Genomic and phenotypic insights into antibiotic resistance and virulence of Klebsiella pneumoniae from the environment in Southern Taiwan

Background Klebsiella pneumoniae is a major human pathogen responsible for healthcare- and community-associated infections and a critical contributor to the global antimicrobial resistance (AMR) crisis. Although widely present in the environment, its role in harboring multidrug-resistant (MDR) and hypervirulent strains (hvKp) remains insufficiently characterized. Methods This study assessed the prevalence, genomic diversity, and pathogenic potential of K. pneumoniae isolated from surface waters in southern Taiwan. A total of 62 sites were sampled, yielding 68 environmental isolates. Whole-genome sequencing (WGS), virulence phenotyping, in vivo infection models, and conjugation assays were used to evaluate resistance, virulence, and gene transfer potential. Results K. pneumoniae was detected at 91.9% of sampled sites. Among 68 isolates, 7.35% were MDR, and virulence-associated phenotypes were common: 26.47% exhibited serum resistance, 13.24% anti-phagocytic activity, 11.76% hypermucoviscosity, 22.06% strong biofilm formation, and 48.53% intestinal cell adhesion. WGS revealed 59 sequence types and 48 capsular types, indicating a high level of genetic diversity among environmental isolates. Hypervirulent clones KL1-ST23 and KL2-ST373 were identified and confirmed to be pathogenic in mice. Based on genomic and in vivo data, hvKp was detected in 5.88% of isolates. Phylogenetic analysis showed close relatedness to clinical reference strains NTUH-K2044 and MGH78578. Conjugation experiments demonstrated successful ciprofloxacin resistance transfer. Conclusions These findings provide evidence that environmental surface waters can serve as reservoirs for antimicrobial resistance and hypervirulence in K. pneumoniae. They highlight the need for integrated environmental surveillance and One Health strategies to address this emerging public health threat.