Comparative genomic analysis of enterotoxigenic  Escherichia coli  O159 strains isolated from diarrheal patients in Korea

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Abstract

Background

Enterotoxigenic Escherichia coli (ETEC) is a common cause of bacterial infection that leads to diarrhea. Although some studies have proposed a potential association between the toxic profile and genetic background, association between toxin of ETEC and phylo-group has not been reported yet. The objective of this study was to examine genomic and phylogenetic characteristics of ETEC strain NCCP15731 and NCCP15733 by whole genome sequencing and comparative genomic analysis of two phylo-groups of O159 reference strains.

Results

Whole genome sequencing showed that genome size of NCCP15731 strain was 4,663,459 bp, containing 4435 CDS and 19 RNAs. The genome size of NCCP15733 was 4,645,336 bp, containing 4369 CDS and 23 RNAs. Both NCCP15731 and NCCP15733 were classified in the phylo-group A, which is one of major E. coli phylogenetic groups. Their serotype was O159:H34. They possessed the virulence factor such as adherence systems, auto transporter systems, and flagella segments of major driving force for ETEC pathogenicity. They also harbored STh enterotoxin. Hierarchical clustering result based on the presence or absence of a total of 108 major virulence factors of 14 O159 ETEC strains showed that seven strains in phylo-group A and seven strains in phylo-group B1 were clustered each other, respectively. Colonization factors (CFs) of NCCP15731 or NCCP15733 were not detected.

Conclusions

Serotype of NCCP15731 and NCCP15733, representing major types of ETEC in Korea, was O159:H34 and their MLST type was ST218. Comparison with other O159 strains revealed that NCCP15731 was specialized for transporter system and secretion system whereas NCCP15733 had unique genes related to capsular polysaccharide. Compared with E159, the most recent common ancestor, these two strains had different toxin type and virulence factors. These results will improve our understanding of ETEC O159 strains to prevent ETEC disease.

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The online version of this article (10.1186/s13099-019-0289-6) contains supplementary material, which is available to authorized users.

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Most cited references 37

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Diarrheagenic Escherichia coli.

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Escherichia coli is the predominant nonpathogenic facultative flora of the human intestine. Some E. coli strains, however, have developed the ability to cause disease of the gastrointestinal, urinary, or central nervous system in even the most robust human hosts. Diarrheagenic strains of E. coli can be divided into at least six different categories with corresponding distinct pathogenic schemes. Taken together, these organisms probably represent the most common cause of pediatric diarrhea worldwide. Several distinct clinical syndromes accompany infection with diarrheagenic E. coli categories, including traveler's diarrhea (enterotoxigenic E. coli), hemorrhagic colitis and hemolytic-uremic syndrome (enterohemorrhagic E. coli), persistent diarrhea (enteroaggregative E. coli), and watery diarrhea of infants (entero-pathogenic E. coli). This review discusses the current level of understanding of the pathogenesis of the diarrheagenic E. coli strains and describes how their pathogenic schemes underlie the clinical manifestations, diagnostic approach, and epidemiologic investigation of these important pathogens.

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Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC.

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Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.

Julian Parkhill, Tetsuya Hayashi, George Henderson … (2008)

Enteropathogenic Escherichia coli (EPEC) was the first pathovar of E. coli to be implicated in human disease; however, no EPEC strain has been fully sequenced until now. Strain E2348/69 (serotype O127:H6 belonging to E. coli phylogroup B2) has been used worldwide as a prototype strain to study EPEC biology, genetics, and virulence. Studies of E2348/69 led to the discovery of the locus of enterocyte effacement-encoded type III secretion system (T3SS) and its cognate effectors, which play a vital role in attaching and effacing lesion formation on gut epithelial cells. In this study, we determined the complete genomic sequence of E2348/69 and performed genomic comparisons with other important E. coli strains. We identified 424 E2348/69-specific genes, most of which are carried on mobile genetic elements, and a number of genetic traits specifically conserved in phylogroup B2 strains irrespective of their pathotypes, including the absence of the ETT2-related T3SS, which is present in E. coli strains belonging to all other phylogroups. The genome analysis revealed the entire gene repertoire related to E2348/69 virulence. Interestingly, E2348/69 contains only 21 intact T3SS effector genes, all of which are carried on prophages and integrative elements, compared to over 50 effector genes in enterohemorrhagic E. coli O157. As E2348/69 is the most-studied pathogenic E. coli strain, this study provides a genomic context for the vast amount of existing experimental data. The unexpected simplicity of the E2348/69 T3SS provides the first opportunity to fully dissect the entire virulence strategy of attaching and effacing pathogens in the genomic context.

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Author and article information

Contributors

Si-yun Chung: wjdtldbs9298@naver.com

Taesoo Kwon: joshuakwon@gmail.com

Young-Seok Bak: emtsos@hanmail.net

Joung Je Park: jjp0812@hanmail.net

Cheorl-Ho Kim: chkimbio@skku.edu

Seung-Hak Cho: skcho38@korea.kr

Won Kim: wonkim@snu.ac.kr

Journal

Journal ID (nlm-ta): Gut Pathog

Journal ID (iso-abbrev): Gut Pathog

Title: Gut Pathogens

Publisher: BioMed Central (London )

ISSN (Electronic): 1757-4749

Publication date (Electronic): 21 February 2019

Publication date PMC-release: 21 February 2019

Publication date Collection: 2019

Volume: 11

Electronic Location Identifier: 9

Affiliations

[1 ]ISNI 0000 0004 0470 5905, GRID grid.31501.36, School of Biological Sciences, , Seoul National University, ; 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742 Republic of Korea

[2 ]Cloud9, 133, Yeonje-gil, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do 28164 Republic of Korea

[3 ]ISNI 0000 0004 0533 4202, GRID grid.412859.3, Department of Emergency Medical Services, , Sun Moon University, ; Asan-si, Chungcheongnam-do 31460 Republic of Korea

[4 ]ISNI 0000 0001 0742 4007, GRID grid.49100.3c, Department of Emergency Medical Service, , Pohang University, ; Heunghae-eup, Sindeok-ro, Pohang-si, Gyeongsangbuk-do Republic of Korea

[5 ]ISNI 0000 0001 2181 989X, GRID grid.264381.a, Glycobiology Unit, Department of Biological Science, , Sungkyunkwan University and Samsung Advanced Institute for Health Sciences and Technology (SAIHST), ; 2066 Seobu-ro, Suwon, 16419 Republic of Korea

[6 ]ISNI 0000 0004 0647 4899, GRID grid.415482.e, Division of Bacterial Disease Research, Center for Infectious Disease Research, , Korea National Institute of Health, ; Cheongju, 363-951 Republic of Korea

Article

Publisher ID: 289

DOI: 10.1186/s13099-019-0289-6

PMC ID: 6383257

SO-VID: dfa545ba-cc42-4814-9a48-a8b8287419f9

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 2 August 2018

Date accepted : 11 February 2019

Funding

Funded by: FundRef http://dx.doi.org/10.13039/501100003566, Ministry of Oceans and Fisheries;

Award ID: marine biotechnology program(genome analysis of marine organisms

Award ID: development of functional applications)

Award Recipient : Won Kim

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ScienceOpen disciplines: Gastroenterology & Hepatology

Keywords: enterotoxigenic escherichia coli o159,whole genome sequencing,virulence factors,colonization factors,phylo-groups

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ScienceOpen disciplines: Gastroenterology & Hepatology

Keywords: enterotoxigenic escherichia coli o159, whole genome sequencing, virulence factors, colonization factors, phylo-groups

Comparative genomic analysis of enterotoxigenic Escherichia coli O159 strains isolated from diarrheal patients in Korea

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Conclusions

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Karger: Gastroenterology

Most cited references 37

Diarrheagenic Escherichia coli.

Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC.

Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.

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