Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments

Abstract

Objective Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease. Design Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed. Results A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034). Conclusion These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis.

Complete genome sequence of Helicobacter pylori B128 7.13 and a single‐step method for the generation of unmarked mutations

“…Here, we reveal the closed genome sequence of H pylori strain B128 7.13 and a method for generating genomic markerless and scarless isogenic mutants. H pylori B128 7.13 is an important strain for the study of H pylori physiology, both in vitro and in vivo . Consistent with previous reports of H pylori genomes, including the draft genomes of B128 7.13 that were recently published, the B128 7.13 genome size is relatively small (1.67 Mbp) in comparison to other gastrointestinal pathogens, such as E coli and S. Typhimurium, where larger genomes are typically observed (5‐6 Mbp).…”

“…Furthermore, in an independent experiment, B128 was used to infect Mongolian gerbils for a total of three times, and a resulting strain, named B8, was recovered . The genome sequence of B8 has been assembled and this strain is routinely used as a reference genome for investigators interested in the biology of B128 7.13 . Although the draft genome of B128 7.13 has been reported using Illumina sequencing technology, the closed genome of this strain has not been reported.…”

“…The genome sequence of B8 has been assembled and this strain is routinely used as a reference genome for investigators interested in the biology of B128 7.13 . Although the draft genome of B128 7.13 has been reported using Illumina sequencing technology, the closed genome of this strain has not been reported. Given that we sought to confirm the mutations present in our mutagenized B128 7.13 strains on a genome‐wide scale and given the importance of the B128 7.13 strain to the wider research community, we used both the PacBio and Illumina sequencing platforms to determine the closed genome sequence of B128 7.13.…”

Pathogenesis of Helicobacter pylori infection

“…Two studies support a role for genetic variation within the infecting population as a strategy to cope with diverse stresses. One study examined genetic changes that accumulated during gerbil infection with and without high salt diet or iron limitation . A second queried genetic changes during challenge after vaccination with a trivalent vaccine containing VacA, CagA, and NapA or placebo .…”

Acetylation‐mediated Siah2 stabilization enhances PHD3 degradation in Helicobacter pylori‐infected gastric epithelial cancer cells

“…Helicobacter pylori are the most potent causative agents for gastric cancer (1,2). Strains possessing the cytotoxinassociated gene (cag) pathogenicity island (PAI) or cag PAI (+) strains are associated with greater disease severity (3,4) despite its short lifespan in epithelial cells (5).…”