Genomic analysis of virulence and antimicrobial resistance in Klebsiella isolates from farmed sika deer

BACKGROUND: Klebsiella species are important opportunistic pathogens whose antimicrobial resistance and virulence evolution have attracted increasing attention. However, their prevalence and genomic characteristics in farmed sika deer remain unclear. RESULTS: A total of 69 Klebsiella isolates (13.40%) were recovered from 443 fecal samples of farmed sika deer. Antimicrobial susceptibility testing showed that all isolates were resistant to ciprofloxacin and sulfonamides (100%), and 17 isolates were identified as multi-drug resistant (MDR). Biofilm assays showed that 63.77% of isolates exhibited biofilm-forming ability. Whole-genome sequencing of 27 representative deer-derived isolates identified 108 antimicrobial resistance genes (ARGs) and diverse virulence factor genes (VFGs), mainly associated with adhesion factors and iron acquisition systems (ent, fep, and iutA). Mobile genetic elements (MGEs), particularly tnpA and IS91, exhibited the highest detection frequencies. Comparative analysis with 511 publicly available genomes identified 263 ARGs, including 17 shared between sika deer- and human-derived strains, and 13 shared MGEs, suggesting a potential role of sika deer as a reservoir of resistance determinants. Phylogenetic analysis demonstrated close genetic relatedness among strains from different hosts, with frequent clustering of deer-derived and human-derived isolates. MLST analysis identified 180 sequence types (STs), with ST11 as the dominant clone across hosts, while several emerging MDR STs (e.g., ST442, ST35, and ST4501) were detected in deer-derived isolates. Correlation and Mantel analyses further revealed a significant association between ARGs and MGEs. CONCLUSION: These findings suggest that farmed sika deer may serve as a potential reservoir for ARGs and contribute to their dissemination across hosts, possibly mediated by MGEs. The observed genetic relatedness between animal- and human-derived strains highlights the potential risk of cross-species transmission. This study underscores the importance of farmed sika deer in the maintenance and dissemination of antimicrobial resistance and highlights the necessity of integrated One Health surveillance approaches.