Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance inVibrio choleraeunder anaerobic conditions

Abstract

Antimicrobial resistance (AMR) in Gram negative enteropathogens is an urgent threat to the antibiotic formulary. These taxa undergo anaerobic respiration within the host, yet little is known about how anaerobic conditions influence antimicrobial resistance (AMR). The facultative enteropathogen Vibrio cholerae was chosen as a model to determine the impact of anaerobic growth on AMR because cholera is one of the few non-invasive diarrhoeal diseases for which antibiotics are indicated, albeit conditionally. V. cholerae isolates from a single outbreak were tested for resistance by minimal inhibitory concentrations (MIC) under aerobic and anaerobic conditions against clinically relevant antibiotics. Here we show that the odds of classifying isolates as resistant under anaerobic compared to aerobic conditions increased over 20 times for ciprofloxacin and 50 times for azithromycin, yet for doxycycline, all isolates remained below the breakpoint for resistance. Genome-wide association studies (GWAS) found significant associations between known and unknown genetic elements and AMR phenotypes that varied by oxygen exposure and antibiotic concentrations. In most cases, AMR phenotypes were more heritable, and more genes significantly associated with AMR were discovered, under anaerobic conditions compared to aerobic conditions. These findings challenge the paradigm of testing facultative enteropathogens for AMR under aerobic conditions alone. This experimental approach establishes a new, more sensitive framework to track and investigate mechanisms of AMR.