Species distribution, antimicrobial resistance, and putative virulence factor profiles of Aeromonas isolates from extra-intestinal clinical specimens: a whole-genome sequencing study

Abstract

Introduction Aeromonas spp. are increasingly recognized opportunistic pathogens of humans, yet integrated genomic and phenotypic data from clinical, extra-intestinal isolates remain limited. We characterized 74 non-duplicate Aeromonas isolates recovered from extra-intestinal clinical specimens at a tertiary hospital in Ningbo, China, between 2020 and 2025, combining whole-genome sequencing (WGS)-based taxonomy, antimicrobial susceptibility testing, and resistome and putative virulence factor (VF) prediction. Methods Species were identified by average nucleotide identity (ANI) analysis and sequence types (STs) by multilocus sequence typing (MLST). Susceptibility to 11 agents was interpreted according to the Clinical and Laboratory Standards Institute (CLSI) guideline M45. Resistance genes were predicted against the Comprehensive Antibiotic Resistance Database (CARD) and VFs against the Virulence Factors of Pathogenic Bacteria database (VFDB); genotype–phenotype concordance was quantified with Cohen’s κ, and VF profiles were analyzed by principal coordinates analysis and permutational multivariate analysis of variance (PERMANOVA). Results Six species were identified, dominated by Aeromonas caviae (32.4%), Aeromonas veronii (25.7%) and Aeromonas dhakensis (24.3%). Bile was the leading source of isolation (51.4%), and species were significantly associated with isolation site (Fisher’s exact test, p < 0.001). The population was genetically diverse (71 STs, 39 novel). Resistance was highest to piperacillin/tazobactam (29.7%), whereas only one isolate was resistant to amikacin. Eighty-five resistance genes were detected, with a ubiquitous intrinsic β-lactamase background (OXA-12-like, cphA/imiH and MOX-type genes in 63.5, 58.1 and 41.9% of isolates, respectively) and the acquired carbapenemase gene blaNDM-1 in three isolates. Genotype–phenotype agreement was substantial for trimethoprim/sulfamethoxazole (κ = 0.773–0.856) and fluoroquinolones (κ = 0.706) but poor for β-lactams. Fifty-six VFs were detected, comprising a conserved 26-VF core virulome and accessory determinants structured by species (PERMANOVA R2 = 0.797, p = 0.001). A. dhakensis and A. hydrophila carried the heaviest VF loads and were enriched for aerolysin, ExoA, MARTX/RtxA and T6SS, whereas A. caviae lacked aerolysin and had the sparsest virulome. Discussion Species identity was the dominant correlate of clinical distribution and virulence potential, supporting genome-based species identification as the basis for risk assessment of clinical Aeromonas isolates.