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The bacterium  Helicobacter pylori  exhibits great genetic diversity, and the pathogenic roles of its virulence factors have been widely studied. However, the evolutionary dynamics of  H. pylori  strains during stomach colonization are not well-characterized. Here, we analyzed the microevolutionary dynamics of the toxigenic strain  vacAs1m1 , the non-toxigenic strain  vacAs2m2 , and a combination of both strains in an animal model over time.  Meriones unguiculatus  were inoculated with the following bacteria: group 1-toxigenic strain  vacAs1m1/cagA+/cagE+/babA2+ ; ST181, group 2-non-toxigenic strain  vacAs2m2/cagA+/cagE+/babA2+ ; ST2901, and group 3-both strains. The gerbils were euthanized at different time points (3, 6, 12, and 18 months). In group 1, genetic alterations were observed at 6 and 12 months. With the combination of both strains, group 3 also exhibited genetic alterations at 3 and 18 months; moreover, a chimera,  vacA m1-m2 , was detected. Additionally, four new sequence types (STs) were reported in the PubMLST database for  H. pylori . Synonymous and non-synonymous mutations were analyzed and associated with alterations in amino acids. Microevolutionary analysis of the STs (PHYLOViZ) identified in each group revealed many mutational changes in the toxigenic ( vacAs1m1 ) and non-toxigenic ( vacAs2m2 ) strains. Phylogenetic assessments (eBURST) did not reveal clonal complexes. Our findings indicate that the toxigenic strain,  vacAs1m1 , and a combination of toxigenic and non-toxigenic strains acquired genetic material by recombination. The allelic combination,  vacAs2m1 , displayed the best adaptation in the animal model over time, and a chimera,  m1-m2 , was also identified, which confirmed previous reports.

Diversification of the vacAs1m1 and vacAs2m2 Strains of Helicobacter pylori in Meriones unguiculatus