Antimicrobial resistance of Vibrio spp. from the coastal California system: discordance between genotypic and phenotypic patterns.

Abstract

Antimicrobial resistance in Vibrio species poses risks to both human and marine mammal health. Whole genome sequencing of Vibrio spp. can be utilized to screen for antimicrobial resistance genes and allelic variants to provide mechanistic insights in ways that PCR screening and phenotypic interpretation cannot. Our goals were to (i) characterize antimicrobial resistance patterns of Vibrio spp. pathogens isolated from southern sea otters (Enhydra lutris nereis), northern sea otters (Enhydra lutris kenyoni), and environmental samples from the central California coast using whole genome sequencing, and (ii) compare the presence of antimicrobial resistance genes with phenotypic interpretation from antibiotic susceptibility testing. Unexpectedly, genomic classification identified an understudied species, Vibrio diabolicus, in sea otter and environmental isolates that were previously identified as Vibrio alginolyticus. A total of 489 Vibrio spp. isolates were sequenced, and frequently detected antimicrobial resistance genes included multidrug efflux pumps and genes associated with resistance to ß-lactams and tetracyclines. Genes associated with resistance to fluoroquinolones, aminoglycosides, chloramphenicol, and sulfonamides were uncommon. Sea otter isolates were phenotypically susceptible to tetracycline despite carrying genes tet34 and tet35. Both between- and within-species variations in ampicillin resistance were observed despite the ubiquitous presence of bla_CARB genes in V. alginolyticus, V. diabolicus, and Vibrio parahaemolyticus. Discordance between phenotypic and genotypic ampicillin resistance was especially noted for V. parahaemolyticus and was partially attributed to the allelic variation of the bla_CARB genes. Tetracyclines and fluoroquinolones, but not ß-lactams, are likely to be effective treatments for vibriosis in sea otters.

Importance: Vibriosis (infection with non-cholera Vibrio spp.) is the most common seafood-borne illness globally, with major impacts on public health, food security, and wildlife health. Potential treatments of antimicrobial-resistant Vibrio spp. in humans, aquaculture, and marine wildlife rehabilitation are complicated by current diagnostic challenges regarding bacterial species identification and interpretation of antimicrobial resistance patterns. Unexpected detection of previously misidentified Vibrio diabolicus in sea otters suggests that a broader taxonomic group of Vibrio infect sea otters than previously described. We also determined that the presence of ß-lactamase genes alone in sea otter isolates does not necessarily correlate with an ampicillin-resistant phenotype, likely due to deleterious amino acid substitutions in certain bla_CARB alleles. Continued monitoring of Vibrio spp. phenotypes and genotypes in sea otters is warranted to observe biologically relevant changes in antimicrobial resistance.