Precise species identification and whole-genome sequencing analysis of Enterobacter cloacae complex causing bloodstream infections in China

作者：Yanbing Li, Ziran Wang, Ge Zhang, Wei Kang, Jin Li, Yingchun Xu, Menglan Zhou · 发表于：Microbiology Spectrum · 年份：2025 · DOI：10.1128/spectrum.02865-25 · 被引用次数：1 · 研究领域：Antibiotic Resistance in Bacteria、Enterobacteriaceae and Cronobacter Research、Infections and bacterial resistance

ABSTRACT The Enterobacter cloacae complex (ECC) is one of the major causes of hospital-acquired infections. However, achieving accurate species identification and comprehensive resistance profiling remains difficult in clinical practice, with a limited understanding of species-specific resistance patterns. ECC isolates were collected from patients with bloodstream infections at Peking Union Medical College Hospital between 2015 and 2020. Whole-genome sequencing (WGS) was performed to identify species, analyze antimicrobial resistance genes, and explore genomic variation in serial isolates. Multi-locus sequence typing (MLST) profiles were extracted from the WGS data. Phylogenetic analysis was conducted based on hsp60 sequences. Eleven hsp60 clusters were identified, with cluster VIII being the most prevalent (28/108). Average nucleotide identity (ANI)-based species classification showed Enterobacter hormaechei (31.5%) and Enterobacter xiangfangensis (15.7%) were dominant species. Five clade-cluster pairs (B-VIII, A-VI, G-XI, D-III, R-IX) accounted for 74% of isolates. A total of 90 sequence types (STs) were detected, including 29 novel STs. Resistance gene analysis revealed a high prevalence of bla ACT , with distinct distribution patterns observed among different species. Twenty isolates were carbapenem-resistant, with three carrying bla NDM-1/5 . Enterobacter roggenkampii was the most common species (5/20) among all carbapenem-resistant isolates, and 83.3% of the isolates sh...