Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by multilocus sequence typing

Fei Yu; Xiao Chen; Shufa Zheng; Dongsheng Han; Yiyin Wang; Ruonan Wang; Baohong Wang; Yu Chen

doi:10.1016/j.ijid.2017.11.025

Prevalence and genetic diversity of human diarrheagenic Escherichia coli isolates by multilocus sequence typing

Int J Infect Dis. 2018 Feb:67:7-13. doi: 10.1016/j.ijid.2017.11.025. Epub 2017 Nov 26.

Authors

Fei Yu¹, Xiao Chen², Shufa Zheng², Dongsheng Han³, Yiyin Wang¹, Ruonan Wang¹, Baohong Wang⁴, Yu Chen⁵

Affiliations

¹ Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
² Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
³ Clinical Medical Examination Center, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China.
⁴ State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
⁵ Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China. Electronic address: chenyuzy@zju.edu.cn.

PMID: 29183841
DOI: 10.1016/j.ijid.2017.11.025

Abstract

Background: The population structure of human diarrheagenic Escherichia coli (DEC) isolates derived from worldwide collections remains undefined.

Methods: A total of 1196 clinical isolates were obtained from a multilocus sequence typing (MLST) database. Genetic diversity analysis, MLST analysis, and phylogenetic analysis combined with different pathotypes were performed through a variety of calculation software applications.

Results: All isolates were categorized as one of 579 different sequence types (STs). The eBURST algorithm resolved these 579 STs into 27 clonal complexes (CCs), 37 concatemers, and 210 singletons, revealing a high level of genetic diversity in the population structure of DEC. CC10 was the most prevalent CC, comprising 276 (23.08%, 276/1196) isolates with 85 (14.68%, 85/579) STs widely distributed in 20 countries. The population structure of five common pathotypes was highly diversified, and isolates with the same ST or CC were heterogeneous for different pathotypes. Sequence variations were more abundant in fumC and gyrB than in the other five genes, and these exhibited the highest degree of nucleotide diversity (0.03886 and 0.03075, respectively) and the greatest number of polymorphic nucleotide sites (137 and 139, respectively). The dN/dS ratios of seven analyzed loci varied from 0.0083 (recA) to 0.0434 (purA), and the ratio for the concatenated sequence was 0.2518, revealing the effects of purifying selection on housekeeping genes during the evolutionary process. Significant allele linkage disequilibrium was detected when the standardized index of association (I^S_A) was calculated both for the entire collection of isolates (0.3174, p<0.001) and for the 579 STs (0.1475, p<0.001).

Conclusions: This study facilitated a comprehensive understanding of the genetic diversity of human DEC distributed across the global population. The results provide genetic evidence that will allow us to uncover the microevolutionary relationships among different pathogenic isolates of DEC.

Keywords: Clonal complex (CC); Diarrheagenic Escherichia coli; Genetic diversity; Multilocus sequence typing (MLST); Phylogenetic analysis; Sequence type (ST).

MeSH terms

Alleles
Diarrhea / microbiology
Escherichia coli / genetics*
Escherichia coli / isolation & purification
Escherichia coli / pathogenicity
Genetic Variation*
Humans
Linkage Disequilibrium
Multilocus Sequence Typing
Phylogeny
Prevalence