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Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China
BACKGROUND: Escherichia coli is an important pathogen that causes diarrhea in both humans and animals. To determine the relationships between putative virulence factors and pathotypes or host taxa, many molecular studies on diarrhea-associated E. coli have been reported. However, little is known reg...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416869/ https://www.ncbi.nlm.nih.gov/pubmed/30866824 http://dx.doi.org/10.1186/s12864-019-5588-2 |
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author | Tang, Fang Wang, Juanfang Li, Dezhi Gao, Song Ren, Jianluan Ma, Liqing Liu, Fei Zhuge, Xiangkai Yan, Genqiang Lu, Yan Dai, Jianjun |
author_facet | Tang, Fang Wang, Juanfang Li, Dezhi Gao, Song Ren, Jianluan Ma, Liqing Liu, Fei Zhuge, Xiangkai Yan, Genqiang Lu, Yan Dai, Jianjun |
author_sort | Tang, Fang |
collection | PubMed |
description | BACKGROUND: Escherichia coli is an important pathogen that causes diarrhea in both humans and animals. To determine the relationships between putative virulence factors and pathotypes or host taxa, many molecular studies on diarrhea-associated E. coli have been reported. However, little is known regarding genome-wide variation of E. coli from animal hosts. In this study, we performed whole genome sequencing of 127 E. coli isolates from sheep and swine with diarrhea in China. We compared isolates to explore the phylogenomic relatedness based on host origin. We explored the relationships of putative virulence factors across host taxa and pathotypes. Antimicrobial resistance was also tested. RESULTS: The E. coli genomes in this study were diverse with clear differences in the SNP, MLST, and O serotypes. Seven putative virulence factors (VFs) were prevalent (> 95%) across the isolates, including Hcp, csgC, dsdA, feoB, fepA, guaA, and malX. Sixteen putative VFs showed significantly different distributions (P < 0.05) in strains from sheep and swine and were primarily adhesion- and toxin-related genes. Some putative VFs were co-occurrent in some specific pathotypes and O serotypes. The distribution of 4525 accessory genes of the 127 strains significantly differed (P < 0.05) between isolates obtained from the two animal species. The 127 animal isolates sequenced in this study were each classified into one of five pathotypes: EAEC, ETEC, STEC, DAEC, and EPEC, with 66.9% of isolates belonging to EAEC. Analysis of stx subtypes and a minimum spanning tree based on MLST revealed that STEC isolates from sheep and EAEC isolates from sheep and swine have low potential to infect humans. Antibiotic resistance analysis showed that the E. coli isolates were highly resistant to ampicillin and doxycycline. Isolates from southeast China were more resistant to antibiotics than isolates from northwest China. Additionally, the plasmid-mediated colist in resistance gene mcr-1 was detected in 15 isolates, including 4 from sheep in Qinghai and 11 from swine in Jiangsu. CONCLUSIONS: Our study provides insight into the genomes of E. coli isolated from animal sources. Distinguishable differences between swine and sheep isolates at the genomic level provides a baseline for future investigations of animal E. coli pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5588-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6416869 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64168692019-03-25 Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China Tang, Fang Wang, Juanfang Li, Dezhi Gao, Song Ren, Jianluan Ma, Liqing Liu, Fei Zhuge, Xiangkai Yan, Genqiang Lu, Yan Dai, Jianjun BMC Genomics Research Article BACKGROUND: Escherichia coli is an important pathogen that causes diarrhea in both humans and animals. To determine the relationships between putative virulence factors and pathotypes or host taxa, many molecular studies on diarrhea-associated E. coli have been reported. However, little is known regarding genome-wide variation of E. coli from animal hosts. In this study, we performed whole genome sequencing of 127 E. coli isolates from sheep and swine with diarrhea in China. We compared isolates to explore the phylogenomic relatedness based on host origin. We explored the relationships of putative virulence factors across host taxa and pathotypes. Antimicrobial resistance was also tested. RESULTS: The E. coli genomes in this study were diverse with clear differences in the SNP, MLST, and O serotypes. Seven putative virulence factors (VFs) were prevalent (> 95%) across the isolates, including Hcp, csgC, dsdA, feoB, fepA, guaA, and malX. Sixteen putative VFs showed significantly different distributions (P < 0.05) in strains from sheep and swine and were primarily adhesion- and toxin-related genes. Some putative VFs were co-occurrent in some specific pathotypes and O serotypes. The distribution of 4525 accessory genes of the 127 strains significantly differed (P < 0.05) between isolates obtained from the two animal species. The 127 animal isolates sequenced in this study were each classified into one of five pathotypes: EAEC, ETEC, STEC, DAEC, and EPEC, with 66.9% of isolates belonging to EAEC. Analysis of stx subtypes and a minimum spanning tree based on MLST revealed that STEC isolates from sheep and EAEC isolates from sheep and swine have low potential to infect humans. Antibiotic resistance analysis showed that the E. coli isolates were highly resistant to ampicillin and doxycycline. Isolates from southeast China were more resistant to antibiotics than isolates from northwest China. Additionally, the plasmid-mediated colist in resistance gene mcr-1 was detected in 15 isolates, including 4 from sheep in Qinghai and 11 from swine in Jiangsu. CONCLUSIONS: Our study provides insight into the genomes of E. coli isolated from animal sources. Distinguishable differences between swine and sheep isolates at the genomic level provides a baseline for future investigations of animal E. coli pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5588-2) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-13 /pmc/articles/PMC6416869/ /pubmed/30866824 http://dx.doi.org/10.1186/s12864-019-5588-2 Text en © The Author(s). 2019 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. |
spellingShingle | Research Article Tang, Fang Wang, Juanfang Li, Dezhi Gao, Song Ren, Jianluan Ma, Liqing Liu, Fei Zhuge, Xiangkai Yan, Genqiang Lu, Yan Dai, Jianjun Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title | Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title_full | Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title_fullStr | Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title_full_unstemmed | Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title_short | Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China |
title_sort | comparative genomic analysis of 127 escherichia coli strains isolated from domestic animals with diarrhea in china |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416869/ https://www.ncbi.nlm.nih.gov/pubmed/30866824 http://dx.doi.org/10.1186/s12864-019-5588-2 |
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