Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome

In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with differen...

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Main Authors:	You, Yuanhai, He, Lihua, Zhang, Maojun, Fu, Jianying, Gu, Yixin, Zhang, Binghua, Tao, Xiaoxia, Zhang, Jianzhong
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368837/

id	pubmed-3368837
recordtype	oai_dc
spelling	pubmed-33688372012-06-13 Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome You, Yuanhai He, Lihua Zhang, Maojun Fu, Jianying Gu, Yixin Zhang, Binghua Tao, Xiaoxia Zhang, Jianzhong Research Article In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases. Public Library of Science 2012-06-06 /pmc/articles/PMC3368837/ /pubmed/22701658 http://dx.doi.org/10.1371/journal.pone.0038528 Text en You et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	You, Yuanhai He, Lihua Zhang, Maojun Fu, Jianying Gu, Yixin Zhang, Binghua Tao, Xiaoxia Zhang, Jianzhong
spellingShingle	You, Yuanhai He, Lihua Zhang, Maojun Fu, Jianying Gu, Yixin Zhang, Binghua Tao, Xiaoxia Zhang, Jianzhong Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
author_facet	You, Yuanhai He, Lihua Zhang, Maojun Fu, Jianying Gu, Yixin Zhang, Binghua Tao, Xiaoxia Zhang, Jianzhong
author_sort	You, Yuanhai
title	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
title_short	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
title_full	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
title_fullStr	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
title_full_unstemmed	Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome
title_sort	comparative genomics of helicobacter pylori strains of china associated with different clinical outcome
description	In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90000 probes covering six sequenced Helicobacter pylori (H. pylori) genomes was designed. This microarray was used to compare the genomic profiles of eight unsequenced strains isolated from patients with different gastroduodenal diseases in Heilongjiang province of China. Since significant genomic variation was found among these strains, an additional 76 H. pylori strains associated with different clinical outcomes were isolated from various provinces of China. These strains were tested by polymerase chain reaction to demonstrate this distinction. We identified several highly variable regions in strains associated with gastritis, gastric ulceration, and gastric cancer. These regions are associated with genes involved in the bacterial type I, type II, and type III R-M systems. They were also associated with the virB gene, which lies on the well-studied cag pathogenic island. While previous studies have reported on the diverse genetic characterization of this pathogenic island, in this study, we find that it is conserved in all strains tested by microarray. Moreover, a number of genes involved in the type IV secretion system, which is related to horizontal DNA transfer between H. pylori strains, were identified in the comparative analysis of the strain-specific genes. These findings may provide insight into new biomarkers for the prediction of gastric diseases.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3368837/
_version_	1611535043212083200

Comparative Genomics of Helicobacter pylori Strains of China Associated with Different Clinical Outcome

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