Comparison of genetic divergence and fitness between two subclones of Helicobacter pylori

Helicobacter pylori has a very plastic genome, reflecting its high rate of recombination and point mutation. This plasticity promotes divergence of th e population by the development of subclones and presumably enhances adapta tion to host niches. We have investigated the genotypic and phenotypic char acteristics of two such subclones isolated from one patient as well as the genetic evolution of these isolates during experimental infection. Whole-ge nome genotyping of the isolates using DNA microarrays revealed that they we re more similar to each other than to a panel of other genotyped strains re covered from different hosts. Nonetheless, they still showed significant di fferences. For example, one isolate (67:21) contained the entire Cag pathog enicity island (PAI), whereas the other (67:20) had excised the PAL Phenoty pic studies disclosed that both isolates expressed adhesins that recognized human histo-blood group Lewis(b) glycan receptors produced by gastric pit and surface mucus cells. In addition, both isolates were able to colonize, to equivalent density and with similar efficiency, germ-free transgenic mic e genetically engineered to synthesize Lewis' glycans in their pit cells (1 2 to 14 mice/isolate). Remarkably, the Cag PAI-negative isolate was unable to colonize conventionally raised Lewis(b) transgenic mice harboring a norm al gastric microflora, whereas the Cag PAI-positive isolate colonized 74% o f the animals (39 to 40 mice/isolate). The genomic evolution of both isolat es during the infection of conventionally raised and germ-free mice was mon itored over the course of 3 months. The Cag PAI-positive isolate was also s urveyed after a 10 month colonization of conventionally raised transgenic a nimals (n = 9 mice). Microarray analysis of the Cag PAI and sequence analys is of the cagA, recA, and 16S rRNA genes disclosed no changes in recovered isolates. Together, these results reveal that the IL pylori population infe cting one individual can undergo significant divergence, creating stable su bclones,vith substantial genotypic and phenotypic differences.