Genomic analysis of Helicobacter pylori from Andhra Pradesh, South India: Molecular evidence for three major genetic clusters

Abstract

Earlier analyses of a very few selected gene loci of the gastric pathogen Helicobacter pylori indicated that different genotypes predominate in different human populations. This interpretation was tested and extended by whole genome fingerprinting and genotyping of fluorescent amplified-fragment length polymorphisms (FAFLP) of H. pylori isolates from Andhra Pradesh. Highly reproducible FAFLP profiles derived from EcoRI/MseI restricted fragments revealed more or less similar genotype for 70 independent isolates with sufficient clonal groupings. These genotypes were however distinct from the European strains (H. pylori J99 and H. pylori 26695) and the reference strain NCTC 11637. We were able to genotype the isolates based on differential amplification of a total of 31 genomic loci representing important genes involved in molecular pathogenicity, adhesion/motility, toxicity/ chemotaxis, DNA replication, translation and metabolism. Phylogenetic analyses revealed major affinities among the isolates and separated them as three different strain groups. This suggests colonization by at least three dominant strain types without much evidence for genetic recombination.