Progressive genomic convergence of twoHelicobacter pyloristrains during mixed infection of a patient with chronic gastritis

Abstract

ObjectiveTo study the detailed nature of genomic microevolution during mixed infection with multiple Helicobacter pylori strains in an individual.DesignWe sampled 18 isolates from a single biopsy from a patient with chronic gastritis and nephritis. Whole-genome sequencing was applied to these isolates, and statistical genetic tools were used to investigate their evolutionary history.ResultsThe genomes fall into two clades, reflecting colonisation of the stomach by two distinct strains, and these lineages have accumulated diversity during an estimated 2.8 and 4.2 years of evolution. We detected about 150 clear recombination events between the two clades. Recombination between the lineages is a continuous ongoing process and was detected on both clades, but the effect of recombination in one clade was nearly an order of magnitude higher than in the other. Imputed ancestral sequences also showed evidence of recombination between the two strains prior to their diversification, and we estimate that they have both been infecting the same host for at least 12 years. Recombination tracts between the lineages were, on average, 895 bp in length, and showed evidence for the interspersion of recipient sequences that has been observed in in vitro experiments. The complex evolutionary history of a phage-related protein provided evidence for frequent reinfection of both clades by a single phage lineage during the past 4 years.ConclusionsWhole genome sequencing can be used to make detailed conclusions about the mechanisms of genetic change of H. pylori based on sampling bacteria from a single gastric biopsy.

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches

“…For example, while Mycobacterium tuberculosis may accumulate approximately four SNPs per genome per 4 years [4], Helicobacter pylori can exhibit over 30 SNPs per genome per year [5]. Recombination, the exchange of genetic material between bacteria, ranges from rare (M. tuberculosis) [6] to strong enough for large-scale confusion of phylogenetic interrelationships in gene trees (Streptococcus pneumoniae, H. pylori) [7,8]. The causes of variability in genome content are large insertions, deletions, genome rearrangements and transfer of exogenous DNA, and extrachromosomal elements such as plasmids and phages.…”

Peer Review #1 of "Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia (v0.1)"

“…H. pylori is a bacterium that can display very fast local adaptive processes via mutation and recombination (Cao Q et al, 2015;Furuta Y et al, 2015). The phylogenetics, population genetics and protein evolutionary analysis suggest that alpA in Colombia has functionally divergent variants that are the result of gene conversion in a staggeringly short period of time.…”

Rapid evolution of distinctHelicobacter pylorisubpopulations in the Americas

“…11, 2016; from the US. Since it has been shown that H. pylori from the same population (hpEastAsia) can exchange 10% of their genome during a single 4-year mixed infection in human [21], the ancestral pattern in US H. pylori implies barriers to recombination between the two populations. Such barriers may be the result of ethnic segregation and thus less diverse co-infections, of differential uptake or incorporation of DNA from different populations, or of efficient competitive exclusion of bacteria from one population by bacteria from the other within individual stomachs.…”