Antimicrobial resistance of
Vibrio
spp. from the coastal California system: discordance between genotypic and phenotypic patterns
Authors: Sebastian Peter J. , Schlesener Cory , Byrne Barbara A. , Miller Melissa , Smith Woutrina , Batac Francesca , Goertz Caroline E. C. , Weimer Bart C. , Johnson Christine K. 
Published: February 2025

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.