Comparing genomes of Helicobacter pylori strains from the high-altitude desert of Ladakh, India

Abstract

The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI as a whole, cagA, vacA, iceA, oipA, babB, and the plasticity cluster) revealed that H. pylori strains from Ladakh are genetically distinct and possibly less virulent than the isolates from East Asian countries, such as China and Japan. Phylogenetic analyses based on the cagA-glr motifs, enterobacterial repetitive intergenic consensus patterns, repetitive extragenic palindromic signatures, the glmM gene mutations, and several genomic markers representing fluorescent amplified fragment length polymorphisms revealed that Ladakhi strains share features of the Indo-European, as well as the East Asian, gene pools. However, the contribution of genetic features from the Indo-European gene pool was more prominent.

FIG. 1.

Genetic rearrangements in Ladakhi strains corresponding to the cag PAI and the region from the extreme right end of the cagA gene to the start of the glutamate racemase (glr) gene. Precise locations of rearrangements have been marked with arrows. LF1, left end of cag PCR product 1; LF2, left end of cag PCR product 2; T, cagT gene; E, cagE gene; APF1, cagA promoter PCR product 1; APF2, cagA promoter PCR product 2; AF1, cagA gene PCR product 1; AF2, cagA gene PCR product 2; Unk1, unknown region 1 as described by Kersulyte et al. (17); RJ, right junction of cagA; glr, glutamate racemase gene.

FIG. 2.

Genomic diversity of H. pylori from Ladakh as revealed by FAFLP-based genotyping (A, B, and C) and polymorphisms within the glmM and babB genes. Part A corresponds to the two-dimensional gel image depicting the number of polymorphic loci that were compared before genetic affinities among Ladakhi, Indian, and Japanese strains were deduced in the form of a phylogenetic tree (C). The Genotyper plot (B) corresponding to FAFLP analysis was developed by the Genescan and Genotyper software (Applied Biosystems). It compares FAFLP allelic profiles of Ladakhi strains with Indo-European and East Asian gene pools. Phylogenetic trees were also deduced based on DNA sequence divergence analyses corresponding to glmM (D) and babB (E) genes.