title: 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.
abstract: The population biology of 78 Helicobacter pylori strains (71 from Swiss Italian, 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 determined. 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 different topologies and were incongruent. The virulence-associated markers were distributed over the dendrograms and no association was found with phylogenetic clusters or clinical manifestations (chronic gastritis, gastric or duodenal ulcer, MALT lymphoma). Moreover, the H ratios (calculated with the homoplasy test) ranged from 0.742 to 0.799, depending on the gene fragment examined. All these observations suggest that H. pylori exists as a recombinant population. The clustering of the strains according to their geographical origin (USA/Europe, East Asia, South Africa) that has recently been demonstrated elsewhere could only be confirmed for the East Asian vacA s1c strains. In contrast, the South African strains clustered together only in the atpD tree. Presumably, recombination at the different loci has masked the evolutionary relationship among the strains.
authors.affiliation: Istituto Cantonale Batteriosierologico, Via Ospedale 6, 6904 Lugano, Switzerland1.
authors.forename: Nadia
authors.initials: N
authors.lastname: Maggi Solcà
authors.affiliation: Istituto Cantonale Batteriosierologico, Via Ospedale 6, 6904 Lugano, Switzerland1.
authors.forename: Marco V
authors.initials: MV
authors.lastname: Bernasconi
authors.affiliation: Istituto Cantonale Batteriosierologico, Via Ospedale 6, 6904 Lugano, Switzerland1.
authors.forename: Claudio
authors.initials: C
authors.lastname: Valsangiacomo
authors.affiliation: Delft Diagnostic Laboratory, R. de Graafweg 7, 2625 AD Delft, The Netherlands2.
authors.forename: Leen-Jan
authors.initials: LJ
authors.lastname: Van Doorn
authors.affiliation: Istituto Cantonale Batteriosierologico, Via Ospedale 6, 6904 Lugano, Switzerland1.
authors.forename: Jean-Claude
authors.initials: JC
authors.lastname: Piffaretti
mesh_terms: D001706:Biopsy; D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D005202:Asia, Eastern; D005798:Genes, Bacterial; D005828:Genetics, Population; D005838:Genotype; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013019:South Africa; D013270:Stomach / Q000382:microbiology / Q000601:surgery; D013557:Switzerland; D014774:Virulence
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial