Longitudinal Molecular Epidemiology and Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae in the Gut of Healthy Individuals in China

Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) was identified by the World Health Organization in 2024 as a key priority bacterium for the development of novel control strategies. While most surveillance studies have focused on clinical isolates, the prevalence and genomic characteristics of CRKP in healthy populations remain poorly understood. Here, we present a nationwide longitudinal descriptive genomic analysis of CRKP isolates from healthy individuals in China in 2016 and from 2019 to 2024. Within this hospital-based health-check cohort, CRKP prevalence was higher in southern regions. Descriptive temporal changes in carbapenemase gene composition were observed, with bla_NDM variants, especially bla_NDM-5, more frequently detected in later years and often associated with IncHI2-IncHI2A plasmids. ST11, primarily represented by capsular types KL47 and KL64, remained the predominant lineage throughout the study period. Gene presence/absence association analysis identified several ST11-enriched loci related to iron acquisition, capsular polysaccharide synthesis, and secretion-associated functions, highlighting candidate lineage-associated features. Comparative genomic analysis with 113 clinical CRKP isolates revealed high genetic similarity (SNP < 100) between some healthy-carrier and clinical strains, suggesting possible clonal relatedness. These findings indicate that healthy individuals in this hospital-based cohort can harbor clinically relevant CRKP, supporting surveillance beyond symptomatic infections while emphasizing the descriptive scope of the present study.

Keywords

Carbapenem-resistant Klebsiella pneumoniae / Healthy individuals / Carbapenemase genes / ST11 / IncHI2-IncHI2A

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