Genomic Epidemiology and Antimicrobial Susceptibility Profile of Enterotoxigenic Escherichia coli From Outpatients With Diarrhea in Shenzhen, China, 2015–2020

Chao Yang,Yinghui Li,Chengsong Wan,Xiaolu Shi,Rui Cai,Xianglilan Zhang,Le Zuo,Yixiang Jiang,Miaomiao Luo,Yujun Cui,Lei Wang,Qinghua Hu,Yiying She,Shuang Wu,Li Xie,Min Jiang

doi:10.3389/fmicb.2021.732068

Abstract

Enterotoxigenic Escherichia coli (ETEC) is the leading cause of severe diarrhea in children and the most common cause of diarrhea in travelers. However, most ETEC infections in Shenzhen, China were from indigenous adults. In this study, we characterized 106 ETEC isolates from indigenous outpatients with diarrhea (77% were adults aged >20 years) in Shenzhen between 2015 and 2020 by whole-genome sequencing and antimicrobial susceptibility testing. Shenzhen ETEC isolates showed a remarkable high diversity, which belonged to four E. coli phylogroups (A: 71%, B1: 13%, E: 10%, and D: 6%) and 15 ETEC lineages, with L11 (25%, O159:H34/O159:H43, ST218/ST3153), novel L2/4 (21%, O6:H16, ST48), and L4 (15%, O25:H16, ST1491) being major lineages. Heat-stable toxin (ST) was most prevalent (76%, STh: 60% STp: 16%), followed by heat-labile toxin (LT, 17%) and ST + LT (7%). One or multiple colonization factors (CFs) were identified in 68 (64%) isolates, with the common CFs being CS21 (48%) and CS6 (34%). Antimicrobial resistance mutation/gene profiles of genomes were concordant with the phenotype testing results of 52 representative isolates, which revealed high resistance rate to nalidixic acid (71%), ampicillin (69%), and ampicillin/sulbactam (46%), and demonstrated that the novel L2/4 was a multidrug-resistant lineage. This study provides novel insight into the genomic epidemiology and antimicrobial susceptibility profile of ETEC infections in indigenous adults for the first time, which further improves our understanding on ETEC epidemiology and has implications for the development of vaccine and future surveillance and prevention of ETEC infections.

Highlights

Enterotoxigenic Escherichia coli (ETEC) is the leading cause of severe diarrhea among young children aged less than five in developing countries, and is the most common cause of diarrhea in travelers to ETEC-endemic areas, accounting for more than 200 million diarrheal cases and 50,000 deaths annually (Khalil et al, 2018; Fleckenstein and Kuhlmann, 2019)
At least 27 known or putative colonization factors (CFs) have been identified to date, including a novel CF, CS30 identified by genomic analysis, and the most prevalent CFs are colonization factor antigen I (CFA/I) and coli surface antigens 1–6 (CS1–CS6) (Gaastra and Svennerholm, 1996; Nada et al, 2011; von Mentzer et al, 2017; Vidal et al, 2019)
There was a close association of ETEC lineage with serotype and Multi-locus sequence type (MLST)-stable toxin (ST), with isolates within a lineage belonging to 1–2 serotypes or STs (Table 1)

Summary

Introduction

Enterotoxigenic Escherichia coli (ETEC) is the leading cause of severe diarrhea among young children aged less than five in developing countries, and is the most common cause of diarrhea in travelers to ETEC-endemic areas, accounting for more than 200 million diarrheal cases and 50,000 deaths annually (Khalil et al, 2018; Fleckenstein and Kuhlmann, 2019). ETEC is defined by production of heat-stable toxin (ST) and/or heatlabile toxin (LT), and ST includes two subtypes, human ST (STh) and porcine ST (STp). Besides the classic virulence factors of enterotoxins and CFs, multiple non-classic virulence factors have been identified in recent years, including a cytoplasmic protein (LeoA), three adhesins (Tia, TibA, and EtpA), an extracytoplasmic protein (CexE), a hemolysin (ClyA), two mucinases (EatA and YghJ), three iron acquisition systems (Irp, Irp, and FyuA), and an enteroaggregative heat-stable toxin 1 (EAST1) (Turner et al, 2006; Pilonieta et al, 2007; Del Canto et al, 2011; Gonzales et al, 2013; Luo et al, 2014; Sjöling et al, 2015)

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Results

Conclusion