Antimicrobial resistance in Vibrio cholerae increases under anaerobic conditions revealing novel genetic targets

Many bacterial pathogens experience anaerobic conditions in the gut, but antimicrobial resistance (AMR) phenotypes are generally tested under ambient aerobic conditions in the lab. To better understand AMR under conditions more similar to natural infections, we used Vibrio cholerae as a model enteric pathogen. We sequenced the genomes and assessed the growth of 62 V. cholerae isolates with different concentrations of three antibiotics, under aerobic and anaerobic conditions. In support of the hypothesis that AMR varies according to oxygen conditions, V. cholerae was more resistant to antibiotics under anaerobic conditions. We found many previously known genes associated with resistance; however, some of these genes were only resistance-associated under aerobic conditions. Resistance to azithromycin and doxycycline only had a detectable genetic component under anaerobic conditions. Together, our results point to distinct genetic mechanisms of resistance under anaerobic conditions and suggest several candidate genes for experimental follow-up.