due to the host’s own inflammatory response. Genetics The genome of S. flexneri and Escherichia coli are nearly indistinguishable at the species level. S. flexneri has a circular chromosome with 4,599,354 base pairs. It is smaller than that of E. coli but the genes are similar. S. flexneri has about 4,084 known genes in the genome. The extensive similarity between E. coli and S. flexneri is proposed to be due to horizontal transfer. All of the genes needed for S. flexneri to invade the epithelial lining of the colon are found on a virulence plasmid called pINV. The genome of pINV is highly conserved between subspecies of S. flexneri. S. flexneri also has two other small multicopy plasmids, but some strains of S. flexneri have more plasmids that are suspected to confer antibiotic resistance. Some strains of S. flexneri have resistance to the antibiotics streptomycin, ampicillin, or trimethoprim. It has been found that chloramphenicol, nalidixic acid, and gentamicin are still effective antibiotics for some strains. Metabolism Shigella flexneri is a heterotroph. It utilizes the Embden-Meyerhof-Parnas (EMP), Entner-Doudoroff (ED), or pentose phosphate pathway (PPP) to metabolize sugars. The products of these pathways then feed into the Citric Acid Cycle (TCA). S. flexneri can metabolize glucose and pyruvate. Supplemented pyruvate allows for the most growth and is believed to be the preferred carbon source. Pyruvate could be supplied by the cell's own metabolism or taken from the host cell. S. flexneri is a facultative anaerobe that is able to perform mixed-acid fermentation of pyruvate. S. flexneri is unable to ferment lactose. This bacterium grows optimally at 37°C but can grow in temperatures as low as 30°C. Small RNA Bacterial small RNAs play important roles in many cellular processes. RnaG and RyhB sRNAs have been well studied in S. flexneri. Ssr1 sRNA, which could play role in resistance to acidic stress and regulation of virulence was shown to exist only in Shigella. Ecology Infectious cycle Shigella flexneri contains a virulence plasmid that codes for three virulence factors: a type-3 secretion system (T3SS), invasion plasmid antigen proteins (IPA proteins), and IcsA (used for cell-to-cell spread). Upon infection, S. flexneri injects the host cell cytoplasm with ipa proteins using the T3SS—a needle-and-syringe-like apparatus common to many Gram-negative pathogens. These ipa proteins induce "membrane ruffling" by the host cell. Membrane ruffling creates membrane pockets which capture and engulf the bacteria. Once inside, S. flexneri uses host