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From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma
- Source :
- BMC Genomics, Vol 11, Iss 1, p 368 (2010), BMC Genomics, BMC Genomics, BioMed Central, 2010, 11 (1), pp.368. ⟨10.1186/1471-2164-11-368⟩, BMC Genomics, 2010, 11 (1), pp.368. ⟨10.1186/1471-2164-11-368⟩, BMC Genomics, BioMed Central, 2010, 11 (1), pp.368. <10.1186/1471-2164-11-368>
- Publication Year :
- 2010
- Publisher :
- BMC, 2010.
-
Abstract
- Background elicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach. Results A set of 254 H. pylori genes was used to perform array-based comparative genomic hybridization among 120 French H. pylori strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with cag PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released H. pylori genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest H. pylori genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the vacA s2m2 allele and lacks the genes encoding the major virulence factors (absence of cag PAI, bab B, bab C, sab B, and hom B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 H. pylori sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38. Conclusion These isolates are deprived of the main H. pylori virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.
- Subjects :
- MESH: Intestinal Diseases
MESH: Genome, Bacterial
Genome
MESH: Nucleic Acid Hybridization
Cluster Analysis
MESH: Genomic Islands
MESH: Lymphoma, B-Cell, Marginal Zone
MESH: Phylogeny
MESH: Bacterial Proteins
Phylogeny
MESH: Evolution, Molecular
Oligonucleotide Array Sequence Analysis
Genetics
0303 health sciences
biology
DNA–DNA hybridization
Nucleic Acid Hybridization
MALT lymphoma
Gastritis
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
MESH: Gastritis
Research Article
Biotechnology
Genomic Islands
lcsh:QH426-470
lcsh:Biotechnology
Evolution, Molecular
03 medical and health sciences
MESH: Gene Expression Profiling
Bacterial Proteins
Species Specificity
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
lcsh:TP248.13-248.65
medicine
Humans
MESH: Species Specificity
030304 developmental biology
Synteny
Comparative genomics
MESH: Humans
Helicobacter pylori
030306 microbiology
Gene Expression Profiling
Lymphoma, B-Cell, Marginal Zone
biology.organism_classification
medicine.disease
MESH: Cluster Analysis
Intestinal Diseases
lcsh:Genetics
Genetic marker
Duodenal Ulcer
MESH: Duodenal Ulcer
MESH: Oligonucleotide Array Sequence Analysis
MESH: Helicobacter pylori
Genome, Bacterial
Comparative genomic hybridization
Subjects
Details
- Language :
- English
- ISSN :
- 14712164
- Volume :
- 11
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....9cdb4fd21f8793ebfc3df98f14305bf3