (enterotoxin and cytotoxin necrotizing factor). The illness is normally relatively mild and self-limiting. However, severe diarrhea and dysentery can develop in infants. In adults, the infection can spread and cause complications such as reactive arthritis, thyroid disorders, endocarditis, glomerulonephritis, eye inflammation, and/or erythema nodosum. Bacteremia may develop in rare cases.

Viral Infections of the Gastrointestinal Tract

Gastroenteritis Caused by Rotaviruses

Rotaviruses are double-stranded RNA viruses in the family Reoviridae. They are responsible for common diarrheal illness, although prevention through vaccination is becoming more common. The virus is primarily spread by the fecal-oral route ([link]).

Gastroenteritis Caused by Noroviruses

Noroviruses, commonly identified as Norwalk viruses, are caliciviruses. Several strains can cause gastroenteritis. There are millions of cases a year, predominately in infants, young children, and the elderly. These viruses are easily transmitted and highly contagious. They are known for causing widespread infections in groups of people in confined spaces, such as on cruise ships. The viruses can be transmitted through direct contact, through touching contaminated surfaces, and through contaminated food. Because the virus is not killed by disinfectants used at standard concentrations for killing bacteria, the risk of transmission remains high, even after cleaning.

Gastroenteritis Caused by Astroviruses

Astroviruses are single-stranded RNA viruses (family Astroviridae) that can cause severe gastroenteritis, especially in infants and children. Signs and symptoms include diarrhea, nausea, vomiting, fever, abdominal pain, headache, and malaise. The viruses are transmitted through the fecal-oral route (contaminated food or water). For diagnosis, stool samples are analyzed. Testing may involve enzyme immunoassays and immune electron microscopy. Treatment involves supportive rehydration and electrolyte replacement if needed.

Hepatitis

Hepatitis is a general term meaning inflammation of the liver, which can have a variety of causes. In some cases, the cause is viral infection. There are five main hepatitis viruses that are clinically significant: hepatitisviruses A (HAV), B (HBV), C (HCV), D, (HDV) and E (HEV) ([link]). Note that other viruses, such as Epstein-Barr virus (EBV), yellow fever, and cytomegalovirus (CMV) can also cause hepatitis and are discussed in Viral Infections of the Circulatory and Lymphatic Systems.

Protozoan Infections of the Gastrointestinal Tract

Giardiasis

Also called backpacker’s diarrhea or beaver fever, giardiasis is a common disease in the United States caused by the flagellated protist *Giardia lamblia*, also known as *Giardia intestinalis* or *Giardia duodenalis* ([link]). To establish infection, *G. lamblia* uses a large adhesive disk to attach to the intestinal mucosa. The disk is comprised of microtubules. During adhesion, the flagella of *G. lamblia* move in a manner that draws fluid out from under the disk, resulting in an area of lower pressure that promotes its adhesion to the intestinal epithelial cells. Due to its attachment, *Giardia* also blocks absorption of nutrients, including fats.

Cryptosporidiosis

Another protozoan intestinal illness is cryptosporidiosis, which is usually caused by *Cryptosporidium* *parvum* or *C. hominis*. ([link]) These pathogens are commonly found in animals and can be spread in feces from mice, birds, and farm animals. Contaminated water and food are most commonly responsible for transmission. The protozoan can also be transmitted through human contact with infected animals or their feces.

Amoebiasis (Amebiasis)

The protozoan parasite *Entamoeba histolytica* causes amoebiasis, which is known as amoebic dysentery in severe cases. *E. histolytica* is generally transmitted through water or food that has fecal contamination. The disease is most widespread in the developing world and is one of the leading causes of mortality from parasitic disease worldwide. Disease can be caused by as few as 10 cysts being transmitted.

Cyclosporiasis

The intestinal disease cyclosporiasis is caused by the protozoan *Cyclospora cayetanensis*. It is endemic to tropical and subtropical regions and therefore uncommon in the United States, although there have been outbreaks associated with contaminated produce imported from regions where the protozoan is more common.

Helminthic Infections of the Gastrointestinal Tract

Ascariasis

Infections caused by the large nematode roundworm *Ascaris lumbricoides*, a soil-transmitted helminth, are called ascariasis. Over 800 million to 1 billion people are estimated to be infected worldwide.[footnote] Infections are most common in warmer climates and at warmer times of year. At present, infections are uncommon in the United States. The eggs of the worms are transmitted through contaminated food and water. This may happen if food is grown in contaminated soil, including when manure is used as fertilizer.

Centers for Disease Control and Prevention. “Parasites–Ascariasis.” Updated May 24, 2016. http://www.cdc.gov/parasites/ascariasis/index.html.

Hookworm

Two species of nematode worms are associated with hookworm infection. Both species are found in the Americas, Africa, and Asia. *Necator americanus* is found predominantly in the United States and Australia. Another species, *Ancylostoma doudenale*, is found in southern Europe, North Africa, the Middle East, and Asia.

Strongyloidiasis

Strongyloidiasis is generally caused by *Strongyloides stercoralis*, a soil-transmitted helminth with both free-living and parasitic forms. In the parasitic form, the larvae of these nematodes generally penetrate the body through the skin, especially through bare feet, although transmission through organ transplantation or at facilities like day-care centers can also occur. When excreted in the stool, larvae can become free-living adults rather than developing into the parasitic form. These free-living worms reproduce, laying eggs that hatch into larvae that can develop into the parasitic form. In the parasitic life cycle, infective larvae enter the skin, generally through the feet. The larvae reach the circulatory system, which allows them to travel to the alveolar spaces of the lungs. They are transported to the pharynx where, like many other helminths, the infected patient coughs them up and swallows them again so that they return to the intestine. Once they reach the intestine, females live in the epithelium and produce eggs that develop asexually, unlike the free-living forms, which use sexual reproduction. The larvae may be excreted in the stool or can reinfect the host by entering the tissue of the intestines and skin around the anus, which can lead to chronic infections.

Pinworms (Enterobiasis)

*Enterobius vermicularis*, commonly called pinworms, are tiny (2–13 mm) nematodes that cause enterobiasis. Of all helminthic infections, enterobiasis is the most common in the United States, affecting as many as one-third of American children.[footnote] Although the signs and symptoms are generally mild, patients may experience abdominal pain and insomnia from itching of the perianal region, which frequently occurs at night when worms leave the anus to lay eggs. The itching contributes to transmission, as the disease is transmitted through the fecal-oral route. When an infected individual scratches the anal area, eggs may get under the fingernails and later be deposited near the individual’s mouth, causing reinfection, or on fomites, where they can be transferred to new hosts. After being ingested, the larvae hatch within the small intestine and then take up residence in the colon and develop into adults. From the colon, the female adult exits the body at night to lay eggs ([link]).

“Roundworms.” *University of Maryland Medical Center Medical Reference Guide*. Last reviewed December 9, 2014. https://umm.edu/health/medical/altmed/condition/roundworms.

Trichuriasis

The nematode whipworm *Trichuris trichiura* is a parasite that is transmitted by ingestion from soil-contaminated hands or food and causes trichuriasis. Infection is most common in warm environments, especially when there is poor sanitation and greater risk of fecal contamination of soil, or when food is grown in soil using manure as a fertilizer. The signs and symptoms may be minimal or nonexistent. When a substantial infection develops, signs and symptoms include painful, frequent diarrhea that may contain mucus and blood. It is possible for the infection to cause rectal prolapse, a condition in which a portion of the rectum becomes detached from the inside of the body and protrudes from the anus ([link]). Severely infected children may experience reduced growth and their cognitive development may be affected.

Trichinosis

Trichinosis (trichenellosis) develops following consumption of food that contains *Trichinella* *spiralis* (most commonly) or other *Trichinella* species. These microscopic nematode worms are most commonly transmitted in meat, especially pork, that has not been cooked thoroughly. *T. spiralis* larvae in meat emerge from cysts when exposed to acid and pepsin in the stomach. They develop into mature adults within the large intestine. The larvae produced in the large intestine are able to migrate into the muscles mechanically via the stylet of the parasite, forming cysts. Muscle proteins are reduced in abundance or undetectable in cells that contain *Trichinella* (nurse cells). Animals that ingest the cysts from other animals can later develop infection ([link]).

Tapeworms (Taeniasis)

Taeniasis is a tapeworm infection, generally caused by pork (*Taenia* *solium*), beef (*Taenia saginata*), and Asian (*Taenia asiatica*) tapeworms found in undercooked meat. Consumption of raw or undercooked fish, including contaminated sushi, can also result in infection from the fish tapeworm (*Diphyllobothrium* *latum*). Tapeworms are flatworms (cestodes) with multiple body segments and a head called a scolex that attaches to the intestinal wall. Tapeworms can become quite large, reaching 4 to 8 meters long ([link]). [link] illustrates the life cycle of a tapeworm.

Hydatid Disease

Another cestode, *Echinococcus granulosus*, causes a serious infection known as hydatid disease (cystic echinococcosis). *E. granulosus* is found in dogs (the definitive host), as well as several intermediate hosts (sheep, pigs, goats, cattle). The cestodes are transmitted through eggs in the feces from infected animals, which can be an occupational hazard for individuals who work in agriculture.

Flukes

Flukes are flatworms that have a leaflike appearance. They are a type of trematode worm, and multiple species are associated with disease in humans. The most common are liver flukes and intestinal flukes ([link]).

Circulatory and Lymphatic System Infections

Introduction

Anatomy of the Circulatory and Lymphatic Systems

The Circulatory System

The circulatory (or cardiovascular) system is a closed network of organs and vessels that moves blood around the body ([link]). The primary purposes of the circulatory system are to deliver nutrients, immune factors, and oxygen to tissues and to carry away waste products for elimination. The heart is a four-chambered pump that propels the blood throughout the body. Deoxygenated blood enters the right atrium through the superior vena cava and the inferior vena cava after returning from the body. The blood next passes through the tricuspid valve to enter the right ventricle. When the heart contracts, the blood from the right ventricle is pumped through the pulmonary arteries to the lungs. There, the blood is oxygenated at the alveoli and returns to the heart through the pulmonary veins. The oxygenated blood is received at the left atrium and proceeds through the mitral valve to the left ventricle. When the heart contracts, the oxygenated blood is pumped throughout the body via a series of thick-walled vessels called arteries. The first and largest artery is called the aorta. The arteries sequentially branch and decrease in size (and are called arterioles) until they end in a network of smaller vessels called capillaries. The capillary beds are located in the interstitial spaces within tissues and release nutrients, immune factors, and oxygen to those tissues. The capillaries connect to a series of vessels called venules, which increase in size to form the veins. The veins join together into larger vessels as they transfer blood back to the heart. The largest veins, the superior and inferior vena cava, return the blood to the right atrium.

The Lymphatic System

The lymphatic system is also a network of vessels that run throughout the body ([link]). However, these vessels do not form a full circulating system and are not pressurized by the heart. Rather, the lymphatic system is an open system with the fluid moving in one direction from the extremities toward two drainage points into veins just above the heart. Lymphatic fluids move more slowly than blood because they are not pressurized. Small lymph capillaries interact with blood capillaries in the interstitial spaces in tissues. Fluids from the tissues enter the lymph capillaries and are drained away ([link]). These fluids, termed lymph, also contain large numbers of white blood cells.

Infections of the Circulatory System

Under normal circumstances, the circulatory system and the blood should be sterile; the circulatory system has no normal microbiota. Because the system is closed, there are no easy portals of entry into the circulatory system for microbes. Those that are able to breach the body’s physical barriers and enter the bloodstream encounter a host of circulating immune defenses, such as antibodies, complement proteins, phagocytes, and other immune cells. Microbes often gain access to the circulatory system through a break in the skin (e.g., wounds, needles, intravenous catheters, insect bites) or spread to the circulatory system from infections in other body sites. For example, microorganisms causing pneumonia or renal infection may enter the local circulation of the lung or kidney and spread from there throughout the circulatory network.

Infections of the Lymphatic System

Like the circulatory system, the lymphatic system does not have a normal microbiota, and the large numbers of immune cells typically eliminate transient microbes before they can establish an infection. Only microbes with an array of virulence factors are able to overcome these defenses and establish infection in the lymphatic system. However, when a localized infection begins to spread, the lymphatic system is often the first place the invading microbes can be detected.

Bacterial Infections of the Circulatory and Lymphatic Systems

Bacterial Sepsis, Septic and Toxic Shock

At low concentrations, pro-inflammatory cytokines such as interleukin 1 (IL-1) and tumor necrosis factor-α (TNF-α) play important roles in the host’s immune defenses. When they circulate systemically in larger amounts, however, the resulting immune response can be life threatening. IL-1 induces vasodilation (widening of blood vessels) and reduces the tight junctions between vascular endothelial cells, leading to widespread edema. As fluids move out of circulation into tissues, blood pressure begins to drop. If left unchecked, the blood pressure can fall below the level necessary to maintain proper kidney and respiratory functions, a condition known as septic shock. In addition, the excessive release of cytokines during the inflammatory response can lead to the formation of blood clots. The loss of blood pressure and occurrence of blood clots can result in multiple organ failure and death.

Puerperal Sepsis

A type of sepsis called puerperal sepsis, also known as puerperal infection, puerperal fever, or childbed fever, is a nosocomial infection associated with the period of puerperium—the time following childbirth during which a person's reproductive system returns to a nonpregnant state. Such infections may originate in the genital tract, breast, urinary tract, or a surgical wound. Initially the infection may be limited to the uterus or other local site of infection, but it can quickly spread, resulting in peritonitis, septicemia, and death. Before the 19th century work of Ignaz Semmelweis and the widespread acceptance of germ theory (see Modern Foundations of Cell Theory), puerperal sepsis was a major cause of mortality among new mothers in the first few days following childbirth.

Infectious Arthritis

Also called septic arthritis, infectious arthritis can be either an acute or a chronic condition. Infectious arthritis is characterized by inflammation of joint tissues and is most often caused by bacterial pathogens. Most cases of acute infectious arthritis are secondary to bacteremia, with a rapid onset of moderate to severe joint pain and swelling that limits the motion of the affected joint. In adults and young children, the infective pathogen is most often introduced directly through injury, such as a wound or a surgical site, and brought to the joint through the circulatory system. Acute infections may also occur after joint replacement surgery. Acute infectious arthritis often occurs in patients with an immune system impaired by other viral and bacterial infections. *S. aureus* is the most common cause of acute septic arthritis in the general population of adults and young children. *Neisseria gonorrhoeae* is an important cause of acute infectious arthritis in sexually active individuals.

Osteomyelitis

Osteomyelitis is an inflammation of bone tissues most commonly caused by infection. These infections can either be acute or chronic and can involve a variety of different bacteria. The most common causative agent of osteomyelitis is *S. aureus*. However, *M. tuberculosis*, *Pseudomonas aeruginosa, Streptococcus pyogenes*, *S. agalactiae*, species in the Enterobacteriaceae*,* and other microorganisms can also cause osteomyelitis, depending on which bones are involved. In adults, bacteria usually gain direct access to the bone tissues through trauma or a surgical procedure involving prosthetic joints. In children, the bacteria are often introduced from the bloodstream, possibly spreading from focal infections. The long bones, such as the femur, are more commonly affected in children because of the more extensive vascularization of bones in the young.[footnote]

M. Vazquez. “Osteomyelitis in Children.” *Current Opinion in Pediatrics* 14, no. 1 (2002):112–115.

Rheumatic Fever

Infections with *S. pyogenes* have a variety of manifestations and complications generally called sequelae. As mentioned, the bacterium can cause suppurative infections like puerperal fever. However, this microbe can also cause nonsuppurative sequelae in the form of acute rheumatic fever (ARF), which can lead to rheumatic heart disease, thus impacting the circulatory system. Rheumatic fever occurs primarily in children a minimum of 2–3 weeks after an episode of untreated or inadequately treated pharyngitis (see Bacterial Infections of the Respiratory Tract). At one time, rheumatic fever was a major killer of children in the US; today, however, it is rare in the US because of early diagnosis and treatment of streptococcal pharyngitis with antibiotics. In parts of the world where diagnosis and treatment are not readily available, acute rheumatic fever and rheumatic heart disease are still major causes of mortality in children.[footnote]

A. Beaudoin et al. “Acute Rheumatic Fever and Rheumatic Heart Disease Among Children—American Samoa, 2011–2012.” *Morbidity and Mortality Weekly Report* 64 no. 20 (2015):555–558.

Bacterial Endocarditis and Pericarditis

The endocardium is a tissue layer that lines the muscles and valves of the heart. This tissue can become infected by a variety of bacteria, including gram-positive cocci such as *Staphylococcus aureus*, viridans streptococci, and *Enterococcus faecalis*, and the gram-negative so-called HACEK bacilli: *Haemophilus* spp., *Actinobacillus actinomycetemcomitans*, *Cardiobacterium hominis*, *Eikenella corrodens*, and *Kingella kingae*. The resulting inflammation is called endocarditis, which can be described as either acute or subacute. Causative agents typically enter the bloodstream during accidental or intentional breaches in the normal barrier defenses (e.g., dental procedures, body piercings, catheterization, wounds). Individuals with preexisting heart damage, prosthetic valves and other cardiac devices, and those with a history of rheumatic fever have a higher risk for endocarditis. This disease can rapidly destroy the heart valves and, if untreated, lead to death in just a few days.

Gas Gangrene

Traumatic injuries or certain medical conditions, such as diabetes, can cause damage to blood vessels that interrupts blood flow to a region of the body. When blood flow is interrupted, tissues begin to die, creating an anaerobic environment in which anaerobic bacteria can thrive. This condition is called ischemia. Endospores of the anaerobic bacterium *Clostridium perfringens* (along with a number of other *Clostridium* spp. from the gut) can readily germinate in ischemic tissues and colonize the anaerobic tissues.

Tularemia

Infection with the gram-negative bacterium *Francisella tularensis* causes tularemia (or rabbit fever), a zoonotic infection in humans. *F. tularensis* is a facultative intracellular parasite that primarily causes illness in rabbits, although a wide variety of domesticated animals are also susceptible to infection. Humans can be infected through ingestion of contaminated meat or, more typically, handling of infected animal tissues (e.g., skinning an infected rabbit). Tularemia can also be transmitted by the bites of infected arthropods, including the dog tick (*Dermacentor variabilis*), the lone star tick (*Amblyomma americanum*), the wood tick (*Dermacentor andersoni*), and deer flies (*Chrysops* spp.). Although the disease is not directly communicable between humans, exposure to aerosols of *F. tularensis* can result in life-threatening infections. *F. tularensis* is highly contagious, with an infectious dose of as few as 10 bacterial cells. In addition, pulmonary infections have a 30%–60% fatality rate if untreated.[footnote] For these reasons, *F. tularensis* is currently classified and must be handled as a biosafety level-3 (BSL-3) organism and as a potential biological warfare agent.

World Health Organization. “WHO Guidelines on Tularaemia.” 2007. http://www.cdc.gov/tularemia/resources/whotularemiamanual.pdf. Accessed July 26, 2016.

Brucellosis

Species in the genus *Brucella* are gram-negative facultative intracellular pathogens that appear as coccobacilli. Several species cause zoonotic infections in animals and humans, four of which have significant human pathogenicity: *B. abortus* from cattle and buffalo, *B. canis* from dogs, *B. suis* from swine, and *B. melitensis* from goats, sheep, and camels. Infections by these pathogens are called brucellosis, also known as undulant fever, “Mediterranean fever,” or “Malta fever.” Alice Katherine Evans first determined that *Brucella* infections present in cows could be transmitted to humans through milk. Her findings were disputed for years before being accepted; people began pasteurizing milk (heating it to interfere with microorganisms), which led to a sharp reduction in the related diseases. Vaccination of animals has made brucellosis a rare disease in the US, but it is still common in the Mediterranean, south and central Asia, Central and South America, and the Caribbean. Human infections are primarily associated with the ingestion of meat or unpasteurized dairy products from infected animals. Infection can also occur through inhalation of bacteria in aerosols when handling animal products, or through direct contact with skin wounds. In the US, most cases of brucellosis are found in individuals with extensive exposure to potentially infected animals (e.g., slaughterhouse workers, veterinarians).

Cat-Scratch Disease

The zoonosis cat-scratch disease (CSD) (or cat-scratch fever) is a bacterial infection that can be introduced to the lymph nodes when a human is bitten or scratched by a cat. It is caused by the facultative intracellular gram-negative bacterium *Bartonella henselae*. Cats can become infected from flea feces containing *B. henselae* that they ingest while grooming. Humans become infected when flea feces or cat saliva (from claws or licking) containing *B. henselae* are introduced at the site of a bite or scratch. Once introduced into a wound, *B. henselae* infects red blood cells.

Rat-Bite Fever

The zoonotic infection rat-bite fever can be caused by two different gram-negative bacteria: *Streptobacillus moniliformis*, which is more common in North America, and *Spirillum minor*, which is more common in Asia. Because of modern sanitation efforts, rat bites are rare in the US. However, contact with fomites, food, or water contaminated by rat feces or body fluids can also cause infections. Signs and symptoms of rat-bite fever include fever, vomiting, myalgia (muscle pain), arthralgia (joint pain), and a maculopapular rash on the hands and feet. An ulcer may also form at the site of a bite, along with some swelling of nearby lymph nodes. In most cases, the infection is self-limiting. Little is known about the virulence factors that contribute to these signs and symptoms of disease.

Plague

The gram-negative bacillus *Yersinia pestis* causes the zoonotic infection plague. This bacterium causes acute febrile disease in animals, usually rodents or other small mammals, and humans. The disease is associated with a high mortality rate if left untreated. Historically, *Y. pestis* has been responsible for several devastating pandemics, resulting in millions of deaths (see Micro Connections: The History of the Plague). There are three forms of plague: bubonic plague (the most common form, accounting for about 80% of cases), pneumonic plague, and septicemic plague. These forms are differentiated by the mode of transmission and the initial site of infection. [link] illustrates these various modes of transmission and infection between animals and humans.

Zoonotic Febrile Diseases

A wide variety of zoonotic febrile diseases (diseases that cause fever) are caused by pathogenic bacteria that require arthropod vectors. These pathogens are either obligate intracellular species of *Anaplasma, Bartonella*, *Ehrlichia, Orientia,* and *Rickettsia*, or spirochetes in the genus *Borrelia*. Isolation and identification of pathogens in this group are best performed in BSL-3 laboratories because of the low infective dose associated with the diseases.

Viral Infections of the Circulatory and Lymphatic Systems

Infectious Mononucleosis and Burkitt Lymphoma

Human herpesvirus 4, also known as Epstein-Barr virus (EBV), has been associated with a variety of human diseases, such as mononucleosis and Burkitt lymphoma. Exposure to the human herpesvirus 4 (HHV-4) is widespread and nearly all people have been exposed at some time in their childhood, as evidenced by serological tests on populations. The virus primarily resides within B lymphocytes and, like all herpes viruses, can remain dormant in a latent state for a long time.

Cytomegalovirus Infections

Also known as cytomegalovirus (CMV), human herpesvirus 5 (HHV-5) is a virus with high infection rates in the human population. It is currently estimated that 50% of people in the US have been infected by the time they reach adulthood.[footnote] CMV is the major cause of non-Epstein-Barr infectious mononucleosis in the general human population. It is also an important pathogen in immunocompromised hosts, including patients with AIDS, neonates, and transplant recipients. However, the vast majority of CMV infections are asymptomatic. In adults, if symptoms do occur, they typically include fever, fatigue, swollen glands, and pharyngitis.

Centers for Disease Control and Prevention. “Cytomegalovirus (CMV) and Congenital CMV Infection: About CMV.” 2016. http://www.cdc.gov/cmv/transmission.html. Accessed July 28, 2016.

Arthropod-Borne Viral Diseases

There are a number of arthropod-borne viruses, or arbovirus**es**, that can cause human disease. Among these are several important hemorrhagic fevers transmitted by mosquitoes. We will discuss three that pose serious threats: yellow fever, chikungunya fever, and dengue fever.

Ebola Virus Disease

The Ebola virus disease (EVD) is a highly contagious disease caused by species of *Ebolavirus*, a BSL-4 filovirus ([link]). Transmission to humans occurs through direct contact with body fluids (e.g., blood, saliva, sweat, urine, feces, or vomit), and indirect contact by contaminated fomites. Infected patients can easily transmit Ebola virus to others if appropriate containment and use of personal protective equipment is not available or used. Handling and working with patients with EVD is extremely hazardous to the general population and health-care workers. In almost every EVD outbreak there have been Ebola infections among health-care workers. This ease of Ebola virus transmission was recently demonstrated in the Ebola epidemic in Guinea, Liberia, and Sierra Leone in 2014, in which more than 28,000 people in 10 countries were infected and more than 11,000 died.[footnote]

HealthMap. “2014 Ebola Outbreaks.” http://www.healthmap.org/ebola/#timeline. Accessed July 28, 2016.

Hantavirus

The genus *Hantavirus* consists of at least four serogroups with nine viruses causing two major clinical (sometimes overlapping) syndromes: hantavirus pulmonary syndrome (HPS) in North America and hemorrhagic fever with renal syndrome (HFRS) in other continents. Hantaviruses are found throughout the world in wild rodents that shed the virus in their urine and feces. Transmission occurs between rodents and to humans through inhalation of aerosols of the rodent urine and feces. Hantaviruses associated with outbreaks in the US and Canada are transmitted by the deer mouse, white-footed mouse, or cotton rat.

Human Immunodeficiency Virus

Human T-lymphotropic viruses (HTLV), also called human immunodeficiency viruses (HIV) are retroviruses that are the causative agent of acquired immune deficiency syndrome (AIDS). There are two main variants of human immunodeficiency virus (HIV). HIV-1 ([link]) occurs in human populations worldwide, whereas HIV-2 is concentrated in West Africa. Currently, the most affected region in the world is sub-Saharan Africa, with an estimated 25.6 million people living with HIV in 2015.[footnote] Sub-Saharan Africa also accounts for two-thirds of the global total of new HIV infections ([link]).[footnote]

World Health Organization. “HIV/AIDS: Fact Sheet.” 2016.http://www.who.int/mediacentre/factsheets/fs360/en/. Accessed July 28, 2016.ibid.

Parasitic Infections of the Circulatory and Lymphatic Systems

Malaria

Despite more than a century of intense research and clinical advancements, malaria remains one of the most important infectious diseases in the world today. Its widespread distribution places more than half of the world’s population in jeopardy. In 2015, the WHO estimated there were about 214 million cases of malaria worldwide, resulting in about 438,000 deaths; about 88% of cases and 91% of deaths occurred in Africa.[footnote] Although malaria is not currently a major threat in the US, the possibility of its reintroduction is a concern. Malaria is caused by several protozoan parasites in the genus *Plasmodium*: *P. falciparum, P. knowlesi, P. malariae, P. ovale,* and *P. vivax. Plasmodium* primarily infect red blood cells and are transmitted through the bite of *Anopheles* mosquitoes.

World Health Organization. “World Malaria Report 2015: Summary.” 2015. http://www.who.int/malaria/publications/world-malaria-report-2015/report/en/. Accessed July 28, 2016.

Toxoplasmosis

The disease toxoplasmosis is caused by the protozoan *Toxoplasma gondii*. *T. gondii* is found in a wide variety of birds and mammals,[footnote] and human infections are common. The Centers for Disease Control and Prevention (CDC) estimates that 22.5% of the population 12 years and older has been infected with *T. gondii*; but immunocompetent individuals are typically asymptomatic, however.[footnote] Domestic cats are the only known definitive hosts for the sexual stages of *T. gondii* and, thus, are the main reservoirs of infection. Infected cats shed *T. gondii* oocysts in their feces, and these oocysts typically spread to humans through contact with fecal matter on cats’ bodies, in litter boxes, or in garden beds where outdoor cats defecate.

A.M. Tenter et al.. “*Toxoplasma gondii*: From Animals to Humans.” *International Journal for Parasitology* 30 no. 12-13 (2000):1217–1258.Centers for Disease Control and Prevention. “Parasites - Toxoplasmosis (Toxoplasma Infection). Epidemiology & Risk Factors.” 2015 http://www.cdc.gov/parasites/toxoplasmosis/epi.html. Accessed July 28, 2016.

Babesiosis

Babesiosis is a rare zoonotic infectious disease caused by *Babesia* spp. These parasitic protozoans infect various wild and domestic animals and can be transmitted to humans by black-legged *Ixodes* ticks. In humans, *Babesia* infect red blood cells and replicate inside the cell until it ruptures. The *Babesia* released from the ruptured red blood cell continue the growth cycle by invading other red blood cells. Patients may be asymptomatic, but those who do have symptoms often initially experience malaise, fatigue, chills, fever, headache, myalgia, and arthralgia. In rare cases, particularly in asplenic (absence of the spleen) patients, the elderly, and patients with AIDS, babesiosis may resemble falciparum malaria, with high fever, hemolytic anemia, hemoglobinuria (hemoglobin or blood in urine), jaundice, and renal failure, and the infection can be fatal. Previously acquired asymptomatic Babesia infection may become symptomatic if a splenectomy is performed.

Chagas Disease

Also called American trypanosomiasis, Chagas disease is a zoonosis classified as a neglected tropical disease (NTD). It is caused by the flagellated protozoan *Trypanosoma cruzi* and is most commonly transmitted to animals and people through the feces of triatomine bugs. The triatomine bug is nicknamed the kissing bug because it frequently bites humans on the face or around the eyes; the insect often defecates near the bite and the infected fecal matter may be rubbed into the bite wound by the bitten individual ([link]). The bite itself is painless and, initially, many people show no signs of the disease. Alternative modes of transmission include contaminated blood transfusions, organ transplants from infected donors, and congenital transmission during pregnancy to a fetus.

Leishmaniasis

Although it is classified as an NTD, leishmaniasis is relatively widespread in tropical and subtropical regions, affecting people in more than 90 countries. It is caused by approximately 20 different species of *Leishmania*, protozoan parasites that are transmitted by sand fly vectors such as *Phlebotomus* spp. and *Lutzomyia* spp. Dogs, cats, sheep, horses, cattle rodents, and humans can all serve as reservoirs.

Schistosomiasis

Schistosomiasis (bilharzia) is an NTD caused by blood flukes in the genus *Schistosoma* that are native to the Caribbean, South America, Middle East, Asia, and Africa. Most human schistosomiasis cases are caused by *Schistosoma mansoni, S. haematobium*, or *S. japonicum*. *Schistosoma* are the only trematodes that invade through the skin; all other trematodes infect by ingestion. WHO estimates that at least 258 million people required preventive treatment for schistosomiasis in 2014.[footnote]

World Health Organization. “Schistosomiasis. Fact Sheet.” 2016. http://www.who.int/mediacentre/factsheets/fs115/en/. Accessed July 29, 2016.

Nervous System Infections

Introduction

Anatomy of the Nervous System

The Central Nervous System

The brain is the most complex and sensitive organ in the body. It is responsible for all functions of the body, including serving as the coordinating center for all sensations, mobility, emotions, and intellect. Protection for the brain is provided by the bones of the skull, which in turn are covered by the scalp, as shown in [link]. The scalp is composed of an outer layer of skin, which is loosely attached to the aponeurosis, a flat, broad tendon layer that anchors the superficial layers of the skin. The periosteum, below the aponeurosis, firmly encases the bones of the skull and provides protection, nutrition to the bone, and the capacity for bone repair. Below the boney layer of the skull are three layers of membranes called meninges that surround the brain. The relative positions of these meninges are shown in [link]. The meningeal layer closest to the bones of the skull is called the dura mater (literally meaning *tough mother*). Below the dura mater lies the arachnoid mater (literally *spider-like mother*). The innermost meningeal layer is a delicate membrane called the pia mater (literally *tender mother*). Unlike the other meningeal layers, the pia mater firmly adheres to the convoluted surface of the brain. Between the arachnoid mater and pia mater is the subarachnoid space. The subarachnoid space within this region is filled with cerebrospinal fluid (CSF). This watery fluid is produced by cells of the choroid plexus—areas in each ventricle of the brain that consist of cuboidal epithelial cells surrounding dense capillary beds. The CSF serves to deliver nutrients and remove waste from neural tissues.

The Peripheral Nervous System

The PNS is formed of the nerves that connect organs, limbs, and other anatomic structures of the body to the brain and spinal cord. Unlike the brain and spinal cord, the PNS is not protected by bone, meninges, or a blood barrier, and, as a consequence, the nerves of the PNS are much more susceptible to injury and infection. Microbial damage to peripheral nerves can lead to tingling or numbness known as neuropathy. These symptoms can also be produced by trauma and noninfectious causes such as drugs or chronic diseases like diabetes.

The Cells of the Nervous System

Tissues of the PNS and CNS are formed of cells called glial cells (neuroglial cells) and neurons (nerve cells). Glial cells assist in the organization of neurons, provide a scaffold for some aspects of neuronal function, and aid in recovery from neural injury.

Meningitis and Encephalitis

Although the skull provides the brain with an excellent defense, it can also become problematic during infections. Any swelling of the brain or meninges that results from inflammation can cause intracranial pressure, leading to severe damage of the brain tissues, which have limited space to expand within the inflexible bones of the skull. The term meningitis is used to describe an inflammation of the meninges. Typical symptoms can include severe headache, fever, photophobia (increased sensitivity to light), stiff neck, convulsions, and confusion. An inflammation of brain tissue is called encephalitis, and patients exhibit signs and symptoms similar to those of meningitis in addition to lethargy, seizures, and personality changes. When inflammation affects both the meninges and the brain tissue, the condition is called meningoencephalitis. All three forms of inflammation are serious and can lead to blindness, deafness, coma, and death.

Bacterial Diseases of the Nervous System

Bacterial Meningitis

Bacterial meningitis is one of the most serious forms of meningitis. Bacteria that cause meningitis often gain access to the CNS through the bloodstream after trauma or as a result of the action of bacterial toxins. Bacteria may also spread from structures in the upper respiratory tract, such as the oropharynx, nasopharynx, sinuses, and middle ear. Patients with head wounds or cochlear implants (an electronic device placed in the inner ear) are also at risk for developing meningitis.

*Clostridium*-Associated Diseases

Species in the genus *Clostridium* are gram-positive, endospore-forming rods that are obligate anaerobes. Endospores of *Clostridium* spp. are widespread in nature, commonly found in soil, water, feces, sewage, and marine sediments. *Clostridium* spp. produce more types of protein exotoxins than any other bacterial genus, including two exotoxins with protease activity that are the most potent known biological toxins: botulinum neurotoxin (BoNT) and tetanus neurotoxin (TeNT). These two toxins have lethal doses of 0.2–10 ng per kg body weight.

Hansen’s Disease (Leprosy)

Hansen’s disease (also known as leprosy) is caused by a long, thin, filamentous rod-shaped bacterium *Mycobacterium leprae*, an obligate intracellular pathogen. *M. leprae* is classified as gram-positive bacteria, but it is best visualized microscopically with an acid-fast stain and is generally referred to as an acid-fast bacterium. Hansen’s disease affects the PNS, leading to permanent damage and loss of appendages or other body parts.

Acellular Diseases of the Nervous System

Viral Meningitis

Although it is much more common than bacterial meningitis, viral meningitis is typically less severe. Many different viruses can lead to meningitis as a sequela of the primary infection, including those that cause herpes, influenza, measles, and mumps. Most cases of viral meningitis spontaneously resolve, but severe cases do occur.

Zika Virus Infection

Zika virus infection is an emerging arboviral disease associated with human illness in Africa, Southeast Asia, and South and Central America; however, its range is expanding as a result of the widespread range of its mosquito vector. The first cases originating in the United States were reported in 2016.The Zika virus was initially described in 1947 from monkeys in the Zika Forest of Uganda through a network that monitored yellow fever. It was not considered a serious human pathogen until the first large-scale outbreaks occurred in Micronesia in 2007;[footnote] however, the virus has gained notoriety over the past decade, as it has emerged as a cause of symptoms similar to other arboviral infections that include fever, skin rashes, conjunctivitis, muscle and joint pain, malaise, and headache. Mosquitoes of the *Aedes* genus are the primary vectors, although the virus can also be transmitted sexually, to a fetus during pregnancy, or through a blood transfusion.

Sikka, Veronica, Vijay Kumar Chattu, Raaj K. Popli, Sagar C. Galwankar, Dhanashree Kelkar, Stanley G. Sawicki, Stanislaw P. Stawicki, and Thomas J. Papadimos, “The Emergence of Zika Virus as a Global Health Security Threat: A Review and a Consensus Statement of the INDUSEM Joint Working Group (JWG),” *Journal of Global Infectious Diseases* 8, no. 1 (2016): 3.

Rabies

Rabies is a deadly zoonotic disease that has been known since antiquity. The disease is caused by rabies virus (RV), a member of the family Rhabdoviridae, and is primarily transmitted through the bite of an infected mammal. Rhabdoviridae are enveloped RNA viruses that have a distinctive bullet shape ([link]); they were first studied by Louis Pasteur, who obtained rabies virus from rabid dogs and cultivated the virus in rabbits. He successfully prepared a rabies vaccine using dried nerve tissues from infected animals. This vaccine was used to first treat an infected human in 1885.

Poliomyelitis

Poliomyelitis (polio), caused by poliovirus, is a primarily intestinal disease that, in a small percentage of cases, proceeds to the nervous system, causing paralysis and, potentially, death. Poliovirus is highly contagious, with transmission occurring by the fecal-oral route or by aerosol or droplet transmission. Approximately 72% of all poliovirus infections are asymptomatic; another 25% result only in mild intestinal disease, producing nausea, fever, and headache.[footnote] However, even in the absence of symptoms, patients infected with the virus can shed it in feces and oral secretions, potentially transmitting the virus to others. In about one case in every 200, the poliovirus affects cells in the CNS.[footnote]

US Centers for Disease Control and Prevention, “Global Health – Polio,” 2014. Accessed June 30, 2016. http://www.cdc.gov/polio/about/index.htm.US Centers for Disease Control and Prevention, “Global Health – Polio,” 2014. Accessed June 30, 2016. http://www.cdc.gov/polio/about/index.htm.

Transmissible Spongiform Encephalopathies

Acellular infectious agents called prions are responsible for a group of related diseases known as transmissible spongiform encephalopathies (TSEs) that occurs in humans and other animals (see Viroids, Virusoids, and Prions). All TSEs are degenerative, fatal neurological diseases that occur when brain tissue becomes infected by prions. These diseases have a slow onset; symptoms may not become apparent until after an incubation period of years and perhaps decades, but death usually occurs within months to a few years after the first symptoms appear.

Fungal and Parasitic Diseases of the Nervous System

Cryptococcocal Meningitis

*Cryptococcus neoformans* is a fungal pathogen that can cause meningitis. This yeast is commonly found in soils and is particularly associated with pigeon droppings. It has a thick capsule that serves as an important virulence factor, inhibiting clearance by phagocytosis. Most *C. neoformans* cases result in subclinical respiratory infections that, in healthy individuals, generally resolve spontaneously with no long-term consequences (see Respiratory Mycoses). In immunocompromised patients or those with other underlying illnesses, the infection can progress to cause meningitis and granuloma formation in brain tissues. *Cryptococcus* antigens can also serve to inhibit cell-mediated immunity and delayed-type hypersensitivity.

Amoebic Meningitis

Primary amoebic meningoencephalitis (PAM) is caused by *Naegleria fowleri*. This amoeboflagellate is commonly found free-living in soils and water. It can exist in one of three forms—the infective amoebic trophozoite form, a motile flagellate form, and a resting cyst form. PAM is a rare disease that has been associated with young and otherwise healthy individuals. Individuals are typically infected by the amoeba while swimming in warm bodies of freshwater such as rivers, lakes, and hot springs. The pathogenic trophozoite infects the brain by initially entering through nasal passages to the sinuses; it then moves down olfactory nerve fibers to penetrate the submucosal nervous plexus, invades the cribriform plate, and reaches the subarachnoid space. The subarachnoid space is highly vascularized and is a route of dissemination of trophozoites to other areas of the CNS, including the brain ([link]). Inflammation and destruction of gray matter leads to severe headaches and fever. Within days, confusion and convulsions occur and quickly progress to seizures, coma, and death. The progression can be very rapid, and the disease is often not diagnosed until autopsy.

Granulomatous Amoebic Encephalitis

*Acanthamoeba* and *Balamuthia* species are free-living amoebae found in many bodies of fresh water. Human infections by these amoebae are rare. However, they can cause amoebic keratitis in contact lens wearers (see Protozoan and Helminthic Infections of the Eyes), disseminated infections in immunocompromised patients, and granulomatous amoebic encephalitis (GAE) in severe cases. Compared to PAM, GAE tend to be subacute infections. The microbe is thought to enter through either the nasal sinuses or breaks in the skin. It is disseminated hematogenously and can invade the CNS. There, the infections lead to inflammation, formation of lesions, and development of typical neurological symptoms of encephalitis ([link]). GAE is nearly always fatal.

Human African Trypanosomiasis

Human African trypanosomiasis (also known as African sleeping sickness) is a serious disease endemic to two distinct regions in sub-Saharan Africa. It is caused by the insect-borne hemoflagellate *Trypanosoma brucei*. The subspecies *Trypanosoma brucei rhodesiense* causes East African trypanosomiasis (EAT), and another subspecies, *Trypanosoma brucei gambiense* causes West African trypanosomiasis (WAT). A few hundred cases of EAT are currently reported each year.[footnote] WAT is more commonly reported and tends to be a more chronic disease. Around 7000 to 10,000 new cases of WAT are identified each year.[footnote]

US Centers for Disease Control and Prevention, “Parasites – African Trypanosomiasis (also known as Sleeping Sickness), East African Trypanosomiasis FAQs,” 2012. Accessed June 30, 2016. http://www.cdc.gov/parasites/sleepingsickness/gen_info/faqs-east.html.US Centers for Disease Control and Prevention, “Parasites – African Trypanosomiasis (also known as Sleeping Sickness), Epidemiology & Risk Factors,” 2012. Accessed June 30, 2016. http://www.cdc.gov/parasites/sleepingsickness/epi.html.

Neurotoxoplasmosis

*Toxoplasma gondii* is an ubiquitous intracellular parasite that can cause neonatal infections. Cats are the definitive host, and humans can become infected after eating infected meat or, more commonly, by ingesting oocysts shed in the feces of cats (see Parasitic Infections of the Circulatory and Lymphatic Systems). *T. gondii* enters the circulatory system by passing between the endothelial cells of blood vessels.[footnote] Most cases of toxoplasmosis are asymptomatic. However, in immunocompromised patients, neurotoxoplasmosis caused by *T. gondii* infections are one of the most common causes of brain abscesses.[footnote] The organism is able to cross the blood-brain barrier by infecting the endothelial cells of capillaries in the brain. The parasite reproduces within these cells, a step that appears to be necessary for entry to the brain, and then causes the endothelial cell to lyse, releasing the progeny into brain tissues. This mechanism is quite different than the method it uses to enter the bloodstream in the first place.[footnote]

Carruthers, Vern B., and Yasuhiro Suzuki, “Effects of *Toxoplasma gondii* Infection on the Brain,” *Schizophrenia Bulletin* 33, no. 3 (2007): 745-51.Uppal, Gulshan, “CNS Toxoplasmosis in HIV,” 2015. Accessed June 30, 2016. http://emedicine.medscape.com/article/1167298-overview#a3.Konradt, Christoph, Norikiyo Ueno, David A. Christian, Jonathan H. Delong, Gretchen Harms Pritchard, Jasmin Herz, David J. Bzik et al., “Endothelial Cells Are a Replicative Niche for Entry of *Toxoplasma gondii* to the Central Nervous System,” *Nature Microbiology* 1 (2016): 16001.

Neurocysticercosis

Cysticercosis is a parasitic infection caused by the larval form of the pork tapeworm, *Taenia solium*. When the larvae invade the brain and spinal cord, the condition is referred to as neurocysticercosis. This condition affects millions of people worldwide and is the leading cause of adult onset epilepsy in the developing world.[footnote]

DeGiorgio, Christopher M., Marco T. Medina, Reyna Durón, Chi Zee, and Susan Pietsch Escueta, “Neurocysticercosis,” *Epilepsy Currents* 4, no. 3 (2004): 107-11.

Fundamentals of Physics and Chemistry Important to Microbiology

Atomic Structure

Life is made up of matter. Matter occupies space and has mass. All matter is composed of **atoms**. All atoms contain **protons**, **electrons**, and **neutrons** ([link]). The only exception is hydrogen (H), which is made of one proton and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a mass of 1 atomic mass unit (amu) and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. Electrons are distributed in different energy levels called electron shells. Electrons have a negligible mass and a charge of –1. Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 amu and no charge (neutral). The positive (proton) and negative (electron) charges balance each other in a neutral atom, which has a net zero charge. Because protons and neutrons each have a mass of 1 amu, the mass of an atom is equal to the number of protons and neutrons of that atom. The number of electrons does not factor into the overall mass because electron mass is so small.

Chemical Elements

All matter is composed of atoms of **elements**. Elements have unique physical and chemical properties and are substances that cannot easily be transformed either physically or chemically into other substances. Each element has been given a name, usually derived from Latin or English. The elements also have one- or two-letter symbols representing the name; for example, sodium (Na), gold (Au), and silver (Ag) have abbreviations derived from their original Latin names *natrium*, *aurum,* and *argentum*, respectively. Examples with English abbreviations are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). A total of 118 different elements (92 of which occur naturally) have been identified and organized into the periodic table of elements. Of the naturally occurring elements, fewer than 30 are found in organisms on Earth, and four of those (C, H, O, and N) make up approximately 96% of the mass of an organism.[footnote]

Schrijver, Karel, and Iris Schrijver. *Living with the Stars: How the Human Body Is Connected to the Life Cycles of the Earth, the Planets, and the Stars*. Oxford University Press, USA, 2015.

Chemical Bonds

There are three types of chemical bonds that are important when describing the interaction of atoms both within and between molecules in microbiology: (1) covalent bonds, which can be either polar or non-polar, (2) ionic bonds, and (3) hydrogen bonds. There are other types of interactions such as *London* dispersion forces and *van der Waals* forces that could also be discussed when describing the physical and chemical properties of the intermolecular interactions of atoms, but we will not include descriptions of these forces here.

Molecular Formula, Molecular Mass, and the Mole

For molecules formed by covalent bonds, the molecular formula represents the number and types of elemental atoms that compose the molecule. As an example, consider a molecule of glucose, which has the molecular formula C6H12O6. This molecular formula indicates that a single molecule of glucose is formed from six carbon atoms, twelve hydrogen atoms, and six oxygen atoms.

Energy

Thermodynamics refers to the study of energy and energy transfer involving physical matter.

Chemical Reactions

**Chemical reactions** occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in a chemical reaction are called the **reactants** (usually found on the left side of a chemical equation), and the substances produced by the reaction are known as the **products** (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a “one-way street.”

Properties of Water and Solutions

The hydrogen and oxygen atoms within water molecules form polar covalent bonds. There is no overall charge to a water molecule, but there is one ∂+ on each hydrogen atom and two ∂– on the oxygen atom. Each water molecule attracts other water molecules because of the positive and negative charges in the different parts of the molecule ([link]). Water also attracts other polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as **hydrophilic** (“water-loving”). Hydrogen bonds are not readily formed with nonpolar substances like oils and fats. These nonpolar compounds are **hydrophobic** (“water-fearing”) and will orient away from and avoid water.

Acids and Bases

The **pH** of a solution is a measure of hydrogen ion (H+) and hydroxide ion (OH–) concentrations and is described as **acidity** or **alkalinity,** respectively. Acidity and alkalinity (also referred to as basicity) can be measured and calculated. pH can be simply represented by the mathematic equation, $\text{pH}={\text{−log}}_{10}\left[{\text{H}}^{+}\right].$ On the left side of the equation, the "p" means "the negative logarithm of " and the H represents the [H+]. On the right side of the equation, [H+] is the concentration of H+ in moles/L . What is not represented in this simple equation is the contribution of the OH–, which also participates in acidity or alkalinity. Calculation of pH results in a number range of 0 to 14 called the pH scale ([link]). A pH value between 0 and 6.9 indicates an acid. It is also referred to as a low pH, due to a high [H+] and low [OH–] concentration. A pH value between 7.1 and 14 indicates an alkali or base. It is also referred to as a high pH, due to a low [H+] and high [OH–] concentration. A pH of 7 is described as a neutral pH and occurs when [H+] equals [OH–].

Mathematical Basics

Squares and Other Powers

An exponent, or a power, is mathematical shorthand for repeated multiplications. For example, the exponent “2” means to multiply the base for that exponent by itself (in the example here, the base is “5”):

Calculating Percents

A percent is a way of expressing a fractional amount of something using a whole divided into 100 parts. A percent is a ratio whose denominator is 100. We use the percent symbol, %, to show percent. Thus, 25% means a ratio of $\frac{25}{100}$, 3% means a ratio of $\frac{3}{100}$, and 100 % percent means $\frac{100}{100}$, or a whole.

Multiplying and Dividing by Tens

In many fields, especially in the sciences, it is common to multiply decimals by powers of 10. Let’s see what happens when we multiply 1.9436 by some powers of 10.

Scientific Notation

Scientific notation is used to express very large and very small numbers as a product of two numbers. The first number of the product, the digit term, is usually a number not less than 1 and not greater than 10. The second number of the product, the exponential term, is written as 10 with an exponent. Some examples of scientific notation are given in [link].

Expressing Numbers in Scientific Notation

Converting any number to scientific notation is straightforward. Count the number of places needed to move the decimal next to the left-most non-zero digit: that is, to make the number between 1 and 10. Then multiply that number by 10 raised to the number of places you moved the decimal. The exponent is positive if you moved the decimal to the left and negative if you moved the decimal to the right. So

Logarithms

The common logarithm (log) of a number is the power to which 10 must be raised to equal that number. For example, the common logarithm of 100 is 2, because 10 must be raised to the second power to equal 100. Additional examples are in [link].

Rounding and Significant Digits

In reporting numerical data obtained via measurements, we use only as many significant figures as the accuracy of the measurement warrants. For example, suppose a microbiologist using an automated cell counter determines that there are 525,341 bacterial cells in a one-liter sample of river water. However, she records the concentration as 525,000 cells per liter and uses this rounded number to estimate the number of cells that would likely be found in 10 liters of river water. In this instance, the last three digits of the measured quantity are not considered *significant.* They are rounded to account for variations in the number of cells that would likely occur if more samples were measured.

Generation Time

It is possible to write an equation to calculate the cell numbers at any time if the number of starting cells and doubling time are known, as long as the cells are dividing at a constant rate. We define *N*0 as the starting number of bacteria, the number at time *t* = 0. *Ni* is the number of bacteria at time *t* = *i*, an arbitrary time in the future. Finally we will set *j* equal to the number of generations, or the number of times the cell population doubles during the time interval. Then we have,

Most Probable Number

The table in [link] contains values used to calculate the most probable number example given in How Microbes Grow.

Metabolic Pathways

Glycolysis

Entner–Doudoroff Pathway

The Pentose-Phosphate Pathway

TCA Cycle

Beta Oxidation

Electron Transport Chain and Oxidative Phosphorylation

Calvin-Benson Cycle

Taxonomy of Clinically Relevant Microorganisms

Bacterial Pathogens

The following tables list the species, and some higher groups, of pathogenic Eubacteria mentioned in the text. The classification of Bacteria, one of the three domains of life, is in constant flux as relationships become clearer through sampling of genetic sequences. Many groups at all taxonomic levels still have an undetermined relationship with other members of the phylogenetic tree of Bacteria. *Bergey’s Manual of Systematics of Archaea and Bacteria* maintains a published list and descriptions of prokaryotic species. The tables here follow the taxonomic organization in the *Bergey’s Manual* Taxonomic Outline.[footnote]

Bergey’s Manual Trust. *Bergey’s Manual of Systematics of Archaea and Bacteria, Taxonomic Outline*. 2012. http://www.bergeys.org/outlines.html

Viral Pathogens

There are several classification systems for viruses. The International Committee on Taxonomy of Viruses (ICTV) is the international scientific body responsible for the rules of viral classification. The ICTV system used here groups viruses based on genetic similarity and presumed monophyly. The viral classification system is separate from the classification system for cellular organisms. The ICTV system groups viruses within seven orders, which contain related families. There is, presently, a large number of unassigned families with unknown affinities to the seven orders. Three of these orders infect only Eubacteria, Archaea, or plants and do not appear in this table. Some families may be divided into subfamilies. There are also many unassigned genera. Like all taxonomies, viral taxonomy is in constant flux. The latest complete species list and classification can be obtained on the ICTV website.[footnote]

International Committee on Taxonomy of Viruses. “ICTV Master Species List.” http://talk.ictvonline.org/files/ictv_documents/m/msl/default.aspx

Fungal Pathogens

The Fungi are one of the kingdoms of the domain Eukarya. Fungi are most closely related to the animals and a few other small groups and more distantly related to the plants and other groups that formerly were categorized as protist. At present, the Fungi are divided into seven phyla (or divisions, a hold over from when fungi were studied with plants), but there are uncertainties about some relationships.[footnote] Many groups of fungi, particularly those that were formerly classified in the phylum Zygomycota, which was not monophyletic, have uncertain relationships to the other fungi. The one species listed in this table that falls into this category is *Rhizopus arrhizus.* Fungal names are governed by the International Code of Nomenclature for Algae, Fungi, and Plants,[footnote] but the International Commission on the Taxonomy of Fungi (ICTF) also promotes taxonomic work on fungi. One activity of the ICTF is publicizing name changes for medically and otherwise important fungal species. Many species that formerly had two names (one for the sexual form and one for the asexual form) are now being brought together under one name.

D. S. Hibbett et al. “A Higher-level Phylogenetic Classification of the Fungi.” *Mycological Research* 111 no. 5 (2007):509–547.J. McNeill et al. *International Code of Nomenclature for Algae, Fungi, and Plants (Melbourne Code)*. Oberreifenerg, Germany. Koeltz Scientific Books; 2012. http://www.iapt-taxon.org/nomen/main.php?

Protozoan Pathogens

The relationships among the organisms (and thus their taxonomy) previously grouped under the name Protists are better understood than they were two or three decades ago, but this is still a work in progress. In 2005, the Eukarya were divided into six supergroups.[footnote] The latest high-level classification combined two of the previous supergroups to produce a system comprising five supergroups.[footnote] This classification was developed for the Society of Protozoologists, but it is not the only suggested approach. One of the five supergroups includes the animals, fungi, and some smaller protist groups. Another contains green plants and three algal groups. The other three supergroups (listed in the three tables below) contain the other protists, many of them which cause disease. In addition, there is a large number of protist groups whose relationships are not understood. In the three supergroups represented here we have indicated the phyla to which the listed pathogens belong.

S.M. Adl et al. “The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists.” *Journal of Eukaryotic Microbiology* 52 no. 5 (2005):399–451.S.M. Adl et al. “The Revised Classification of Eukaryotes.” *Journal of Eukaryotic Microbiology* 59 no. 5 (2012):429–514.

Parasitic Helminths

The taxonomy of parasitic worms, all of which belong to the kingdom Animalia still contains many uncertainties. The pathogenic species are found in two phyla: the Nematoda, or roundworms, and the Platyhelminthes, or flat worms. The Nematoda is tentatively divided into two classes[footnote], one of which, Chromadorea, probably contains unrelated groups. The parasitic flatworms are contained within three classes of flatworm, of which two are important to humans, the trematodes and the cestodes.

National Center for Biotechnology Information. “Taxonomy Browser: Nematoda.” http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=6231

Glossary