Bridging sea and clinic: genomic evidence of shared AMR and virulence determinants in Vibrio fluvialis from human disease and the environment.

BACKGROUND

Vibrio fluvialis is an emerging enteric pathogen increasingly implicated in diarrhoeal disease outbreaks and sporadic infections, particularly in low- and middle-income countries. Reports of multidrug resistance (MDR) in this species are rising; however, comprehensive genomic data from Indian clinical isolates remain limited. A detailed understanding of its antimicrobial resistance (AMR) determinants, virulence repertoire, and population structure is essential for guiding surveillance and public health interventions.

METHODS

We performed whole-genome sequencing of clinical V. fluvialis isolates collected in India between 2019 and 2025. High-quality draft genomes were subjected to in silico analyses to identify acquired AMR genes, chromosomal resistance determinants, virulence-associated genes, and mobile genetic elements including plasmids and integrative elements. To contextualize Indian isolates within the global population structure, we conducted single nucleotide polymorphism (SNP)-based phylogenetic analysis incorporating publicly available V. fluvialis genomes from diverse geographic and ecological sources. Phylogenetic clustering was examined to explore evolutionary relationships and potential links between clinical, environmental, and non-human isolates.

RESULTS

Indian clinical isolates demonstrated considerable genomic diversity and harbored a broad array of AMR genes conferring resistance to commonly used antimicrobial classes. Several resistance determinants were associated with mobile genetic elements, underscoring the role of horizontal gene transfer in shaping the resistome. Virulence profiling identified genes linked to adhesion, toxin production, and intestinal colonization. SNP-based phylogeny revealed that Indian isolates were distributed across multiple global lineages, with certain clusters including environmental and non-human isolates, suggesting potential environmental reservoirs and transmission interfaces.

CONCLUSIONS

This study provides a comprehensive genomic overview of contemporary Indian clinical V. fluvialis isolates within a global framework. The findings highlight the genetic diversity, MDR potential, and possible environmental connectivity of this emerging pathogen, reinforcing the need for sustained genomic surveillance and a One Health approach to its monitoring and control.