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Short nucleotide sequence inserts within the signal (s) and mid (m) regions of the vacuolating cytotoxin gene (vacA) of Helicobacter pylori provide the basis for defining the allelic forms widely used for strain typing and as markers for toxin functionality and severity of interactions with host gastric epithelial cells. Here 484 signal region and 411 mid-region sequences (new and from public databases) from 32 countries were analysed to determine the effect of geographical location on insert diversity, which is currently undefined. Short (27 bp) inserts of 52 mol% G+C from 201 sequences (98 %) of the s2 allelic family encoded a highly conserved nine amino acid sequence irrespective of geographical origin. The longer (75 bp) mid-region insert of 38 mol% G+C in 255 sequences of the m2 allelic family was more diverse and represented by 23 peptide variants, with one predominant sequence (MRI type 4) representing 62 % of inserts. Mid-region inserts were widespread throughout European/North American (Western) sequences in the dataset whereas a lower insert frequency was a geographical feature of East Asian sequences. Each insert was preceded by an associated conserved motif that provided a marker of the insertion sites within vacA, and facilitated identification of the Chinese m2b genotype. It is concluded that the observed sequence conservation supports the continued global use of vacA genotyping, and that inserts could have a functional significance in the mature protein, particularly the s2 form of the toxin, as the same combination of signal and mid-region insert type and preinsert motif was highly conserved.

Phenotypic and phylogenetic studies were performed on four Campylobacter-like organisms recovered from three seals and a porpoise. Comparative 16S rRNA gene sequencing studies demonstrated that the organisms represent a hitherto unknown subline within the genus Campylobacter, associated with a subcluster containing Campylobacter jejuni, Campylobacter coli and Campylobacter lari. DNA-DNA hybridization studies confirmed that the bacteria belonged to a single species, for which the name Campylobacter insulaenigrae sp. nov. is proposed. The type strain of Campylobacter insulaenigrae sp. nov. is NCTC 12927(T) (=CCUG 48653(T)).

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'.

Helicobacter pylori, a Gram-negative bacterium, is a causal agent of peptic ulcers and is estimated to infect the gastric mucosa of at least half of the world's population. As primary infections are acquired mainly by household contact, studies on family clusters provide a model for investigating transmission and the natural history of initial infection. Here, sequence typing exploiting genetic variation in core fragments of three key housekeeping loci (ureI, atpA and ahpC) was used to determine clonal descent amongst isolates of ten members of four families in Northern Ireland and a family with three generations in central England. Phylogenetic analysis of each locus for 73 strains of H. pylori from 11 countries indicated high background intraspecific diversity, apart from identical paired isolates from five unrelated patients and strains with identical sequence types (STs) detected in adult members of two families. In several families carrying strains with different STs, evidence of residual clonal descent was detected at one or two loci by comparison of nucleotide and amino acid sequences. Pathogenicity-associated genotypes were heterogeneous with respect to ST and amino acid type. Analysis of these three housekeeping genes provides unique evidence for precise tracing of clonal descent in isolates of H. pylori in family groups.