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Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni

Thépault Amandine, Méric Guillaume, Rivoal Katell, Ben Pascoe Orcid Logo, Mageiros Leonardos, Touzain Fabrice, Rose Valérie, Béven Véronique, Chemaly Marianne, K Samuel

Applied and Environmental Microbiology, Volume: 83, Issue: 7, Start page: e03085-16

Swansea University Author: Ben Pascoe Orcid Logo

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DOI (Published version): 10.1128/AEM.03085-16

Abstract

<p>Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially m...

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Published in: Applied and Environmental Microbiology
ISSN: 0099-2240 1098-5336
Published: American Society for Microbiology 2017
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URI: https://cronfa.swan.ac.uk/Record/cronfa33246
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fullrecord <?xml version="1.0"?><rfc1807><datestamp>2018-04-18T14:39:25.5271104</datestamp><bib-version>v2</bib-version><id>33246</id><entry>2017-05-07</entry><title>Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni</title><swanseaauthors><author><sid>4660c0eb7e6bfd796cd749ae713ea558</sid><ORCID>0000-0001-6376-5121</ORCID><firstname>Ben</firstname><surname>Pascoe</surname><name>Ben Pascoe</name><active>true</active><ethesisStudent>false</ethesisStudent></author></swanseaauthors><date>2017-05-07</date><deptcode>PMSC</deptcode><abstract>&lt;p&gt;Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multi-locus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles, at 7 MLST loci, among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1810 genes identified through gene-by-gene comparison of 884 genomes of C. jejuni isolates from animal reservoirs, the environment and clinical cases. Fifteen loci, involved in metabolic activities, protein modification, signal transduction and stress response, or coding for hypothetical proteins, were selected as host-segregating markers and used to attribute the source of 42 French and 281 UK clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software, attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the UK. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modelling to account for differences in production, behaviour and food consumption.&lt;/p&gt;&lt;p&gt;IMPORTANCE: Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France. A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and UK clinical isolates attributed to each host reservoir illustrates a potential role for local/national variations in C. jejuni transmission dynamics.&lt;/p&gt;</abstract><type>Journal Article</type><journal>Applied and Environmental Microbiology</journal><volume>83</volume><journalNumber>7</journalNumber><paginationStart>e03085-16</paginationStart><publisher>American Society for Microbiology</publisher><issnPrint>0099-2240</issnPrint><issnElectronic>1098-5336</issnElectronic><keywords/><publishedDay>23</publishedDay><publishedMonth>1</publishedMonth><publishedYear>2017</publishedYear><publishedDate>2017-01-23</publishedDate><doi>10.1128/AEM.03085-16</doi><url/><notes/><college>COLLEGE NANME</college><department>Medicine</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>PMSC</DepartmentCode><institution>Swansea University</institution><apcterm/><lastEdited>2018-04-18T14:39:25.5271104</lastEdited><Created>2017-05-07T00:18:38.7533165</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Medicine</level></path><authors><author><firstname>Th&#xE9;pault</firstname><surname>Amandine</surname><order>1</order></author><author><firstname>M&#xE9;ric</firstname><surname>Guillaume</surname><order>2</order></author><author><firstname>Rivoal</firstname><surname>Katell</surname><order>3</order></author><author><firstname>Ben</firstname><surname>Pascoe</surname><orcid>0000-0001-6376-5121</orcid><order>4</order></author><author><firstname>Mageiros</firstname><surname>Leonardos</surname><order>5</order></author><author><firstname>Touzain</firstname><surname>Fabrice</surname><order>6</order></author><author><firstname>Rose</firstname><surname>Val&#xE9;rie</surname><order>7</order></author><author><firstname>B&#xE9;ven</firstname><surname>V&#xE9;ronique</surname><order>8</order></author><author><firstname>Chemaly</firstname><surname>Marianne</surname><order>9</order></author><author><firstname>K</firstname><surname>Samuel</surname><order>10</order></author></authors><documents/><OutputDurs/></rfc1807>
spelling 2018-04-18T14:39:25.5271104 v2 33246 2017-05-07 Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni 4660c0eb7e6bfd796cd749ae713ea558 0000-0001-6376-5121 Ben Pascoe Ben Pascoe true false 2017-05-07 PMSC <p>Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multi-locus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles, at 7 MLST loci, among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1810 genes identified through gene-by-gene comparison of 884 genomes of C. jejuni isolates from animal reservoirs, the environment and clinical cases. Fifteen loci, involved in metabolic activities, protein modification, signal transduction and stress response, or coding for hypothetical proteins, were selected as host-segregating markers and used to attribute the source of 42 French and 281 UK clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software, attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the UK. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modelling to account for differences in production, behaviour and food consumption.</p><p>IMPORTANCE: Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France. A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and UK clinical isolates attributed to each host reservoir illustrates a potential role for local/national variations in C. jejuni transmission dynamics.</p> Journal Article Applied and Environmental Microbiology 83 7 e03085-16 American Society for Microbiology 0099-2240 1098-5336 23 1 2017 2017-01-23 10.1128/AEM.03085-16 COLLEGE NANME Medicine COLLEGE CODE PMSC Swansea University 2018-04-18T14:39:25.5271104 2017-05-07T00:18:38.7533165 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Thépault Amandine 1 Méric Guillaume 2 Rivoal Katell 3 Ben Pascoe 0000-0001-6376-5121 4 Mageiros Leonardos 5 Touzain Fabrice 6 Rose Valérie 7 Béven Véronique 8 Chemaly Marianne 9 K Samuel 10
title Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
spellingShingle Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
Ben Pascoe
title_short Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
title_full Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
title_fullStr Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
title_full_unstemmed Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
title_sort Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni
author_id_str_mv 4660c0eb7e6bfd796cd749ae713ea558
author_id_fullname_str_mv 4660c0eb7e6bfd796cd749ae713ea558_***_Ben Pascoe
author Ben Pascoe
author2 Thépault Amandine
Méric Guillaume
Rivoal Katell
Ben Pascoe
Mageiros Leonardos
Touzain Fabrice
Rose Valérie
Béven Véronique
Chemaly Marianne
K Samuel
format Journal article
container_title Applied and Environmental Microbiology
container_volume 83
container_issue 7
container_start_page e03085-16
publishDate 2017
institution Swansea University
issn 0099-2240
1098-5336
doi_str_mv 10.1128/AEM.03085-16
publisher American Society for Microbiology
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
document_store_str 0
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description <p>Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multi-locus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles, at 7 MLST loci, among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1810 genes identified through gene-by-gene comparison of 884 genomes of C. jejuni isolates from animal reservoirs, the environment and clinical cases. Fifteen loci, involved in metabolic activities, protein modification, signal transduction and stress response, or coding for hypothetical proteins, were selected as host-segregating markers and used to attribute the source of 42 French and 281 UK clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software, attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the UK. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modelling to account for differences in production, behaviour and food consumption.</p><p>IMPORTANCE: Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France. A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and UK clinical isolates attributed to each host reservoir illustrates a potential role for local/national variations in C. jejuni transmission dynamics.</p>
published_date 2017-01-23T03:40:54Z
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