Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation
Identifieur interne : 000261 ( Main/Exploration ); précédent : 000260; suivant : 000262Correlation between the genomic o454-nlpD region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal Escherichia coli (ExPEC) enables pathotyping irrespective of host, disease and source of isolation
Auteurs : Christa Ewers [Allemagne] ; Flavia Dematheis [Allemagne] ; Haritha Devi Singamaneni [Allemagne] ; Nishant Nandanwar [Allemagne, Inde] ; Angelika Fruth [Allemagne] ; Ines Diehl [Allemagne] ; Torsten Semmler [Allemagne] ; Lothar H. Wieler [Allemagne]Source :
- Gut Pathogens [ 1757-4749 ] ; 2014.
Abstract
The
Size variation in the
Four main structures (patterns I-IV) of the
The significant association between pattern III and group B2 strains suggested the
Url:
DOI: 10.1186/s13099-014-0037-x
PubMed: 25349632
PubMed Central: 4209514
Affiliations:
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35392</wicri:regionArea><wicri:noRegion>35392</wicri:noRegion><wicri:noRegion>35392</wicri:noRegion><wicri:noRegion>35392</wicri:noRegion></affiliation></author><author><name sortKey="Dematheis, Flavia" sort="Dematheis, Flavia" uniqKey="Dematheis F" first="Flavia" last="Dematheis">Flavia Dematheis</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Singamaneni, Haritha Devi" sort="Singamaneni, Haritha Devi" uniqKey="Singamaneni H" first="Haritha Devi" last="Singamaneni">Haritha Devi Singamaneni</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Nandanwar, Nishant" sort="Nandanwar, Nishant" uniqKey="Nandanwar N" first="Nishant" last="Nandanwar">Nishant Nandanwar</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, Gachibowli, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, Gachibowli</wicri:regionArea><wicri:noRegion>Gachibowli</wicri:noRegion></affiliation></author><author><name sortKey="Fruth, Angelika" sort="Fruth, Angelika" uniqKey="Fruth A" first="Angelika" last="Fruth">Angelika Fruth</name><affiliation wicri:level="1"><nlm:aff id="I4">National Reference Centre for Salmonella and Other Enteric Pathogens, Robert Koch Institute, Burgstr. 37, Wernigerode, 38855, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>National Reference Centre for Salmonella and Other Enteric Pathogens, Robert Koch Institute, Burgstr. 37, Wernigerode, 38855</wicri:regionArea><wicri:noRegion>38855</wicri:noRegion><wicri:noRegion>38855</wicri:noRegion><wicri:noRegion>38855</wicri:noRegion></affiliation></author><author><name sortKey="Diehl, Ines" sort="Diehl, Ines" uniqKey="Diehl I" first="Ines" last="Diehl">Ines Diehl</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Semmler, Torsten" sort="Semmler, Torsten" uniqKey="Semmler T" first="Torsten" last="Semmler">Torsten Semmler</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Wieler, Lothar H" sort="Wieler, Lothar H" uniqKey="Wieler L" first="Lothar H" last="Wieler">Lothar H. Wieler</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25349632</idno><idno type="pmc">4209514</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209514</idno><idno type="RBID">PMC:4209514</idno><idno type="doi">10.1186/s13099-014-0037-x</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000292</idno><idno type="wicri:Area/Pmc/Curation">000292</idno><idno type="wicri:Area/Pmc/Checkpoint">000223</idno><idno type="wicri:Area/Ncbi/Merge">000267</idno><idno type="wicri:Area/Ncbi/Curation">000267</idno><idno type="wicri:Area/Ncbi/Checkpoint">000267</idno><idno type="wicri:Area/Main/Merge">000261</idno><idno type="wicri:Area/Main/Curation">000261</idno><idno type="wicri:Area/Main/Exploration">000261</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Correlation between the genomic <italic>o454-nlpD</italic> region polymorphisms, virulence gene equipment and phylogenetic group of extraintestinal <italic>Escherichia coli</italic> (ExPEC) enables pathotyping irrespective of host, disease and source of isolation</title><author><name sortKey="Ewers, Christa" sort="Ewers, Christa" uniqKey="Ewers C" first="Christa" last="Ewers">Christa Ewers</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, Giessen, 35392, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-Universität Giessen, Frankfurter Str. 85-89, Giessen, 35392</wicri:regionArea><wicri:noRegion>35392</wicri:noRegion><wicri:noRegion>35392</wicri:noRegion><wicri:noRegion>35392</wicri:noRegion></affiliation></author><author><name sortKey="Dematheis, Flavia" sort="Dematheis, Flavia" uniqKey="Dematheis F" first="Flavia" last="Dematheis">Flavia Dematheis</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Singamaneni, Haritha Devi" sort="Singamaneni, Haritha Devi" uniqKey="Singamaneni H" first="Haritha Devi" last="Singamaneni">Haritha Devi Singamaneni</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Nandanwar, Nishant" sort="Nandanwar, Nishant" uniqKey="Nandanwar N" first="Nishant" last="Nandanwar">Nishant Nandanwar</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, Gachibowli, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, Gachibowli</wicri:regionArea><wicri:noRegion>Gachibowli</wicri:noRegion></affiliation></author><author><name sortKey="Fruth, Angelika" sort="Fruth, Angelika" uniqKey="Fruth A" first="Angelika" last="Fruth">Angelika Fruth</name><affiliation wicri:level="1"><nlm:aff id="I4">National Reference Centre for Salmonella and Other Enteric Pathogens, Robert Koch Institute, Burgstr. 37, Wernigerode, 38855, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>National Reference Centre for Salmonella and Other Enteric Pathogens, Robert Koch Institute, Burgstr. 37, Wernigerode, 38855</wicri:regionArea><wicri:noRegion>38855</wicri:noRegion><wicri:noRegion>38855</wicri:noRegion><wicri:noRegion>38855</wicri:noRegion></affiliation></author><author><name sortKey="Diehl, Ines" sort="Diehl, Ines" uniqKey="Diehl I" first="Ines" last="Diehl">Ines Diehl</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Semmler, Torsten" sort="Semmler, Torsten" uniqKey="Semmler T" first="Torsten" last="Semmler">Torsten Semmler</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Wieler, Lothar H" sort="Wieler, Lothar H" uniqKey="Wieler L" first="Lothar H" last="Wieler">Lothar H. Wieler</name><affiliation wicri:level="3"><nlm:aff id="I2">Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin, 14163</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></analytic><series><title level="j">Gut Pathogens</title><idno type="eISSN">1757-4749</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The <italic>mutS</italic>-<italic>rpoS</italic> intergenic region in <italic>E. coli</italic> displays a mosaic structure which revealed pathotype specific patterns. To assess the importance of this region as a surrogate marker for the identification of highly virulent extraintestinal pathogenic <italic>E. coli</italic> (ExPEC) strains we aimed to: (i) characterize the genetic diversity of the <italic>mutS</italic> gene and the <italic>o454-nlpD</italic> genomic region among 510 <italic>E. coli</italic> strains from animals and humans; (ii) delineate associations between the polymorphism of this region and features such as phylogenetic background of <italic>E. coli</italic>, pathotype, host species, clinical condition, serogroup and virulence associated genes (VAG)s; and (iii) identify the most important VAGs for classification of the <italic>o454-nlpD</italic> region.</p></sec><sec><title>Methods</title><p>Size variation in the <italic>o454-nlpD</italic> region was investigated by PCR amplification and sequencing. Phylogenetic relationships were assessed by Ecor- and Multilocus sequence- typing (MLST), and a comparative analysis between <italic>mutS</italic> gene phylogenetic tree obtained with RAxML and the MLST grouping method was performed. Correlation between <italic>o454-nlpD</italic> patterns and the features described above were analysed. In addition, the importance of 47 PCR-amplified ExPEC-related VAGs for classification of <italic>o454-nlpD</italic> patterns was investigated by means of Random Forest algorithm.</p></sec><sec><title>Results</title><p>Four main structures (patterns I-IV) of the <italic>o454-nlpD</italic> region among ExPEC and commensal <italic>E. coli</italic> strains were identified. Statistical analysis showed a positive and exclusive association between pattern III and the ExPEC strains. A strong association between pattern III and either the Ecor group B2 or the sequence type complexes known to represent the phylogenetic background of highly virulent ExPEC strains (such as STC95, STC73 and STC131) was found as well. RF analyses determined five genes (<italic>csgA</italic>, <italic>malX</italic>, <italic>chuA</italic>, <italic>sit</italic>, and <italic>vat</italic>) to be suitable to predict pattern III strains.</p></sec><sec><title>Conclusion</title><p>The significant association between pattern III and group B2 strains suggested the <italic>o454-nlpD</italic> region to be of great value in identifying highly virulent strains among the mixed population of <italic>E. coli</italic> promising to be the basis of a future typing tool for ExPEC and their gut reservoir. Furthermore, top-ranked VAGs for classification and prediction of pattern III were identified. These data are most valuable for defining ExPEC pathotype in future <italic>in vivo</italic> assays.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kaper, Jb" uniqKey="Kaper J">JB Kaper</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brzuszkiewicz, E" uniqKey="Brzuszkiewicz E">E Brzuszkiewicz</name></author><author><name sortKey="Gottschalk, G" uniqKey="Gottschalk G">G Gottschalk</name></author><author><name sortKey="Ron, E" uniqKey="Ron E">E Ron</name></author><author><name sortKey="Hacker, J" uniqKey="Hacker J">J Hacker</name></author><author><name sortKey="Dobrindt, U" uniqKey="Dobrindt U">U Dobrindt</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Russo, Ta" uniqKey="Russo T">TA Russo</name></author><author><name sortKey="Johnson, Jr" uniqKey="Johnson J">JR Johnson</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Dh" uniqKey="Huson D">DH Huson</name></author><author><name sortKey="Scornavacca, C" uniqKey="Scornavacca C">C Scornavacca</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Plackett, Rl" uniqKey="Plackett R">RL Plackett</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Campbell, I" uniqKey="Campbell I">I Campbell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, D" uniqKey="Meyer D">D Meyer</name></author><author><name sortKey="Zeileis, A" uniqKey="Zeileis A">A Zeileis</name></author><author><name sortKey="Hornik, K" uniqKey="Hornik K">K Hornik</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sheskin, Dj" uniqKey="Sheskin D">DJ Sheskin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Strobl, C" uniqKey="Strobl C">C Strobl</name></author><author><name sortKey="Boulesteix, Al" uniqKey="Boulesteix A">AL Boulesteix</name></author><author><name sortKey="Kneib, T" uniqKey="Kneib T">T Kneib</name></author><author><name sortKey="Augustin, T" uniqKey="Augustin T">T Augustin</name></author><author><name sortKey="Zeileis, A" uniqKey="Zeileis A">A Zeileis</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>Inde</li></country><region><li>Berlin</li></region><settlement><li>Berlin</li></settlement></list><tree><country name="Allemagne"><noRegion><name sortKey="Ewers, Christa" sort="Ewers, Christa" uniqKey="Ewers C" first="Christa" last="Ewers">Christa Ewers</name></noRegion><name sortKey="Dematheis, Flavia" sort="Dematheis, Flavia" uniqKey="Dematheis F" first="Flavia" last="Dematheis">Flavia Dematheis</name><name sortKey="Diehl, Ines" sort="Diehl, Ines" uniqKey="Diehl I" first="Ines" last="Diehl">Ines Diehl</name><name sortKey="Fruth, Angelika" sort="Fruth, Angelika" uniqKey="Fruth A" first="Angelika" last="Fruth">Angelika Fruth</name><name sortKey="Nandanwar, Nishant" sort="Nandanwar, Nishant" uniqKey="Nandanwar N" first="Nishant" last="Nandanwar">Nishant Nandanwar</name><name sortKey="Semmler, Torsten" sort="Semmler, Torsten" uniqKey="Semmler T" first="Torsten" last="Semmler">Torsten Semmler</name><name sortKey="Singamaneni, Haritha Devi" sort="Singamaneni, Haritha Devi" uniqKey="Singamaneni H" first="Haritha Devi" last="Singamaneni">Haritha Devi Singamaneni</name><name sortKey="Wieler, Lothar H" sort="Wieler, Lothar H" uniqKey="Wieler L" first="Lothar H" last="Wieler">Lothar H. Wieler</name></country><country name="Inde"><noRegion><name sortKey="Nandanwar, Nishant" sort="Nandanwar, Nishant" uniqKey="Nandanwar N" first="Nishant" last="Nandanwar">Nishant Nandanwar</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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