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Genome analysis of E. coli isolated from Crohn’s disease patients
BACKGROUND: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from C...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517970/ https://www.ncbi.nlm.nih.gov/pubmed/28724357 http://dx.doi.org/10.1186/s12864-017-3917-x |
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author | Rakitina, Daria V. Manolov, Alexander I. Kanygina, Alexandra V. Garushyants, Sofya K. Baikova, Julia P. Alexeev, Dmitry G. Ladygina, Valentina G. Kostryukova, Elena S. Larin, Andrei K. Semashko, Tatiana A. Karpova, Irina Y. Babenko, Vladislav V. Ismagilova, Ruzilya K. Malanin, Sergei Y. Gelfand, Mikhail S. Ilina, Elena N. Gorodnichev, Roman B. Lisitsyna, Eugenia S. Aleshkin, Gennady I. Scherbakov, Petr L. Khalif, Igor L. Shapina, Marina V. Maev, Igor V. Andreev, Dmitry N. Govorun, Vadim M. |
author_facet | Rakitina, Daria V. Manolov, Alexander I. Kanygina, Alexandra V. Garushyants, Sofya K. Baikova, Julia P. Alexeev, Dmitry G. Ladygina, Valentina G. Kostryukova, Elena S. Larin, Andrei K. Semashko, Tatiana A. Karpova, Irina Y. Babenko, Vladislav V. Ismagilova, Ruzilya K. Malanin, Sergei Y. Gelfand, Mikhail S. Ilina, Elena N. Gorodnichev, Roman B. Lisitsyna, Eugenia S. Aleshkin, Gennady I. Scherbakov, Petr L. Khalif, Igor L. Shapina, Marina V. Maev, Igor V. Andreev, Dmitry N. Govorun, Vadim M. |
author_sort | Rakitina, Daria V. |
collection | PubMed |
description | BACKGROUND: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS: We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. CONCLUSIONS: Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3917-x) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5517970 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-55179702017-08-16 Genome analysis of E. coli isolated from Crohn’s disease patients Rakitina, Daria V. Manolov, Alexander I. Kanygina, Alexandra V. Garushyants, Sofya K. Baikova, Julia P. Alexeev, Dmitry G. Ladygina, Valentina G. Kostryukova, Elena S. Larin, Andrei K. Semashko, Tatiana A. Karpova, Irina Y. Babenko, Vladislav V. Ismagilova, Ruzilya K. Malanin, Sergei Y. Gelfand, Mikhail S. Ilina, Elena N. Gorodnichev, Roman B. Lisitsyna, Eugenia S. Aleshkin, Gennady I. Scherbakov, Petr L. Khalif, Igor L. Shapina, Marina V. Maev, Igor V. Andreev, Dmitry N. Govorun, Vadim M. BMC Genomics Research Article BACKGROUND: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS: We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons. CONCLUSIONS: Our findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3917-x) contains supplementary material, which is available to authorized users. BioMed Central 2017-07-19 /pmc/articles/PMC5517970/ /pubmed/28724357 http://dx.doi.org/10.1186/s12864-017-3917-x Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Rakitina, Daria V. Manolov, Alexander I. Kanygina, Alexandra V. Garushyants, Sofya K. Baikova, Julia P. Alexeev, Dmitry G. Ladygina, Valentina G. Kostryukova, Elena S. Larin, Andrei K. Semashko, Tatiana A. Karpova, Irina Y. Babenko, Vladislav V. Ismagilova, Ruzilya K. Malanin, Sergei Y. Gelfand, Mikhail S. Ilina, Elena N. Gorodnichev, Roman B. Lisitsyna, Eugenia S. Aleshkin, Gennady I. Scherbakov, Petr L. Khalif, Igor L. Shapina, Marina V. Maev, Igor V. Andreev, Dmitry N. Govorun, Vadim M. Genome analysis of E. coli isolated from Crohn’s disease patients |
title | Genome analysis of E. coli isolated from Crohn’s disease patients |
title_full | Genome analysis of E. coli isolated from Crohn’s disease patients |
title_fullStr | Genome analysis of E. coli isolated from Crohn’s disease patients |
title_full_unstemmed | Genome analysis of E. coli isolated from Crohn’s disease patients |
title_short | Genome analysis of E. coli isolated from Crohn’s disease patients |
title_sort | genome analysis of e. coli isolated from crohn’s disease patients |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517970/ https://www.ncbi.nlm.nih.gov/pubmed/28724357 http://dx.doi.org/10.1186/s12864-017-3917-x |
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