Population genetics of Helicobacter pylori in the southern part of Switzerland analysed by sequencing of four housekeeping genes (atpD, glnA, scoB and recA), and by vacA, cagA, iceA and IS605 genotyping

The population biology of 78 Helicobacter pylori strains (71 from Swiss Ita lian. 4 from East Asian and 3 from South African patients) was investigated by sequence analysis of four housekeeping genes: atpD, scoB, glnA and recA . The vacA genotype, the presence of cagA and IS605. the iceA allelic type. and the resistance to metronidazole. clarithromycin and amoxycillin were d etermined. A high percentage of DNA polymorphic sites (19.8% for atpD. 21.3 % for scoB, 23.7% for glnA and 20.3% for recA) was found. The phylogenetic trees based on the nucleotide sequences of the four gene fragments showed d ifferent topologies and were incongruent. The virulence-associated markers were distributed over the dendrograms and no association was found with phy logenetic clusters or clinical manifestations (chronic gastritis, gastric o r duodenal ulcer. MALT lymphoma). Moreover, the H ratios (calculated with t he homoplasy test) ranged from 0.742 to 0.799. depending on the gene fragme nt examined. All these observations suggest that H. pylori exists as a reco mbinant population. The clustering of the strains according to their geogra phical origin (USA/Europe. East Asia, South Africa) that has recently been demonstrated elsewhere could only be confirmed for the East Asian vacA sie strains. In contrast, the South African strains clustered together only in the atpD tree. Presumably, recombination at the different loci has masked t he evolutionary relationship among the strains.