Carbapenem-resistant enterobacterales in sterile body fluids: ten-year population genomics and clinical risk factors in a tertiary hospital, 2016-2025.

OBJECTIVES

To clarify the molecular epidemiology, resistance gene profiles, virulence characteristics, and clinical prognosis-related factors of Carbapenem-Resistant Enterobacterales (CRE) isolated from sterile body fluids. This study provides microbiological evidence for clinical management and infection control surveillance.

METHODS

62 non-duplicate sterile fluid CRE strains from 2016-2025 were retrospectively analyzed. VITEK-2 Compact detected MICs per CLSI M100. Illumina NovaSeq whole-genome sequencing was assembled via ABySS and GapCloser. Databases analyzed resistance, virulence, plasmid and MLST profiles. SNP phylogenetic analysis identified clonal clusters and strain genetic relationships.

RESULTS

Among the 62 CRE isolates, Klebsiella pneumoniae was the predominant species (77.4%, 48/62), followed by Escherichia coli (12.9%, 8/62) and Enterobacter cloacae complex (6.5%, 4/62). Additionally, single isolates of Klebsiella aerogenes and Citrobacter freundii were recovered. A total of 6 sequence types (STs) were identified, with ST11 being the most prevalent (87.5%, 42/48) among K. pneumoniae isolates. Carbapenemase genes were detected in 91.7% (44/48) of K. pneumoniae strains, with blaKPC-2 (85.4%, 41/48) and blaNDM-1 (10.4%, 5/48) as the main types. Three strains co-harbored blaKPC-2 and blaNDM-1, and one strain carried blaNDM-5 alone. These strains also carried class C β-lactamase (AmpC), extended-spectrum β-lactamases (ESBLs), and aminoglycoside/quinolone resistance genes. The rmpA2 virulence gene was detected in 75.0% (36/48) of K. pneumoniae isolates. Among E. coli, blaNDM-5 (4/8) and blaNDM-13 (2/8) were predominant. One ST155 isolate exhibited ertapenem resistance potentially mediated by AmpC promoter mutations and porin loss based on genomic prediction. Additionally, mcr-1.1 was detected in one ST361 isolate. All four E. cloacae complex belonged to ST171 and harboured blaNDM-1; one co-carried mcr-9.1. Clonal analysis revealed five major clusters within ST11 (Clade A-E), with Clade B comprising genetically related dual-carbapenemase isolates from multiple wards (8-10 SNPs). Twelve patients (19.4%) died. Intensive Care Unit (ICU) admission was significantly associated with mortality (83.3% vs. 30.0%, P=0.002).

CONCLUSIONS

CRE from sterile body fluids were dominated by ST11 K. pneumoniae carrying blaKPC-2, with complex multidrug resistance and frequent carriage of rmpA2 and other virulence-associated genes. Continuous molecular surveillance of dominant clones and monitoring of high-risk patient populations may inform strategies to reduce CRE burden.