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

International Journal of Infectious Diseases (Feb 2018)

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

Affiliations

Fei Yu: 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
Xiao Chen: 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
Shufa Zheng: 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
Dongsheng Han: Clinical Medical Examination Center, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu, China
Yiyin Wang: 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
Ruonan Wang: 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
Baohong Wang: 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
Yu Chen: 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

DOI: https://doi.org/10.1016/j.ijid.2017.11.025
Journal volume & issue: Vol. 67, no. C
pp. 7 – 13

Abstract

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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 (ISA) 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.

Published in International Journal of Infectious Diseases

ISSN: 1201-9712 (Print); 1878-3511 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Internal medicine: Infectious and parasitic diseases
Website: http://www.journals.elsevier.com/international-journal-of-infectious-diseases/

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