Genomic characteristics and phylogenetic analyses of enteroaggregative Escherichia coli infection in diarrhea outpatients in Pudong New Area， Shanghai
10.19428/j.cnki.sjpm.2025.24576
- VernacularTitle:上海市浦东新区腹泻门诊病例肠集聚性大肠埃希菌基因组特征及系统发育分析
- Author:
Qiqi CUI
1
;
Yuchen LU
1
;
Suping WU
2
;
Yinwen ZHANG
1
;
Bing ZHAO
1
;
Lifeng PAN
1
;
Yingjie ZHENG
3
;
Lipeng HAO
1
Author Information
1. Pudong New District Center for Disease Control and Prevention, Pudong Institute of Preventive Medicine, Fudan University, Shanghai 200136, China
2. Unit 94969 of the Chinese People’s Liberation Army, Shanghai 200137, China
3. School of Public Health, Fudan University, Shanghai 200032, China
- Publication Type:Journal Article
- Keywords:
enteroaggregative Escherichia coli;
whole genome sequencing;
pan-genome;
molecular characteristic;
phylogenetic evolution
- From:
Shanghai Journal of Preventive Medicine
2025;37(4):342-349
- CountryChina
- Language:Chinese
-
Abstract:
ObjectiveTo investigate the whole genomic characteristics and phylogenetic relationships of clinical isolates of enteroaggregative Escherichia coli (EAEC) in diarrhea outpatients in Pudong New Area, Shanghai. MethodsBased on the diarrheal disease surveillance network in Pudong New Area, Shanghai, whole-genome sequencing was performed on a total of 55 EAEC strains isolated from fecal samples of the diarrhea outpatients from January 2015 to December 2019. The genome analyses based on raw sequencing data encompassed genome size, coding genes, dispersed repeat sequences, genomic islands, and protein coding regions, and pan-genome analyses were conducted simultaneously. Contigs sequences assays were performed to analyze molecular characteristics including serotypes, antibiotic resistance genes, and virulence factors. The phylogenetic clusters and multilocus sequence typing (MLST) were identified, and a phylogenetic tree was constructed. ResultsEAEC exhibited an open pan-genome. The predominant serotype of EAEC in diarrhea outpatients in Pudong New Area was O130:H27, and the carriage rate of β-lactam resistance genes was the highest (67.27%, 37/55). A total of 29 virulence factors and 106 virulence genes were identified, phylogenic group B1 was the predominant group, and clonal group CC31 was the dominant clonal group. The strain distribution was highly heterogeneous. ConclusionThe genomic characteristics of EAEC displayed significant strain polymorphism. It is necessary to develop effective strategies for differential diagnosis and improve detection capabilities for infection with EAEC of different serotypes and genotypes.
