Helicobacter pylori: recombination, population structure and human migrations
ABSTRACT Helicobacter pylori shows extensive genetic diversity and variability due to frequent intraspecific recombination during mixed infection. In the last years, modern genetic and genomic technology as well as cutting-edge population genetic analysis have been used to investigate the population structure and genetic variability of this pathogen. This review article summarizes recent developments in this rapidly moving field.
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ABSTRACT: The integron/gene cassette system contributes to lateral gene transfer of genetic information in bacterial communities, with gene cassette-encoded proteins potentially playing an important role in adaptation to stress. Class 1 integrons are a particularly important class as they themselves seem to be broadly disseminated among the Proteobacteria and have an established role in the spread of antibiotic resistance genes. The abundance and structure of class 1 integrons in freshwater sediment bacterial communities was assessed through sampling of 30 spatially distinct sites encompassing different substrate and catchment types from the Greater Melbourne Area of Victoria, Australia. Real-time PCR was used to demonstrate that the abundance of intI1 was increased as a result of ecosystem perturbation, indicated by classification of sample locations based on the catchment type and a strong positive correlation with the first principal component factor score, comprised primarily of the heavy metals zinc, mercury, lead and copper. Additionally, the abundance of intI1 at sites located downstream from treated sewage outputs was associated with the percentage contribution of the discharge to the basal flow rate. Characterization of class 1 integrons in bacteria cultured from selected sediment samples identified an association with complete Tn402-like transposition modules, and the potential for coselection of heavy-metal and antibiotic resistance mechanisms in benthic environments.FEMS Microbiology Ecology 04/2010; 72(1):35-46. DOI:10.1111/j.1574-6941.2009.00823.x · 3.88 Impact Factor
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ABSTRACT: The genomic methylation analysis is useful to type bacteria that have a high number of expressed type II methyltransferases. Methyltransferases are usually committed to Restriction and Modification (R-M) systems, in which the restriction endonuclease imposes high pressure on the expression of the cognate methyltransferase that hinder R-M system loss. Conventional cluster methods do not reflect this tendency. An algorithm was developed for dendrogram construction reflecting the propensity for conservation of R-M Type II systems. The new algorithm was applied to 52 Helicobacter pylori strains from different geographical regions and compared with conventional clustering methods. The algorithm works by first grouping strains that share a common minimum set of R-M systems and gradually adds strains according to the number of the R-M systems acquired. Dendrograms revealed a cluster of African strains, which suggest that R-M systems are present in H.pylori genome since its human host migrates from Africa. The software files are available at http://www.ff.ul.pt/paginas/jvitor/Bioinformatics/MCRM_algorithm.zip.Bioinformatics 03/2008; 24(3):383-8. DOI:10.1093/bioinformatics/btm621 · 4.62 Impact Factor
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ABSTRACT: In this review, we summarize how genomic approaches contributed to the understanding of the biology of the recently discovered pathogen Helicobacter pylori. Comparative genomics provided new insights into H. pylori's spectacular genetic diversity and generated exiting hypotheses on its evolutionary history. Transcriptomic studies provided original information on the mechanisms of H. pylori gastric adaptation that are central to its virulence.FEMS Immunology & Medical Microbiology 08/2007; 50(2):165-76. DOI:10.1111/j.1574-695X.2007.00244.x · 2.55 Impact Factor