Article

Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer

Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232-2605, USA.
BMC Genomics (Impact Factor: 4.04). 01/2009; 10:3. DOI: 10.1186/1471-2164-10-3
Source: PubMed

ABSTRACT Persistent colonization of the human stomach by Helicobacter pylori is associated with asymptomatic gastric inflammation (gastritis) and an increased risk of duodenal ulceration, gastric ulceration, and non-cardia gastric cancer. In previous studies, the genome sequences of H. pylori strains from patients with gastritis or duodenal ulcer disease have been analyzed. In this study, we analyzed the genome sequences of an H. pylori strain (98-10) isolated from a patient with gastric cancer and an H. pylori strain (B128) isolated from a patient with gastric ulcer disease.
Based on multilocus sequence typing, strain 98-10 was most closely related to H. pylori strains of East Asian origin and strain B128 was most closely related to strains of European origin. Strain 98-10 contained multiple features characteristic of East Asian strains, including a type s1c vacA allele and a cagA allele encoding an EPIYA-D tyrosine phosphorylation motif. A core genome of 1237 genes was present in all five strains for which genome sequences were available. Among the 1237 core genes, a subset of alleles was highly divergent in the East Asian strain 98-10, encoding proteins that exhibited <90% amino acid sequence identity compared to corresponding proteins in the other four strains. Unique strain-specific genes were identified in each of the newly sequenced strains, and a set of strain-specific genes was shared among H. pylori strains associated with gastric cancer or premalignant gastric lesions.
These data provide insight into the diversity that exists among H. pylori strains from diverse clinical and geographic origins. Highly divergent alleles and strain-specific genes identified in this study may represent useful biomarkers for analyzing geographic partitioning of H. pylori and for identifying strains capable of inducing malignant or premalignant gastric lesions.

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    • "Helicobacter pylori strain 26695 (20) was used as in previous studies (25) for tandem affinity purification (TAP) taking Hp-RNase J and RhpA as baits (Supplementary Table S1). For all other experiments, we used H. pylori strain B128 (26) in which the inducible plasmids could be introduced and stably maintained (Supplementary Table S1). For the details of bacterial growth conditions, see Supplementary Methods. "
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    Nucleic Acids Research 10/2012; 41(1). DOI:10.1093/nar/gks945 · 9.11 Impact Factor
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    • "The amino acid identities range between 65-100%. Among these core genes are housekeeping (HK) genes that are essential for H. pylori survival, and the genetic variability in these genes remains very low [10,11]. This conservation is reflected in phylogenetic analysis, where HK genes have been used to trace human migration, indicating co-evolution between H. pylori and its host. "
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