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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...

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Autores principales: Suzuki, Haruo, Tomita, Masaru, Tsai, Pei-Jane, Ko, Wen-Chien, Hung, Yuan-Pin, Huang, I-Hsiu, Chen, Jenn-Wei
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
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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.
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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
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