Frontiers in cellular and infection microbiology · 2026
Carbapenem-resistant enterobacterales in sterile body fluids: ten-year population genomics and clinical risk factors in a tertiary hospital, 2016-2025.
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Cao Shenyun, Wang Peng, Liu Yonghua, Qi Lijuan, Wang Xinying, Li Lin, Zhang Zhijun
Аннотация
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.
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.
Предметные рубрики MeSH
HumansTertiary Care CentersCarbapenem-Resistant EnterobacteriaceaeEnterobacteriaceae InfectionsMicrobial Sensitivity Testsbeta-LactamasesAnti-Bacterial AgentsRetrospective StudiesRisk FactorsBody FluidsBacterial ProteinsMultilocus Sequence TypingPhylogenyCarbapenemsWhole Genome SequencingMolecular EpidemiologyVirulence FactorsPlasmidsGenomicsVirulence