Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China

You, Yuanhai; Liu, Lin; Zhang, Maojun; Han, Xifang; He, Lihua; Zhu, Yuanfang; Ni, Peixiang; Zhang, Jianzhong

doi:10.1128/jb.01399-12

Cited by 9 publications

(4 citation statements)

References 18 publications

(4 reference statements)

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“…YN1–91 was isolated from a Han gastritis patient. The strains were cultured on a Columbia agar base supplemented with 5% sheep blood, and DNA was extracted as previously described [ 31 , 32 ].…”

Section: Methodsmentioning

confidence: 99%

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Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

You

Zhang

et al. 2015

PLoS ONE

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Helicobacter pylori is a common pathogen correlated with several severe digestive diseases. It has been reported that isolates associated with different geographic areas, different diseases and different individuals might have variable genomic features. Here, we describe draft genomic sequences of H. pylori strains YN4-84 and YN1-91 isolated from patients with gastritis from the Naxi and Han populations of Yunnan, China, respectively. The draft sequences were compared to 45 other publically available genomes, and a total of 1059 core genes were identified. Genes involved in restriction modification systems, type four secretion system three (TFS3) and type four secretion system four (TFS4), were identified as highly divergent. Both YN4-84 and YN1-91 harbor intact cag pathogenicity island (cagPAI) and have EPIYA-A/B/D type at the carboxyl terminal of cagA. The vacA gene type is s1m2i1. Another major finding was a 32.5-kb prophage integrated in the YN4-84 genome. The prophage shares most of its genes (30/33) with Helicobacter pylori prophage KHP30. Moreover, a 1,886 bp transposable sequence (IS605) was found in the prophage. Our results imply that the Naxi ethnic minority isolate YN4-84 and Han isolate YN1-91 belong to the hspEAsia subgroup and have diverse genome structure. The genome has been extensively modified in several regions involved in horizontal DNA transfer. The important roles played by phages in the ecology and microevolution of H. pylori were further emphasized. The current data will provide valuable information regarding the H. pylori genome based on historic human migrations and population structure.

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Section: Methodsmentioning

confidence: 99%

“…We have reported draft genome sequences for three H . pylori strains isolated from Heilongjiang province, which has quite a high incidence of gastric disease [ 31 , 32 ]. Additionally, we recently completed draft genomes of two other isolates recovered from gastritis patients from Yunnan province.…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

You

Zhang

et al. 2015

PLoS ONE

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“…The complete genome sequence would likely be helpful in understanding the adaptation of this bacterium to patients living in high‐altitude areas and the reason for high infection rate in the Tibetan plateau. Contributing to the diversity of strains from regions with high incidence of gastrointestinal diseases, draft genomes of three strains isolated from two atrophic gastritis (HLJ193 and HLJ256), and one gastric ulcer (HLJ271) disease patients from Heilongjiang province, China, were also made available .…”

Section: Newly Sequenced H Pylori Genomesmentioning

confidence: 99%

Helicobacter pylori in 2013: Multiplying Genomes, Emerging Insights

et al. 2013

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We describe features of key additions to the existing pool of publicly accessible Helicobacter pylori genome sequences and sequences of Helicobacter pylori phages from April 2012 to March 2013. In addition, important studies involving H. pylori genomes, especially those pertaining to genomic diversity, disease outcome, H. pylori population structure and evolution are reviewed. High degree of homologous recombination contributes to increased diversity of H. pylori genomes. New methods of resolving H. pylori population structure to an ultrafine level led to the proposal of new subpopulations. As the magnitude of diversity in the H. pylori gene pool becomes more and more clear, geographic and demographic factors should be brought to analysis while identifying disease-specific biomarkers and defining new virulence mechanisms.

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“…In a previous study, we published genome sequences of three strains recovered from patients with ulcers and atrophic gastritis in Heilongjiang province [ 13 ]. It is well known that H. pylori strains isolated from different geographic areas show dramatic genomic diversity [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China

et al. 2014

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BackgroundHelicobacter pylori is well known for its relationship with the occurrence of several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are less well known. In this study, we report the genome sequence and genomic characterizations of H. pylori strain HLJ039 that was isolated from a patient with gastric cancer in the Chinese province of Heilongjiang, where there is a high incidence of gastric cancer. To investigate potential genomic features that may be involved in pathogenesis of carcinoma, the genome was compared to three previously sequenced genomes in this area.ResultWe obtained 42 contigs with a total length of 1,611,192 bp and predicted 1,687 coding sequences. Compared to strains isolated from gastritis and ulcers in this area, 10 different regions were identified as being unique for HLJ039; they mainly encoded type II restriction-modification enzyme, type II m6A methylase, DNA-cytosine methyltransferase, DNA methylase, and hypothetical proteins. A unique 547-bp fragment sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC BAA-847 was not present in any other previous H. pylori strains. Phylogenetic analysis based on core genome single nucleotide polymorphisms shows that HLJ039 is defined as hspEAsia subgroup, which belongs to the hpEastAsia group.ConclusionDNA methylations, variations of the genomic regions involved in restriction and modification systems, are the “hot” regions that may be related to the mechanism of H. pylori-induced gastric cancer. The genome sequence will provide useful information for the deep mining of potential mechanisms related to East Asian gastric cancer.

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Genome Sequences of Three Helicobacter pylori Strains Isolated from Atrophic Gastritis and Gastric Ulcer Patients in China

Cited by 9 publications

References 18 publications

Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

Comparative Genomics of a Helicobacter pylori Isolate from a Chinese Yunnan Naxi Ethnic Aborigine Suggests High Genetic Divergence and Phage Insertion

Helicobacter pylori in 2013: Multiplying Genomes, Emerging Insights

Genomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China

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