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

UNLABELLED

Antimicrobial resistance in species poses risks to both human and marine mammal health. Whole genome sequencing of 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 spp. pathogens isolated from southern sea otters (), northern sea otters (), 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, , in sea otter and environmental isolates that were previously identified as . A total of 489 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 and . Both between- and within-species variations in ampicillin resistance were observed despite the ubiquitous presence of genes in , , and . Discordance between phenotypic and genotypic ampicillin resistance was especially noted for and was partially attributed to the allelic variation of the 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 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 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 in sea otters suggests that a broader taxonomic group of 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 alleles. Continued monitoring of spp. phenotypes and genotypes in sea otters is warranted to observe biologically relevant changes in antimicrobial resistance.