Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity.
Identifieur interne : 000195 ( PubMed/Checkpoint ); précédent : 000194; suivant : 000196Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity.
Auteurs : Amber C A. Hendriks [Pays-Bas] ; Frans A G. Reubsaet [Pays-Bas] ; A M D Mirjam Kooistra-Smid [Pays-Bas] ; John W A. Rossen [Pays-Bas] ; Bas E. Dutilh [Pays-Bas] ; Aldert L. Zomer [Pays-Bas] ; Maaike J C. Van Den Beld [Pays-Bas]Source :
- BMC genomics [ 1471-2164 ] ; 2020.
Abstract
We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control.
DOI: 10.1186/s12864-020-6555-7
PubMed: 32041522
Affiliations:
- Pays-Bas
- Groningue (province), Utrecht (province)
- Groningue, Utrecht
- Université d'Utrecht, Université de Groningue
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Hendriks</name><affiliation wicri:level="1"><nlm:affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Reubsaet, Frans A G" sort="Reubsaet, Frans A G" uniqKey="Reubsaet F" first="Frans A G" last="Reubsaet">Frans A G. Reubsaet</name><affiliation wicri:level="1"><nlm:affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author><author><name sortKey="Kooistra Smid, A M D Mirjam" sort="Kooistra Smid, A M D Mirjam" uniqKey="Kooistra Smid A" first="A M D Mirjam" last="Kooistra-Smid">A M D Mirjam Kooistra-Smid</name><affiliation wicri:level="3"><nlm:affiliation>Department of Medical Microbiology, Certe, Groningen, the Netherlands.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Medical Microbiology, Certe, Groningen</wicri:regionArea><placeName><settlement type="city">Groningue</settlement><region nuts="2" type="province">Groningue (province)</region></placeName></affiliation></author><author><name sortKey="Rossen, John W A" sort="Rossen, John W A" uniqKey="Rossen J" first="John W A" last="Rossen">John W A. Rossen</name><affiliation wicri:level="4"><nlm:affiliation>Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.</nlm:affiliation><country xml:lang="fr" wicri:curation="lc">Pays-Bas</country><wicri:regionArea>Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen</wicri:regionArea><placeName><settlement type="city">Groningue</settlement><region nuts="2" type="province">Groningue (province)</region></placeName><orgName type="university">Université de Groningue</orgName></affiliation></author><author><name sortKey="Dutilh, Bas E" sort="Dutilh, Bas E" uniqKey="Dutilh B" first="Bas E" last="Dutilh">Bas E. Dutilh</name><affiliation wicri:level="4"><nlm:affiliation>Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht</wicri:regionArea><placeName><settlement type="city">Utrecht</settlement><region nuts="2" type="province">Utrecht (province)</region></placeName><orgName type="university">Université d'Utrecht</orgName></affiliation></author><author><name sortKey="Zomer, Aldert L" sort="Zomer, Aldert L" uniqKey="Zomer A" first="Aldert L" last="Zomer">Aldert L. Zomer</name><affiliation wicri:level="4"><nlm:affiliation>Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht</wicri:regionArea><placeName><settlement type="city">Utrecht</settlement><region nuts="2" type="province">Utrecht (province)</region></placeName><orgName type="university">Université d'Utrecht</orgName></affiliation></author><author><name sortKey="Van Den Beld, Maaike J C" sort="Van Den Beld, Maaike J C" uniqKey="Van Den Beld M" first="Maaike J C" last="Van Den Beld">Maaike J C. Van Den Beld</name><affiliation wicri:level="1"><nlm:affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands. maaike.van.den.beld@rivm.nl.</nlm:affiliation><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven</wicri:regionArea><wicri:noRegion>Bilthoven</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32041522</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>16</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>1</Issue><PubDate><Year>2020</Year><Month>Feb</Month><Day>10</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity.</ArticleTitle><Pagination><MedlinePgn>138</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-020-6555-7</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">To conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hendriks</LastName><ForeName>Amber C A</ForeName><Initials>ACA</Initials><AffiliationInfo><Affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Reubsaet</LastName><ForeName>Frans A G</ForeName><Initials>FAG</Initials><AffiliationInfo><Affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kooistra-Smid</LastName><ForeName>A M D Mirjam</ForeName><Initials>AMDM</Initials><AffiliationInfo><Affiliation>Department of Medical Microbiology, Certe, Groningen, the Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rossen</LastName><ForeName>John W A</ForeName><Initials>JWA</Initials><AffiliationInfo><Affiliation>Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dutilh</LastName><ForeName>Bas E</ForeName><Initials>BE</Initials><AffiliationInfo><Affiliation>Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zomer</LastName><ForeName>Aldert L</ForeName><Initials>AL</Initials><AffiliationInfo><Affiliation>Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>van den Beld</LastName><ForeName>Maaike J C</ForeName><Initials>MJC</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8720-8434</Identifier><AffiliationInfo><Affiliation>Infectious Disease Research, Diagnostics and laboratory Surveillance, Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands. maaike.van.den.beld@rivm.nl.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands. maaike.van.den.beld@rivm.nl.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><CollectiveName>IBESS group</CollectiveName></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>864.14.004</GrantID><Agency>Nederlandse Organisatie voor Wetenschappelijk Onderzoek</Agency><Country></Country></Grant><Grant><GrantID>Not applicable</GrantID><Agency>Dutch National Insitute for Public Health and the Environment for local Public Health Services</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>02</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Disease control guidelines</Keyword><Keyword MajorTopicYN="N">Disease severity</Keyword><Keyword MajorTopicYN="N">E. coli</Keyword><Keyword MajorTopicYN="N">EIEC</Keyword><Keyword MajorTopicYN="N">Escherichia coli</Keyword><Keyword MajorTopicYN="N">GWAS</Keyword><Keyword MajorTopicYN="N">Shigella</Keyword><Keyword MajorTopicYN="N">Shigellosis</Keyword><Keyword MajorTopicYN="N">Symptoms</Keyword></KeywordList><InvestigatorList><Investigator ValidYN="Y"><LastName>van den Beld</LastName><ForeName>M J C</ForeName><Initials>MJC</Initials></Investigator><Investigator ValidYN="Y"><LastName>Warmelink</LastName><ForeName>E</ForeName><Initials>E</Initials></Investigator><Investigator ValidYN="Y"><LastName>Kooistra-Smid</LastName><ForeName>A M D</ForeName><Initials>AMD</Initials></Investigator><Investigator ValidYN="Y"><LastName>Friedrich</LastName><ForeName>A W</ForeName><Initials>AW</Initials></Investigator><Investigator ValidYN="Y"><LastName>Reubsaet</LastName><ForeName>F A G</ForeName><Initials>FAG</Initials></Investigator><Investigator ValidYN="Y"><LastName>Notermans</LastName><ForeName>D W</ForeName><Initials>DW</Initials></Investigator><Investigator ValidYN="Y"><LastName>Petrignani</LastName><ForeName>M W F</ForeName><Initials>MWF</Initials></Investigator><Investigator ValidYN="Y"><LastName>Waegemaekers</LastName><ForeName>C H F M</ForeName><Initials>CHFM</Initials></Investigator><Investigator ValidYN="Y"><LastName>Rossen</LastName><ForeName>J W A</ForeName><Initials>JWA</Initials></Investigator><Investigator ValidYN="Y"><LastName>van 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