Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China
Abstract 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 k...
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2019-03-01
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Series: | BMC Genomics |
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Online Access: | http://link.springer.com/article/10.1186/s12864-019-5588-2 |
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doaj-f966f4684e374133aabb206d7624d472 |
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Article |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fang Tang Juanfang Wang Dezhi Li Song Gao Jianluan Ren Liqing Ma Fei Liu Xiangkai Zhuge Genqiang Yan Yan Lu Jianjun Dai |
spellingShingle |
Fang Tang Juanfang Wang Dezhi Li Song Gao Jianluan Ren Liqing Ma Fei Liu Xiangkai Zhuge Genqiang Yan Yan Lu Jianjun Dai Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in China BMC Genomics Escherichia coli Genome Putative virulence factor Diarrhea Animal isolates |
author_facet |
Fang Tang Juanfang Wang Dezhi Li Song Gao Jianluan Ren Liqing Ma Fei Liu Xiangkai Zhuge Genqiang Yan Yan Lu Jianjun Dai |
author_sort |
Fang Tang |
title |
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_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_sort |
comparative genomic analysis of 127 escherichia coli strains isolated from domestic animals with diarrhea in china |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-03-01 |
description |
Abstract 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. |
topic |
Escherichia coli Genome Putative virulence factor Diarrhea Animal isolates |
url |
http://link.springer.com/article/10.1186/s12864-019-5588-2 |
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1724903632708567040 |
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doaj-f966f4684e374133aabb206d7624d4722020-11-25T02:13:41ZengBMCBMC Genomics1471-21642019-03-0120111110.1186/s12864-019-5588-2Comparative genomic analysis of 127 Escherichia coli strains isolated from domestic animals with diarrhea in ChinaFang Tang0Juanfang Wang1Dezhi Li2Song Gao3Jianluan Ren4Liqing Ma5Fei Liu6Xiangkai Zhuge7Genqiang Yan8Yan Lu9Jianjun Dai10Key Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityKey Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityKey Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou UniversityKey Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityQinghai Academy of veterinary Medicine and Animal Science, Qinghai UniversityCAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesKey Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityCollege of Animal Science and Technology, Shihezi UniversityQinghai Academy of veterinary Medicine and Animal Science, Qinghai UniversityKey Lab Animal Bacteriology, Ministry of Agriculture; Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural UniversityAbstract 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.http://link.springer.com/article/10.1186/s12864-019-5588-2Escherichia coliGenomePutative virulence factorDiarrheaAnimal isolates |