Does long term use of antibiotics in humans actually lead to a greater risk of infection?
does long term use of antibiotics breed these strains in the bodies of antibiotic users[,] and increase the risk of various bodily infections?


Yes to the first question (although I would use the words select for). No, not usually for the second question in the individual(*), yes in the population.

This should be looked at as a problem in populations of both people/animals and bacterial populations in general. Given time, any living organism will be favored if a mutation involving a selective pressure (like an antibiotic) is introduced, not only in those towards which the antibiotic is directed but also among the normal microbiota. The longer the selective pressure (antibiotic treatment), the greater the probability that a resistant strain of one bacteria or another will develop. 

That's why there's a push (in studies) to limit the number of days of antibiotic use necessary to the least number needed which still proves efficient in eradicating an infection. (The trend is towards kill 'em quick and kill 'em all - higher doses for shorter periods, or make it strong and only long enough to cause the extinction of the illness-causing bacteria and not long enough for selection of resistance mutations.)

It is quite normal to have potentially pathogenic bacteria as part of one's microbiome. Usually other beneficial bacteria and conditions keep these in check. But antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized (up to four years in one study). This gives even a small population of resistant bacteria to genetically transfer resistance to others.

Short-term use is less likely to select for resistance in one individual, but, in terms of populations of people, antibiotics are used so ubiquitously that resistant strains will be selected for in shorter treatment intervals by sheer numbers of people being treated.


  When resistant and susceptible organisms compete to colonize or infect hosts, and use of an antibiotic has a greater impact on the transmission of susceptible bacteria than resistant ones, then increasing use of the antibiotic will result in an increase in frequency of organisms resistant to that drug in the population, even if the risk for treated patients is modest. Antimicrobial use and patient-to-patient transmission are not independent pathways for promoting of antimicrobial resistance, rather they are inextricably linked. 


"Long term use" in one individual is relatively uncommon and unnecessary, but if necessary, usually does more good than harm to that individual. Almost all (if not all) of the population of the bacteria you're trying to eliminate from one site will be susceptible to the antibiotic and will die, leaving, in a few cases, a few resistant ones that your body can handle naturally, or that can repopulate to "normal" levels without causing illness. But they are then there, the resistant ones, to spread within a population of the individual's microbiome, and the population of people. The next person with a problem, who might have picked up that resistant strain, will not respond well to the same antibiotic. Nor will the patient who was initially treated, if the problem recurs with an antibiotic resistant strain. So, as I said, yes and no.

That's why people (doctors, vets, and - with help - patients) should consider a risk-to-benefit-ratio whenever using an antibiotic. From that standpoint, it is always unethical to use an antibiotic for what is probably a virus, because the benefit to a patient is very small, but the risk - to that patient, who might suffer complications from its use, and to the population if a resistant strain is selected for - is relatively high. Better to wait it out to see if it is bacterial (if one can't test for it directly), and treat it if it does turn out to be. Of course, the risk of not treating in certain populations must also be considered: the elderly, the immunosuppressed, infants, and people with other illnesses or predispositions to infection.

It's not just use of antibiotics in patients/humans that causes problems; its use in any situation can lead to selection for resistance. This is well documented to occur in the meat industry, where a grower often tries to minimize the effect of cost-efficient but insalubrious growing conditions by giving antibiotics to the entire population of meat-animals (beef or poultry) to cut the monetary losses associated with potential illnesses.

It's a multifactorial, and often monetarily driven, problem. Doctors share the blame, but so do patients who demand antibiotics thinking they know better than the doctor, and who will doctor-shop until they find one who will do their bidding, or make a stink for the doctor who refuses. Some doctors still refuse, but they pay a heavy (non-monetary and sometimes monetary) price for doing so.

In the meat industry, it's always a monetarily driven process.


  This review focuses on agricultural antimicrobial drug use as a major driver of antimicrobial resistance worldwide for four reasons: It is the largest use of antimicrobials worldwide; much of the use of antimicrobials in agriculture results in subtherapeutic exposures of bacteria; drugs of every important clinical class are utilized in agriculture; and human populations are exposed to antimicrobial-resistant pathogens via consumption of animal products as well as through widespread release into the environment.


What YOU can do:
Do not take an antibiotic for a viral infection like a cold or the flu.
Do not save some of your antibiotic for the next time you get sick.
Take an antibiotic exactly as the healthcare provider tells you. Complete the prescribed course of treatment even if you are feeling better. If treatment stops too soon, some bacteria may survive and re-infect.
Do not take antibiotics prescribed for someone else.
If your healthcare provider determines that you do not have a bacterial infection, ask about ways to help relieve your symptoms. Do not pressure your provider to prescribe an antibiotic.  

Antibiotic resistance: delaying the inevitable
Get Smart: Know When Antibiotics Work
Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome
Antimicrobial Use and Antimicrobial Resistance: A Population Perspective
Comparison of 8 vs 15 Days of Antibiotic Therapy for Ventilator-Associated Pneumonia in AdultsA Randomized Trial
Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria
Industrial Food Animal Production, Antimicrobial Resistance, and Human Health