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.
"It is recognised that the distribution of some bacteria may be related to geographical patterns, such as climatic zones and movement of human populations [9–11]. However, the spatial distribution of genetic variants can shed light on pathogen evolution and transmission. "
[Show abstract][Hide abstract] ABSTRACT: Technological advances in high-throughput genome sequencing have led to an enhanced appreciation of the genetic diversity found within populations of pathogenic bacteria. Methods based on single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) build upon the framework established by multi-locus sequence typing (MLST) and permit a detailed, targeted analysis of variation within related organisms. Robust phylogenetics, when combined with epidemiologically informative data, can be applied to study ongoing temporal and geographical fluctuations in bacterial pathogens. As genome sequencing, SNP detection and geospatial information become more accessible these methods will continue to transform the way molecular epidemiology is used to study populations of bacterial pathogens.
Current opinion in microbiology 10/2010; 13(5):640-5. DOI:10.1016/j.mib.2010.08.002 · 5.90 Impact Factor
"Bacteria represent a globally ubiquitous domain of life, exhibiting a high degree of functional diversity (Nealson, 1997); however, investigation into the vertical transmission of information via recombination (Milkman, 1997; Coenye & LiPuma, 2003; Suerbaum & Achtman, 2004; Coscolla & Gonzalez-Candelas, 2007) and mutation (Lawrence & Ochman , 1998) has failed to account for this diversity (Syvanen, 1994; Davison, 1999). Comparative analysis of variation in bacterial genomes has provided evidence that adaptive evolution is largely facilitated by lateral gene transfer (LGT). "
[Show abstract][Hide abstract] 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.
"This explanation does not reconcile well with the observation by Wirth et al.  that in the Ladakh population genes of European ancestry were found despite the population being in a more pristine region. It has previously been suggested that AE1 originated in Central Asia because it shares phylogenetic signals with isolates from Estonia, Finland and Ladakh [12,36]. Since the ancestors of Malaysian Indians and the Ladakhis resided in the same region and their H. pylori belong to hpAsia2, it seems likely that this biased share of the gene pool by the Malaysian Indian/Malay isolates with the AE1 subpopulation is due to an earlier common ancestry. "
[Show abstract][Hide abstract] ABSTRACT: Helicobacter pylori is a major gastric bacterial pathogen. This pathogen has been shown to follow the routes of human migration by their geographical origin and currently the global H. pylori population has been divided into six ancestral populations, three from Africa, two from Asia and one from Europe. Malaysia is made up of three major ethnic populations, Malay, Chinese and Indian, providing a good population for studying recent H. pylori migration and admixture.
Seventy eight H. pylori isolates, including 27 Chinese, 35 Indian and 16 Malay isolates from Malaysia were analysed by multilocus sequence typing (MLST) of seven housekeeping genes and compared with the global MLST data. STRUCTURE analysis assigned the isolates to previously identified H. pylori ancestral populations, hpEastAsia, hpAsia2 and hpEurope, and revealed a new subpopulation, hspIndia, within hpAsia2. Statistical analysis allowed us to identify population segregation sites that divide the H. pylori populations and the subpopulations. The majority of Malay isolates were found to be grouped together with Indian isolates.
The majority of the Malay and Indian H. pylori isolates share the same origin while the Malaysian Chinese H. pylori is distinctive. The Malay population, known to have a low infection rate of H. pylori, was likely to be initially H. pylori free and gained the pathogen only recently from cross infection from other populations.
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