Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective

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Enhanced representation of sampling locations and prevalence of carbapenem-resistant Klebsiella spp. in urban aquatic environments of China, Nepal, and Sri Lanka. Regions are color-coded by sampling prevalence, with circular charts detailing Klebsiella species and carbapenemase types. Wastewater management practices are visualized for hospitals to correlate with ARG dissemination patterns. • Significant disparities in CRKP prevalence found between China and Nepal’s urban waters. • CRKP isolates exhibit high resistance, especially qnr and tmexCD-toprJ genes in Nepal. • High-virulence CRKP strains in Nepal confirmed via Galleria mellonella model. • Geographic patterns show distinct CRKP resistance profiles in China and Nepal. • Urban waters act as reservoirs for resistance genes, urging integrated management. Antibiotic resistance, particularly carbapenem-resistant Klebsiella pneumoniae (CRKP), poses significant clinical and environmental threats, especially in urban aquatic ecosystems and hospital wastewaters. This study aims to analyze the epidemiological and genomic features of CRKP isolates in urban aquatic environments and evaluate their public health and environmental impacts. Water samples were collected from 113 rivers and 3 hospitals in China, Sri Lanka, and Nepal to isolate carbapenem-resistant Klebsiella spp. isolates. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics analyses were performed to characterize resistance phenotypes, antibiotic resistance genes (ARGs), and evolutionary trends. Big data analysis further elucidated the genomic characteristics of CRKP in global water sources, and Galleria mellonella larvae were used to assess virulence. Statistical analysis validated the findings. A total of 192 carbapenem-resistant Klebsiella spp. isolates were identified from urban aquatic ecosystems in China (n = 60) and Nepal (n = 132), with CRKP (n = 161) being the predominant species. All CRKP isolates exhibited a multidrug-resistant phenotype, yet significant differences in resistance profiles and associated ARGs were observed between isolates from the two countries. Nine carbapenem resistance genes (CRGs) were detected, with bla NDM-1 being the most prevalent (57.8 %). Correlation analysis revealed a strong association between these CRGs and multiple Inc-type plasmids. Global genomic analysis of CRKP from water sources across eight countries identified ten distinct CRGs across 45 serotypes, with KL64 being the most predominant. Notably, carbapenem-resistant hypervirulent Klebsiella pneumoniae was detected in water samples from Nepal. Our findings highlight significant regional disparities in CRKP prevalence and ARG dissemination across urban aquatic environments, with Nepal showing the highest prevalence, particularly in untreated rivers. China exhibited lower prevalence but distinct resistance gene profiles, while no CRKP was detected in Sri Lanka, underscoring the impact of environmental management and healthcare infrastructure on ARG spread.