Analysis of geospecific markers for Helicobacter pylori variants in patients from Japan and Nigeria by triple-locus nucleotide sequence typing

Abstract

Human migrations and geographical separation over long periods may have resulted in ecologically distinct populations of Helicobacter pylori infecting individuals in different continents. This study used nucleotide sequence analysis with the aim of defining population-specific genomic motifs in isolates from East Asian and African dyspeptic patients. Sequences of internal fragments (542-627 bp) of three housekeeping genes (ureI, ahpC and atpA) were analysed for 85 isolates from individuals in Japan and China (30 isolates), Nigeria and South Africa (14 isolates), the United Kingdom (32 isolates), and nine miscellaneous reference strains. Phylogenetic analyses showed a high degree of intra-set relatedness amongst sequences from the Japanese and Nigerian isolates, with each robustly segregated as distinct lineages irrespective of cagA presence and vacA allelic type. All strains had unique combined sequence types except for identical paired (antrum/corpus) isolates. Population-specific polymorphisms were identified within each gene which were combined to provide unique motifs defining the Japanese and Nigerian regional populations. The alleles were present at variable frequencies in UK and South African isolates. The findings provide unique evidence of positive selection for conserved nucleotide sites linked to the geographical separation in Japan of a strain subpopulation for which we propose the designation H. pylori geovar 'orientalis'.

The association of vacA genotype and Helicobacter pylori-related disease in Latin American and African populations

“…'Mix' indicates the number of patients infected with two or more different vacA genotypes. Owen et al [48] published the data from the Nigeria and South Africa populations. When patients were found to be infected with multiple Helicobacter pylori strains, each H. pylori strain was analysed separately [18,22,42,47].…”

Geographical conservation of short inserts in the signal and middle regions of the Helicobacter pylori vacuolating cytotoxin gene

“…Data on human populations in European, African and North American countries as well as in China show that the frequency of the s2/m2 allelic family is low (generally around 10 %). In Japanese human populations, the s2/m2 form appears even rarer: for example, such forms were found in only 4 % of H. pylori infecting patients in Okinawa (Zhou et al, 2004b) and were completely absent from isolates infecting adult gastritis patients in Tokyo (Owen et al, 2004). In Japanese children the predominant genotype reported was s1c/m1b (Azuma et al, 2004).…”

“…All isolates originated from gastric biopsies of unrelated patients undergoing routine upper gastrointestinal endoscopic investigation for various presentations between 1990 and 2002. The study included Japanese (Tokyo) isolates collected as part of the UK/Japan Gastritis Study from 16 patients (eight males and eight females) aged between 23 and 79 years (mean 55.6 years) described previously (Owen et al, 2004;Naylor et al, 2006). Nine reference cultures of H. pylori were obtained in lyophilized form from the National Collection of Type Cultures (NCTC, London): NCTC 11637 (type strain, Australia); NCTC 11638 (Australia); NCTC 13081 (strain Tx30a, USA); NCTC 13082 (Canada), NCTC 13085 (strain 60190, England), NCTC 13086 (Canada), NCTC 11916 (England), NCTC 13207 (CCUG 38772), NCTC 12455 (strain 26695, genome sequenced strain, England; Tomb et al, 1997).…”

“…The East Asian (Eastern-type) isolates, particularly those of Japanese and Chinese origin, appear to represent a distinct modern subpopulation. Furthermore, Japanese-specific polymorphisms have been identified within several housekeeping genes (Owen et al, 2004). Geographical separation of H. pylori in distinct separately evolving populations is supported by analyses of the gene encoding CagA, a marker of the cag pathogenicity island, as well as by vacA, in which characteristic differences were identified between isolates originating from China and Japan (East Asian type) compared to those from the USA and Europe (Western type) (van der Ende et al, 1998;Ito et al, 1997;Pan et al, 1998;van Doorn et al, 1998;Yamaoka et al, 1998;van Doorn et al, 1999;Kersulyte et al, 2000).…”

The Human Microbiota as a Marker for Migrations of Individuals and Populations

“…Genetic studies of H. pylori reveal that recombination is extensive (Suerbaum & Achtman 2004) and that H. pylori represents a nearly panmictic population (Falush et al 2003b, Suerbaum et al 1998). Early studies of current H. pylori populations focused on single genes, such as oipA (Yamaoka et al 2000), hspA (Ng et al 1999), vacA (Garza-Gonzalez et al 2004, Ghose et al 2002, van Doorn et al 1998a, Yamaoka et al 2002, and ureI, ahpC, and atpA (Owen et al 2004). Although these have been nearly supplanted by multilocus sequence typing (MLST) approaches (see below), the studies of vacA provided early evidence of the utility of studying diversity to understand human population movements.…”