Phenotypic and genotypic characterization of colonization and infection with carbapenem-resistant Enterobacteriaceae: A prospective cohort study in China

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Objectives A prospective multicenter study was conducted to elucidate the phenotypic and genotypic characteristics of carbapenem-resistant Enterobacteriaceae (CRE) colonization and infection strains. Methods Strains were collected within one year from ten intensive care units (ICUs) in Anhui Province, China. Antimicrobial susceptibility testing and whole-genome sequencing (WGS) were performed. Results Among 310 colonization and 108 infection strains, Klebsiella pneumoniae predominated (74.4%), followed by Escherichia coli (18.4%). Resistance rates were low to tigecycline (2.6%) and colistin (4.2%) and high (>97.9%) to carbapenems, cephalosporins, and β -lactam/ β- lactamase inhibitor combinations. Both sequence types (STs) and capsular serotypes showed substantial geographic diversity. ST11 was the predominant ST, while ST15-KL19 (34.4%) was the most frequent combination in colonization and infection strains. Notably, the ST48-KL62 clone was significantly more prevalent in infection strains than in colonization strains. Moreover, 86.6% of strains produced carbapenemases, primarily bla KPC-2 (64.4%), and 1.9% co-produced KPC- and MBL-type enzymes. High-risk E. coli ST167 strains carrying bla NDM-5 were identified. All CR Kp carried biosynthetic genes for the siderophore (e.g., fepABCDG , iutA , iroEN ). Virulence factors, including iucABCD , irp1/2 , ybtAEPQSTUX , and fyuA , were significantly more prevalent in CR Kp infection strains. However, ST15-KL19 lacked classic high-virulence factors (e.g., iucABCD , rmpA , rmpA2 ). Closely related strains were found within and across hospitals, indicating regional spread and intra-hospital transmission. Conclusions This study not only characterizes the distinct regional and genomic distribution patterns of CRE but also associates specific clones and virulence determinants with infection risk, thereby providing molecular markers to identify high-risk carriers and facilitate targeted treatment, prevention, and control measures.

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