One Health genomic epidemiology reveals emerging tropical pathogens and antimicrobial resistance in coastal marine ecosystems of Gujarat, India

Introduction Microbial community structures and dissemination of antimicrobial resistance (AMR) are shifting in tropical coastal ecosystems amid rapid urbanization and anthropogenic pressure. However, integrated genomic surveillance of pathogens, resistome, and bacterial hosts along the Gujarat coastline remains incomplete, limiting environmental risk assessment based on the One Health approach. In this study, integrated shotgun metagenomics was performed to understand the microbial diversities, priority pathogens, antimicrobial resistance genes (ARGs), and organism-level ARG- host associations in the Gujarat Coast and the anthropogenic factors influencing the resistome structure. Methods In present study, whole metagenome shotgun sequencing was performed on surface-water samples collected from ten coastal sites, comprising both enriched and control sites. Taxonomic profiles were obtained using Kraken2 and antimicrobial resistance genes using AMRFinderPlus. The resistance determinants were cross-referenced with other sequences in the contigs and then compared with the Comprehensive Antibiotic Resistance Database (CARD), an online resource containing over 200,000 antibiotic resistance genes. Spatial variation and resistance patterns were assessed using alpha diversity, Bray–Curtis ordination, hierarchical clustering, and functional resistome profiling. Results Spatial variation was highly apparent, as Pseudomonadota and Bacillota dominated most sites, and anthropogenically influenced sites had site-specific enrichment of WHO priority bacterial genera. The high-priority Pseudomonas , and the critical-priority Enterobacterales ( Escherichia, Enterobacter, Citrobacter ) were found mainly in Ghogha, Daman, and Dumas. Some genera of fish pathogens, such as Aeromonas and Photobacterium , were found to be distributed locally, whereas some genera associated with tropical diseases, such as Vibrio and Burkholderia , were present at low levels. The resistome consisted mainly of antimicrobial resistance genes, with significant metal resistance and virulence-associated genes, consistent with potential co-selection under multiple environmental stressors. All alpha diversity, principal coordinates analysis, and hierarchical clustering statistics identified geographic location as the primary factor influencing resistome composition, and not enrichment treatment. A total of 699 bacterial host species were found to contain bacterial ARG, only 72 of which were linked to CARD, resulting in a large number of new ARG-host associations in the environment and a significantly increased diversity of host species for potential ARG reservoirs. Discussion This study represents a single-time-point pilot survey across ten coastal sites; findings are descriptive, genus-level, and based on genotypic resistance detection. To our knowledge, this study provides the among the first genomic baseline of pathogens, resistome, and ARG-host associations along the Gujarat coastline. The results highlight the usefulness of One Health surveillance of metagenomic data at the contig level and the need for specific environmental monitoring and antimicrobial resistance mitigation in anthropogenic hotspots.