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

Zelin Yan·Yan Li·Xiaoyang Ju·Hanyu Wang·Jing Zhang·Yanyan Zhang·Yuchen Wu·Chunzhen Wang·Dev Raj Joshi·Tista Prasai Joshi·Yu Zhang·Ruichao Li·Rong Zhang
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Abstract

INTRODUCTION: Antibiotic resistance, particularly carbapenem-resistant Klebsiella pneumoniae (CRKP), poses significant clinical and environmental threats, especially in urban aquatic ecosystems and hospital wastewaters. OBJECTIVES: 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. METHODS AND RESULTS: 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 blaNDM-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. CONCLUSION: 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.

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HumansAnti-Bacterial AgentsMicrobial Sensitivity TestsAnimalsWater MicrobiologyChinaKlebsiellaDrug Resistance, BacterialKlebsiella pneumoniaeNepalGenomicsKlebsiella InfectionsCarbapenem-resistant Klebsiella pneumoniaeHypervirulent Klebsiella pneumoniaeUrban aquatic environmentsWastewater treatmentJournal ArticleResearch Support, Non-U.S. Gov't

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Zelin Yan, Yan Li, Xiaoyang Ju, Hanyu Wang, Jing Zhang, Yanyan Zhang, Yuchen Wu, Chunzhen Wang, Dev Raj Joshi, Tista Prasai Joshi, Yu Zhang, Ruichao Li, Rong Zhang. 2025-09-12. Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective.. https://doi.org/10.1016/j.jare.2025.09.020

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