Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age

Abstract

The bacterium Helicobacter pylori colonizes the gastric mucosa of half of the human population, resulting in chronic gastritis, ulcers, and cancer. We sequenced ten gene fragments from pairs of strains isolated sequentially at a mean interval of 1.8 years from 26 individuals. Several isolates had acquired small mosaic segments from other H. pylori or point mutations. The maximal mutation rate, the import size, and the frequency of recombination were calculated by using a Bayesian model. The calculations indicate that the last common ancestor of H. pylori existed at least 2,500-11,000 years ago. Imported mosaics have a median size of 417 bp, much smaller than for other bacteria, and recombination occurs frequently (60 imports spanning 25,000 bp per genome per year). Thus, the panmictic population structure of H. pylori results from very frequent recombination during mixed colonization by unrelated strains.

Figure 1

Sequence comparisons of ten gene fragments from 26 pairs of isolates of H. pylori. The ten loci are indicated by tiny maps at the top of the figure (colors: core fragments, tan; flanking genes, gray; noncoding regions, white). The sources of the isolates are indicated by patient codes at the left (Colombia, three digits; Louisiana, four digits). The boxes indicate the lengths of the sequenced fragments, distinguished by color (white, identical sequences; yellow, SNPs; pink, clustered polymorphisms). Vertical lines within the boxes indicate the positions of sequence polymorphisms. The patients are separated into five groups (right) on the basis of all genetic changes between the paired isolates (1, no polymorphisms; 2, only SNPs; 3, clustered polymorphisms; 4, related isolates with numerous polymorphic fragments; 5, unrelated isolates). Mathematical analysis was only performed with data from patients in groups 1–3.

Figure 2

Sequence lengths used in the model as described in Materials and Methods.

Figure 3

Probability of identity (p_ident) between sequences versus length. The black curves are pairwise comparisons between the initial isolates within Colombia or Louisiana. The weighted average of these curves is shown in blue. The green curve is from pairwise comparisons between Louisiana and Colombia. Data from within polymorphic stretches from paired isolates (Fig. 1, part 3) are in red.

Figure 4

Parameters estimated by the model for the data in Fig. 1, parts 1–3. (A) Contour plot of marginal likelihoods (posterior/prior) of recombination parameters. (B) Marginal likelihood of mutation rates. The arrow indicates a maximum below which different mutation rates were not distinguished at the 5% level.