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

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.

Colonizing and Virulence Factors in Enterotoxigenic Escherichia coli from Peru

“…12,16 The prevalence of specific CFs varies according to the geographic origin of the isolates, with CFA/I, CSI, CS2, CS3, CS6, CS14, and CS21 ranking among the most widely described. 15,23,31 In agreement, the present data show that CS21, CS6, CS3, and CS1 are the most frequently detected but differ in the relevance of CFA/I, CS2, and especially CS14, which was only detected in one isolate. On the other hand, the prevalence of CS20 was greater than 11% and, in all cases, was presented alone with no other concomitant CF.…”

Spread of Extended-Spectrum-β-Lactamase-Producing Pathogenic Escherichia coli Clonal Complex 10 in the Republic of Korea

“…Five isolates (20121544,20180444,20181364,20181484,20181747) from this study were similar to isolates collected from patients in China between 2017 and 2019 (6 to 91 SNP differences); they also harbored blaCTX-M-15 or blaCTX-M-14 and had mutations in quinolone resistance-determining regions (E18090, E18013, E19033, E19059, E15052, E20033, E17113, E19010, E17090) [10].…”

Distribution of Extended-Spectrum-β-Lactamase-Producing Diarrheagenic Escherichia coli Clonal Complex 10 Isolates from Patients with Diarrhea in the Republic of Korea

“…Five isolates (20121544, 20180444, 20181364, 20181484, and 20181747) from this study were similar to isolates collected from patients in China between 2017 and 2019 (6 to 91 SNP differences); they also harbored bla CTX-M-15 or bla CTX-M-14 and had mutations in quinolone resistance-determining regions (E18090, E18013, E19033, E19059, E15052, E20033, E17113, E19010 or E17090) [13].…”

“…Comparison of the WGS-based population structure of the 57 CC10 strains from the pathogenic E. coli from patients with diarrhea that were sporadically isolated from 10 regions showed that the strains were clonally related, with less than 70 SNPs separating them. When compared with the dissemination of CC10 worldwide, five isolates were highly similar to ETEC isolates from diarrhea patients in China collected from 2017 to 2019 [13]. Among the five isolates, one isolate was collected in 2012, and the other four isolates were collected in 2018.…”