Development of novel tools for monitoring antimicrobial resistance in complex microbial communities and their application to improving our stewardship of antimicrobials in livestock

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Beyi, Ashenafi Feyisa
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Plummer, Paul J
Zhang, Qijing
Phillips, Gregory J
Mochel, Jonathan P
Kreuder, Amanda J
Committee Member
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Veterinary Microbiology and Preventative Medicine
The use of medically important antibiotics in livestock is considered a potential factor that significantly contributes to the emergence and dissemination of antibiotic resistance (AMR) in humans. Thus, the strengthening of antibiotic stewardship programs on farms is critically important. Fluoroquinolones (FQs) are medically important antimicrobials used to treat different human ailments, including gastrointestinal infections caused by foodborne pathogens. In this study, the impacts of FQ drugs such as danofloxacin and enrofloxacin, which are used to prevent and control bovine respiratory disease complex in beef cattle, on gut microbiota were investigated. Furthermore, a novel proximity ligation-based metagenomic method was explored to detect resistance genes with their associated bacterial hosts in a complex microbial community. Young calves with no history of antibiotic exposure were challenged with Mannheimia haemolytica and then treated with FQs to examine the responses of gut microbiota. The main observations in this study are summarized as follows. 1) The proximity ligation approach employed to identify resistance genes with their hosts in a sample from digital dermatitis cases has provided results that are consistent with the literature. 2) We demonstrated that subcutaneously administered a single therapeutic dose of danofloxacin has affected fecal microbiota, resistome profiles, and the relative abundance of Campylobacter. 3) A single therapeutic dose of enrofloxacin has been shown to alter fecal microbiota and resistome irrespective of its dose. Finally, we conducted pharmacokinetic analyses of FQs in plasma and feces, which have revealed the accumulation of significantly high concentrations of danofloxacin, enrofloxacin, and its active metabolite ciprofloxacin in the intestine. In conclusion, our study shows that parenterally administered therapeutic doses of FQs are deposited in the intestine in high amounts, which are capable of negatively impacting microbial integrity and enhancing the development and spread of antimicrobial resistance genes. The new resistance gene tracking approach holds a promising potential to study horizontal gene transfer in microbial communities. In addition, the difference in pharmacokinetics and impacts on gut microbiota between danofloxacin and different doses of enrofloxacin shown in this study provides an opportunity to investigate further and select the FQ drug that has minimal side effects but is still effective in clearing bovine respiratory infections.