Genome-wide mining reveals the genetic plasticity of antibiotic resistance/virulence factor genes in Enterobacter hormaechei subsp. xiangfangensis

Aims This study aims to systematically characterize the genetic basis and intra-species differentiation of antibiotic resistance/virulence factor genes (ARGs/VFGs) in Enterobacter hormaechei subsp. xiangfangensis. Methods and Results A high-quality metagenome-assembled genome of E. hormaechei subsp. xiangfangensis bin99 (97.22% completeness, 1.63% contamination) was acquired. Phylogenomic and average nucleotide identity (≥ 95%) analyses confirmed its taxonomic assignment. Pan-genomic analysis revealed an open configuration (Heap's exponent B = 0.34) with a large accessory genome (approximate 2 965 genes) and a stabilized core genome (1 139 genes). Critically, a strong positive correlation (r = 0.86, P < 2.2e−16) was observed between mobile genetic elements (MGEs) and accessory gene abundance, probably suggesting horizontal gene transfer (HGT) as a potential driver of genome diversity. Functional annotation highlighted distinct roles: core genes enriched in essential metabolism, while accessory/strain-specific genes were linked to adaptation. Screening identified significant inter-strain variation in ARGs (n = 31) and VFGs (n = 35). Bin99 itself harbored 19 ARGs (e.g. multidrug: soxS, ramA, oqxB) and 40 VFGs (e.g. flagella, T6SS). Importantly, MGE abundance showed a significant positive correlation with ARGs (r = 0.67, P < 2.2e−16) but a negative correlation with VFGs (r = -0.29, P < 3.7e−9), suggesting that ARGs were frequently linked to MGEs facilitating HGT-mediated spread, while VFGs might rely less on this route. Conclusions The findings provide genome-wide evidence for distinct genetic plasticity underlying ARG and VFG evolution in E. hormaechei subsp. xiangfangensis, highlighting implications for resistance and virulence dissemination.