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Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with  bla  CMY–2  +   Escherichia coli , 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and  Lactobacillus  rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially  Escherichia/Shigella . However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with  bla  CMY–2  +   E. coli , oral Amp also led to the increase of Proteobacteria, dominated by  Klebsiella  and  Escherichia / Shigella , and a reduction of Firmicutes. Specifically within Firmicutes,  Enterococcus, Clostridium , etc. were enriched but  Lactobacillus  was diminished. The fecal resistome including Amp r  genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted  bla  CMY–2  +  gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Amp r - or multidrug resistance-encoding genes other than  bla  CMY–2  + . These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.

frontiers in microbiology

Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry