Cargando…
Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan
BACKGROUND: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficil...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708112/ https://www.ncbi.nlm.nih.gov/pubmed/29213333 http://dx.doi.org/10.1186/s13099-017-0219-4 |
_version_ | 1783282590381244416 |
---|---|
author | Suzuki, Haruo Tomita, Masaru Tsai, Pei-Jane Ko, Wen-Chien Hung, Yuan-Pin Huang, I-Hsiu Chen, Jenn-Wei |
author_facet | Suzuki, Haruo Tomita, Masaru Tsai, Pei-Jane Ko, Wen-Chien Hung, Yuan-Pin Huang, I-Hsiu Chen, Jenn-Wei |
author_sort | Suzuki, Haruo |
collection | PubMed |
description | BACKGROUND: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses. RESULTS: The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage [Formula: see text] CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage [Formula: see text] NCKUH-21. The prophage [Formula: see text] NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome. CONCLUSIONS: This is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan. Due to the high identity with [Formula: see text] CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13099-017-0219-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5708112 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-57081122017-12-06 Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan Suzuki, Haruo Tomita, Masaru Tsai, Pei-Jane Ko, Wen-Chien Hung, Yuan-Pin Huang, I-Hsiu Chen, Jenn-Wei Gut Pathog Genome Report BACKGROUND: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses. RESULTS: The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage [Formula: see text] CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage [Formula: see text] NCKUH-21. The prophage [Formula: see text] NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome. CONCLUSIONS: This is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan. Due to the high identity with [Formula: see text] CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13099-017-0219-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-11-29 /pmc/articles/PMC5708112/ /pubmed/29213333 http://dx.doi.org/10.1186/s13099-017-0219-4 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 | Genome Report Suzuki, Haruo Tomita, Masaru Tsai, Pei-Jane Ko, Wen-Chien Hung, Yuan-Pin Huang, I-Hsiu Chen, Jenn-Wei Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title | Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title_full | Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title_fullStr | Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title_full_unstemmed | Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title_short | Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan |
title_sort | comparative genomic analysis of clostridium difficile ribotype 027 strains including the newly sequenced strain nckuh-21 isolated from a patient in taiwan |
topic | Genome Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708112/ https://www.ncbi.nlm.nih.gov/pubmed/29213333 http://dx.doi.org/10.1186/s13099-017-0219-4 |
work_keys_str_mv | AT suzukiharuo comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT tomitamasaru comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT tsaipeijane comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT kowenchien comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT hungyuanpin comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT huangihsiu comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan AT chenjennwei comparativegenomicanalysisofclostridiumdifficileribotype027strainsincludingthenewlysequencedstrainnckuh21isolatedfromapatientintaiwan |