Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked t...
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doaj-5370e46e01bb4b2eb43d859fd5f952b92021-05-06T16:05:14ZengTaylor & Francis GroupVirulence2150-55942150-56082021-01-011211258127010.1080/21505594.2021.19207621920762Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicityFeng Yang0Jinghao Zhang1Su Wang2Zhaoyang Sun3Jun Zhou4Feng Li5Yue Liu6Li Ding7Yixin Liu8Wenjing Chi9Tao Liu10Yongqun He11Ping Xiang12Zhijun Bao13Michal A. Olszewski14Hu Zhao15Yanmei Zhang16Research Center on Aging and Medicine, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityHuadong Hospital, Fudan UniversityAnd Center for Computational Medicine and Bioinformatics, University of Michigan Medical SchoolHuadong Hospital, Fudan UniversityGerontology Institute of Shanghai, Huadong Hospital, Fudan UniversityUniversity of Michigan and Research Service, VA Ann Arbor Healthcare SystemResearch Center on Aging and Medicine, Fudan UniversityResearch Center on Aging and Medicine, Fudan UniversitySevere Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai H. pylori isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai H. pylori isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in H. pylori.http://dx.doi.org/10.1080/21505594.2021.1920762helicobacter pylorigastric diseasesgenomic featurespathogenicitygenomic islandcrisprpopulation structure |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Feng Yang Jinghao Zhang Su Wang Zhaoyang Sun Jun Zhou Feng Li Yue Liu Li Ding Yixin Liu Wenjing Chi Tao Liu Yongqun He Ping Xiang Zhijun Bao Michal A. Olszewski Hu Zhao Yanmei Zhang |
spellingShingle |
Feng Yang Jinghao Zhang Su Wang Zhaoyang Sun Jun Zhou Feng Li Yue Liu Li Ding Yixin Liu Wenjing Chi Tao Liu Yongqun He Ping Xiang Zhijun Bao Michal A. Olszewski Hu Zhao Yanmei Zhang Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity Virulence helicobacter pylori gastric diseases genomic features pathogenicity genomic island crispr population structure |
author_facet |
Feng Yang Jinghao Zhang Su Wang Zhaoyang Sun Jun Zhou Feng Li Yue Liu Li Ding Yixin Liu Wenjing Chi Tao Liu Yongqun He Ping Xiang Zhijun Bao Michal A. Olszewski Hu Zhao Yanmei Zhang |
author_sort |
Feng Yang |
title |
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
title_short |
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
title_full |
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
title_fullStr |
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
title_full_unstemmed |
Genomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
title_sort |
genomic population structure of helicobacter pylori shanghai isolates and identification of genomic features uniquely linked with pathogenicity |
publisher |
Taylor & Francis Group |
series |
Virulence |
issn |
2150-5594 2150-5608 |
publishDate |
2021-01-01 |
description |
Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai H. pylori isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai H. pylori isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in H. pylori. |
topic |
helicobacter pylori gastric diseases genomic features pathogenicity genomic island crispr population structure |
url |
http://dx.doi.org/10.1080/21505594.2021.1920762 |
work_keys_str_mv |
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