Sequences of three gene fragments ( flaA, flaB, and vacA) from Helicobacter pylori strains isolated from patients in Germany, Canada, and South Africa were analyzed for diversity and for linkage equilibrium by using the Homoplasy Test and compatibility matrices. Horizontal genetic exchange in H. pylori is so frequent that different loci and polymorphisms within each locus are all at linkage equilibrium. These results indicate that H. pylori is panmictic. Comparisons with sequences from Escherichia coli, Neisseria meningitidis, and Drosophila melanogaster showed that recombination in H. pylori was much more frequent than in other species. In contrast, when multiple family members infected with H. pylori were investigated, some strains were indistinguishable at all three loci. Thus, H. pylori is clonal over short time periods after natural transmission.Helicobacter pylori is genetically one of the most diverse bacterial species so far reported. It also is subject to the highest known rate of intraspecific recombination. This paper presents the evidence for these two assertions and discusses their significance. In particular, is there a causal connection between high variability and high recombination rate?Infection with H. pylori, a common human pathogen, causes chronic type B gastritis and is a prerequisite for the development of duodenal ulcers and most gastric ulcers (1). H. pylori infection is also an important risk factor for gastric malignancies such as adenocarcinoma (2) and mucosa-associated lymphoid tissue lymphoma (3). Most microbiological studies of H. pylori have concentrated on virulence factors (4) and much less is known about its population biology. DNA fingerprinting (5-7), multilocus enzyme electrophoresis (MLEE) (8) and DNA sequence analysis of the ureC͞glmM and cagA genes (9-11) have revealed an unusually high degree of genetic variability within this species, whose origin is unclear.Motility is essential for the virulence of H. pylori and is based on a flagellar apparatus with several unique features (12). The flagellar filament is composed of two flagellins, FlaA and FlaB, which are covered by a flagellar sheath and therefore thought to be shielded from antibody selection. Little has been published about the sequence variability of the flaA and flaB genes. VacA is a secreted vacuolating cytotoxin thought to be involved in ulcerogenesis (13), whose sequence variability seems to reflect mosaicism (14). During sequence analyses of the flaB gene directed to better understanding of its role in virulence, we noticed a degree of sequence variability which seemed unprecedented in the bacterial kingdom. We extended these analyses to data available in GenBank from gene fragments of the flaA and vacA genes and tested the sequence diversity of these three gene fragments among strains isolated from individuals in three different study groups. The sequence data were analyzed for evidence of recombination using a novel tool, the Homoplasy Test (15), which has been designed to test recombination in nu...

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