Structural analysis of the CARB β-lactamase from Vibrio parahaemolyticus facilitates application of the β-lactam/β-lactamase inhibitor therapy

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

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 blaCARB 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 blaCARB 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 blaCARB alleles. Continued monitoring of Vibrio spp. phenotypes and genotypes in sea otters is warranted to observe biologically relevant changes in antimicrobial resistance.

Eco-Evolutionary Drivers of Vibrio parahaemolyticus Sequence Type 3 Expansion: Retrospective Machine Learning Approach

BACKGROUND

Environmentally sensitive pathogens exhibit ecological and evolutionary responses to climate change that result in the emergence and global expansion of well-adapted variants. It is imperative to understand the mechanisms that facilitate pathogen emergence and expansion, as well as the drivers behind the mechanisms, to understand and prepare for future pandemic expansions.

OBJECTIVE

The unique, rapid, global expansion of a clonal complex of Vibrio parahaemolyticus (a marine bacterium causing gastroenteritis infections) named Vibrio parahaemolyticus sequence type 3 (VpST3) provides an opportunity to explore the eco-evolutionary drivers of pathogen expansion.

METHODS

The global expansion of VpST3 was reconstructed using VpST3 genomes, which were then classified into metrics characterizing the stages of this expansion process, indicative of the stages of emergence and establishment. We used machine learning, specifically a random forest classifier, to test a range of ecological and evolutionary drivers for their potential in predicting VpST3 expansion dynamics.

RESULTS

We identified a range of evolutionary features, including mutations in the core genome and accessory gene presence, associated with expansion dynamics. A range of random forest classifier approaches were tested to predict expansion classification metrics for each genome. The highest predictive accuracies (ranging from 0.722 to 0.967) were achieved for models using a combined eco-evolutionary approach. While population structure and the difference between introduced and established isolates could be predicted to a high accuracy, our model reported multiple false positives when predicting the success of an introduced isolate, suggesting potential limiting factors not represented in our eco-evolutionary features. Regional models produced for 2 countries reporting the most VpST3 genomes had varying success, reflecting the impacts of class imbalance.

CONCLUSIONS

These novel insights into evolutionary features and ecological conditions related to the stages of VpST3 expansion showcase the potential of machine learning models using genomic data and will contribute to the future understanding of the eco-evolutionary pathways of climate-sensitive pathogens.

Beta-lactamase genes in bacteria from food animals, retail meat, and human surveillance programs in the United States from 2002 to 2021

The spread of beta-lactamase-producing bacteria is a global public-health concern. This study aimed to explore the distribution of beta-lactamases reported in three sampling sources (cecal, retail meat, and human) collected as part of integrated surveillance in the United States. We retrieved and analyzed data from the United States National Antimicrobial Resistance Monitoring Systems (NARMS) from 2002 to 2021. A total of 115 beta-lactamase genes were detected in E. coli, Salmonella enterica, Campylobacter, Shigella and Vibrio: including 35 genes from cecal isolates, 32 genes from the retail meat isolates, and 104 genes from the human isolates. Three genes in E. coli (blaCMY-2,blaTEM-1A, and blaTEM-1B), 6 genes in Salmonella enterica (blaCARB-2, blaCMY-2, blaCTXM-65, blaTEM-1A, blaTEM-1B, and blaHERA-3), and 2 genes in Campylobacter spp. (blaOXA-61 and blaOXA-449) have been detected across food animals (cattle, chicken, swine, and turkey) and humans over the study period. blaCTXM-55 has been detected in E. coli isolates from the four food animal sources while blaCTXM-15 and blaCTXM-27 were found only in cattle and swine. In Salmonella enterica, blaCTXM-2, blaCTXM-9, blaCTXM-14, blaCTXM-15, blaCTXM-27, blaCTXM-55, and blaNDM-1 were only detected among human isolates. blaOXAs and blaCARB were bacteria-specific and the only beta-lactamase genes detected in Campylobacter spp. and Vibrio spp respectively. The proportions of beta-lactamase genes detected varies from bacteria to bacteria. This study provided insights on the beta-lactamase genes detected in bacteria in food animals and humans in the United States. This is necessary for better understanding the molecular epidemiology of clinically important beta-lactamases in one health interface.

Prevalence and antimicrobial resistance profiles of Vibrio spp. and Enterococcus spp. in retail shrimp in Northern California

Shrimp is one of the most consumed seafood products globally. Antimicrobial drugs play an integral role in disease mitigation in aquaculture settings, but their prevalent use raises public health concerns on the emergence and spread of antimicrobial resistant microorganisms. Vibrio spp., as the most common causative agents of seafood-borne infections in humans, and Enterococcus spp., as an indicator organism, are focal bacteria of interest for the monitoring of antimicrobial resistance (AMR) in seafood. In this study, 400 samples of retail shrimp were collected from randomly selected grocery stores in the Greater Sacramento, California, area between September 2019 and June 2020. The prevalence of Vibrio spp. and Enterococcus spp. was 60.25% (241/400) and 89.75% (359/400), respectively. Subsamples of Vibrio (n = 110) and Enterococcus (n = 110) isolates were subjected to antimicrobial susceptibility testing (AST). Vibrio isolates had high phenotypic resistance to ampicillin (52/110, 47.27%) and cefoxitin (39/110, 35.45%). Enterococcus were most frequently resistant to lincomycin (106/110, 96.36%), quinupristin-dalfopristin (96/110, 87.27%), ciprofloxacin (93/110, 84.55%), linezolid (86/110, 78.18%), and erythromycin (58/110, 52.73%). For both Vibrio and Enterococcus, no significant associations were observed between multidrug resistance (MDR, resistance to ≥3 drug classes) in isolates from farm raised and wild caught shrimp (p > 0.05) and in isolates of domestic and imported origin (p > 0.05). Whole genome sequencing (WGS) of a subset of Vibrio isolates (n = 42) speciated isolates as primarily V. metschnikovii (24/42; 57.14%) and V. parahaemolyticus (12/42; 28.57%), and detected 27 unique antimicrobial resistance genes (ARGs) across these isolates, most commonly qnrVC6 (19.05%, 8/42), dfrA31 (11.90%, 5/42), dfrA6 (9.5%, 4/42), qnrVC1 (9.5%, 4/42). Additionally, WGS predicted phenotypic resistance in Vibrio isolates with an overall sensitivity of 11.54% and specificity of 96.05%. This study provides insights on the prevalence and distribution of AMR in Vibrio spp. and Enterococcus spp. from retail shrimp in California which are important for food safety and public health and exemplifies the value of surveillance in monitoring the spread of AMR and its genetic determinants.

Characteristics of Antimicrobial-Resistant Vibrio parahaemolyticus Strains and Identification of Related Antimicrobial Resistance Gene Mutations

Multidrug-resistant (MDR) Vibrio parahaemolyticus strains have become a great threat to public health. The purpose of this study was to investigate differences in biological characteristics and antimicrobial resistance gene (ARG) mutations of V. parahaemolyticus that displayed different levels of antimicrobial resistance. The susceptibility of 74 V. parahaemolyticus strains to 9 common antimicrobials was investigated, of which 88% were resistant to 3-4 antimicrobials and 3% to 5-7 antimicrobials. Interestingly, only 9% were resistant to 1-2 antimicrobials. The MDR strains possessed longer growth lag time than the non-MDR strains and displayed weaker swimming abilities. Whole genome sequencing was performed on strains VP41, VP44, 460, and 469 that were resistant to two to three classes of antimicrobials. ARGs were identified and compared with that of reference strain ATCC17802, and some important mutations were deduced. The Val189Ile mutation emerged in qnr gene of a single strain. Besides, the nonsynonymous mutations existed in four ARGs in different strains, including CatB (Pro165Ser, Gly208Asp), VmeA (Ile313Thr), VmeC (Glu329Ala), and VmeD (Asn205Ser). These results linked resistance gene mutations to enhance resistance in V. parahaemolyticus strains and provide a reference for more effective monitoring and prevention of V. parahaemolyticus infections.

Crystal structure of the antibiotic- and nitrite-responsive histidine kinase VbrK sensor domain from Vibrio rotiferianus

Vibrio species are prevalent in the aquatic environments and can infect humans and aquatic organisms. Vibrio parahaemolyticus counteracts β-lactam antibiotics and enhances virulence using a regulation mechanism mediated by a two-component regulatory system (TCS) consisting of the VbrK histidine kinase and the VbrR response regulator. The periplasmic sensor domain of VbrK (VbrK^SD) detects β-lactam antibiotics or undergoes S-nitrosylation in response to host nitrites. Although V. parahaemolyticus VbrK^SD (vpVbrK^SD) has recently been characterized through structural studies, it is unclear whether its structural features that are indispensable for biological functions are conserved in other VbrK orthologs. To structurally define the functionally critical regions of VbrK and address the structural dynamics of VbrK, we determined the crystal structures of Vibrio rotiferianus VbrK^SD (vrVbrK^SD) in two crystal forms and performed a comparative analysis of diverse VbrK structures. vrVbrK^SD folds into a curved rod-shaped two-domain structure as observed in vpVbrK^SD. The membrane-distal end of the vrVbrK^SD structure, including the α3 helix and its neighboring loops, harbors both S-nitrosylation and antibiotic-sensing sites and displays high structural flexibility and diversity. Noticeably, the distal end is partially stabilized by a disulfide bond, which is formed by the cysteine residue that is S-nitrosylated in response to nitrite. Therefore, the distal end of VbrK^SD plays a key role in initiating the VbrK-VbrR TCS pathway activation, and it is involved in the nitrosylation-mediated regulation of the structural dynamics of VbrK.