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Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

You Y, He L, Zhang M, Fu J, Gu Y, Zhang B, Tao X, Zhang J - PLoS ONE (2012)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

ABSTRACT
In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 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.

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Related in: MedlinePlus

Gene content analysis of TFS4 and TFS3 in eighty-four H. pylori isolates by PCR.The presence of individual genes is indicated in red, and their absence in green. Non-specific amplicon is shown in black.
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pone-0038528-g005: Gene content analysis of TFS4 and TFS3 in eighty-four H. pylori isolates by PCR.The presence of individual genes is indicated in red, and their absence in green. Non-specific amplicon is shown in black.

Mentions: A heatmap of variable genes detected among the three H. pylori test strains was also confirmed using PCR. Green denotes absence of genes; red indicates presence of genes. The distinct regions of the three test strains were clustered with a dendrogram, which was constructed by hierarchical analysis of the presence or absence of genes. Amplification of some genes showing a weak PCR product band or a band of incorrect size are represented in black. One possible explanation for this is that sequence variation in these genes occurs in the primer binding region. The twenty variable genes of the TFSS3 and TFSS4 in the eight GC isolates observed by ADaCGH were confirmed by PCR, showing concordance with the microarray data. The prevalence of these genes in isolates from 76 additional patients was tested by PCR (Figure 5). These genes were found to be absent in 18 of 33 GC strains (55%). Other strains harbor two or more of these gene. These data support the association of the loss of these genes in isolates from GC patients.


Comparative genomics of Helicobacter pylori strains of China associated with different clinical outcome.

You Y, He L, Zhang M, Fu J, Gu Y, Zhang B, Tao X, Zhang J - PLoS ONE (2012)

Gene content analysis of TFS4 and TFS3 in eighty-four H. pylori isolates by PCR.The presence of individual genes is indicated in red, and their absence in green. Non-specific amplicon is shown in black.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3368837&req=5

pone-0038528-g005: Gene content analysis of TFS4 and TFS3 in eighty-four H. pylori isolates by PCR.The presence of individual genes is indicated in red, and their absence in green. Non-specific amplicon is shown in black.
Mentions: A heatmap of variable genes detected among the three H. pylori test strains was also confirmed using PCR. Green denotes absence of genes; red indicates presence of genes. The distinct regions of the three test strains were clustered with a dendrogram, which was constructed by hierarchical analysis of the presence or absence of genes. Amplification of some genes showing a weak PCR product band or a band of incorrect size are represented in black. One possible explanation for this is that sequence variation in these genes occurs in the primer binding region. The twenty variable genes of the TFSS3 and TFSS4 in the eight GC isolates observed by ADaCGH were confirmed by PCR, showing concordance with the microarray data. The prevalence of these genes in isolates from 76 additional patients was tested by PCR (Figure 5). These genes were found to be absent in 18 of 33 GC strains (55%). Other strains harbor two or more of these gene. These data support the association of the loss of these genes in isolates from GC patients.

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

ABSTRACT
In this study, a whole-genome CombiMatrix Custom oligonucleotide tiling microarray with 90,000 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.

Show MeSH
Related in: MedlinePlus