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Background   Helicobacter pylori  recurrence after successful eradication is an important problem. Children are particularly vulnerable to reinfection, by intrafamilial transmission which facilitates the acquisition or recombination of new genetic information by this bacterium. We investigated the evolutionary dynamics of 80  H. pylori  strains isolated from two paediatric patients with recurrent infection (recrudescence and reinfection).    Results  We characterized the virulence genes  vacA  ( s1 ,  m1 ,  s2 , and  m2 ),  cagA ,  cagE , and  babA2  and performed multilocus sequence typing (MLST) on 7 housekeeping genes ( atpA ,  efp ,  ureI ,  ppa ,  mutY ,  trpC , and  yphC ) to infer the evolutionary dynamics of the  H. pylori  strains through phylogenetic and genealogic inference analyses, genetic diversity analysis and the exploration of recombination events during recurrent infections. The virulence genotype  vacAs1m1/cagA+/cagE+/babA2  was present at a high frequency, as were the EPIYA motifs EPIYA-A, −B and -C. Furthermore, the housekeeping genes of the  H. pylori  strains exhibited high genetic variation, comprising 26 new alleles and 17 new Sequence Type (ST). In addition, the hpEurope (76.5%) and hspWAfrica (23.5%) populations predominated among the paediatric strains. All strains, regardless of their ancestral affiliation, harboured western EPIYA motifs.    Conclusions  This study provides evidence of the evolutionary dynamics of the  H. pylori  strains in two paediatric patients during recrudescence and reinfection events. In particular, our study shows that the strains changed during these events, as evidenced by the presence of different STs that emerged before and after treatment; these changes may be due to the accumulation of mutations and recombination events during the diversification process and recolonization of the patients by different genotypes.    Electronic supplementary material  The online version of this article (10.1186/s12866-019-1554-z) contains supplementary material, which is available to authorized users.

Inference from the analysis of genetic structure of Helicobacter pylori strains isolates from two paediatric patients with recurrent infection