Prevalence, antimicrobial resistance, and genomic characteristics of fish-derived Aeromonas veronii in the freshwater food chain in Xinjiang, China.

Aeromonas veronii is an important opportunistic pathogen in freshwater aquaculture, yet its epidemiological and genomic characteristics remain poorly defined in inland aquaculture systems of northwestern China. In this study, we investigated the occurrence, antimicrobial resistance, and genomic diversity of fish-derived A. veronii across aquaculture farms and aquatic-product markets in Xinjiang, China. A. veronii was isolated from 25.87% (208/804) of samples, with significant variation among fish species, sample types, and seasons; isolation was highest in autumn and no isolates were recovered in winter. Phenotypic antimicrobial susceptibility testing showed a high multidrug resistance (MDR) burden, with 88.94% (185/208) of isolates classified as MDR and particularly high resistance to amoxicillin-clavulanate, ampicillin, and sulfadiazine. Whole-genome sequencing of a purposively selected MDR-enriched subset of 39 isolates revealed marked genomic heterogeneity. Thirty-two sequence types (STs) were identified, including eight previously unregistered STs represented by 10 isolates. The sequenced isolates carried 37 non-redundant antimicrobial-resistance determinants and 167 virulence-associated genes. Resistance determinants and virulence-associated genes, including T3SS- and T6SS-associated genes, occurred across multiple STs and phylogenetic backgrounds rather than being restricted to a single lineage. The IncU_1 replicon was detected in three isolates, and resistance determinants co-occurred on IncU_1-bearing contigs in two, identifying candidate plasmid-associated resistance regions for further validation. Pan-genome analysis of the 39 study isolates together with 20 reference genomes demonstrated extensive accessory-genome diversity and an open pan-genome pattern. Taken together, fish-derived A. veronii in Xinjiang showed a high phenotypic MDR burden, while the 39 selected MDR isolates displayed substantial genomic and lineage diversity rather than evidence of expansion of a single dominant clone. This study establishes a regional epidemiological and genomic baseline for A. veronii across the aquaculture-to-market continuum in the under-sampled inland region of Xinjiang.