Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genome-wide association reveals host-specific genomic traits in Escherichia coli

View ORCID ProfileSumeet K. Tiwari, View ORCID ProfileBoas C.L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Álvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Domínguez, María Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, View ORCID ProfileTorsten Semmler, View ORCID ProfileConstance Schultsz
doi: https://doi.org/10.1101/2022.02.08.479532
Sumeet K. Tiwari
1Robert Koch Institute, Genome sequencing and genomic epidemiology, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sumeet K. Tiwari
Boas C.L. van der Putten
2Amsterdam UMC, Department of Global Health, Amsterdam, Netherlands
3Amsterdam UMC, Department of Medical Microbiology, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Boas C.L. van der Putten
Thilo M. Fuchs
4Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Trung N. Vinh
5Oxford University Clinical Research Unit, Vietnam
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin Bootsma
6UMC Utrecht, Utrecht, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Rik Oldenkamp
2Amsterdam UMC, Department of Global Health, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roberto La Ragione
7Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sebastien Matamoros
3Amsterdam UMC, Department of Medical Microbiology, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ngo T. Hoa
5Oxford University Clinical Research Unit, Vietnam
8Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
9Microbiology Department and the Micro-Parasitology Unit of the Center for Bio-Medical Research, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christian Berens
4Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joy Leng
7Department of Pathology and Infectious Diseases, School of Veterinary Medicine, University of Surrey, Guildford, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Julio Álvarez
10VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
11Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marta Ferrandis-Vila
4Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jenny M. Ritchie
12School of Biosciences and Medicine, University of Surrey, Guildford, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Angelika Fruth
13Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stefan Schwarz
14Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lucas Domínguez
10VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
11Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
María Ugarte-Ruiz
10VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Astrid Bethe
14Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Institute of Microbiology and Epizootics, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Charlotte Huber
15Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vanessa Johanns
15Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ivonne Stamm
16Vet Med Labor GmbH, Division of IDEXX Laboratories, Ludwigsburg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lothar H. Wieler
17Robert Koch Institute, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christa Ewers
18Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amanda Fivian-Hughes
12School of Biosciences and Medicine, University of Surrey, Guildford, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Herbert Schmidt
19Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christian Menge
4Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Torsten Semmler
1Robert Koch Institute, Genome sequencing and genomic epidemiology, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Torsten Semmler
  • For correspondence: semmlert@rki.de
Constance Schultsz
2Amsterdam UMC, Department of Global Health, Amsterdam, Netherlands
3Amsterdam UMC, Department of Medical Microbiology, Amsterdam, Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Constance Schultsz
  • For correspondence: semmlert@rki.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Escherichia coli is an opportunistic pathogen that can colonize or infect various host species. There is a significant gap in our understanding to what extent genetic lineages of E. coli are adapted or restricted to specific hosts. In addition, genomic determinants underlying such host specificity are unknown.By analyzing a randomly sampled collection of 1198 whole-genome sequenced E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, we demonstrate that certain lineages of E. coli are frequently detected in specific hosts. We report a novel nan gene cluster, designated nan-9, putatively encoding acetylesterases and determinants of uptake and metabolism of sialic acid, to be associated with the human host as identified through genome wide association studies. In silico characterization predicts nan-9 to be involved in sialic acid (Sia) metabolism. In vitro growth experiments with a representative Δnan E. coli mutant strain, using sialic acids 5-N-acetyl neuraminic acid (Neu5Ac) and N-glycolyl neuraminic acid (Neu5Gc) as the sole carbon source, indicate an impaired growth behaviour compared to the wild-type. In addition, we identified several additional E. coli genes that are potentially associated with adaptation to human, cattle and chicken hosts, but not for the pig host. Collectively, this study provides an extensive overview of genetic determinants which may mediate host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted February 09, 2022.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Genome-wide association reveals host-specific genomic traits in Escherichia coli
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genome-wide association reveals host-specific genomic traits in Escherichia coli
Sumeet K. Tiwari, Boas C.L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Álvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Domínguez, María Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, Torsten Semmler, Constance Schultsz
bioRxiv 2022.02.08.479532; doi: https://doi.org/10.1101/2022.02.08.479532
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Genome-wide association reveals host-specific genomic traits in Escherichia coli
Sumeet K. Tiwari, Boas C.L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Álvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Domínguez, María Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, Torsten Semmler, Constance Schultsz
bioRxiv 2022.02.08.479532; doi: https://doi.org/10.1101/2022.02.08.479532

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4395)
  • Biochemistry (9613)
  • Bioengineering (7110)
  • Bioinformatics (24912)
  • Biophysics (12642)
  • Cancer Biology (9978)
  • Cell Biology (14377)
  • Clinical Trials (138)
  • Developmental Biology (7967)
  • Ecology (12131)
  • Epidemiology (2067)
  • Evolutionary Biology (16008)
  • Genetics (10937)
  • Genomics (14763)
  • Immunology (9886)
  • Microbiology (23701)
  • Molecular Biology (9491)
  • Neuroscience (50963)
  • Paleontology (370)
  • Pathology (1544)
  • Pharmacology and Toxicology (2688)
  • Physiology (4031)
  • Plant Biology (8677)
  • Scientific Communication and Education (1512)
  • Synthetic Biology (2402)
  • Systems Biology (6446)
  • Zoology (1346)