Region-specific genomic signatures of multidrug-resistant Helicobacter pylori isolated from East and South India

Helicobacter pylori is a ubiquitous bacterium and contributes significantly to the burden of chronic gastritis, peptic ulcers, and gastric cancer across the world. Adaptive phenotypes and virulence factors in H. pylori are heterogeneous and dynamic. However, limited information is available about the molecular nature of antimi-crobial resistance phenotypes and virulence factors of H. pylori strains circulating in India. In the present study, we analyzed the whole genome sequences of 143 H. pylori strains, of which 32 are isolated from two different regions (eastern and southern) of India. Genomic repertoires of individual strains show distinct region-specific signatures. We observed lower resistance phenotypes and genotypes in the East Indian (Kolkata) H. pylori iso-lates against amoxicillin and furazolidone antibiotics, whereas higher resistance phenotypes to metronidazole and clarithromycin. Also, at molecular level, a greater number of AMR genes were observed in the east Indian H. pylori isolates as compared to the southern Indian isolates. From our findings, we suggest that metronidazole and clarithromycin antibiotics should be used judicially in the eastern India. However, no horizontally acquired antimicrobial resistance gene was observed in the current H. pylori strains. The comparative genome analysis shows that the number of genes involved in virulence, disease and resistance of H. pylori isolated from two different regions of India is significantly different. Single-nucleotide polymorphisms (SNPs) based phylogenetic analysis distinguished H. pylori strains into different clades according to their geographical locations. Condi-tionally beneficial functions including antibiotic resistance phenotypes that are linked with faster evolution rates in the Indian isolates.

Automated summary

This study analyzed the whole genome sequences of 143 Helicobacter pylori strains isolated from different regions of India and found distinct genomic signatures and antimicrobial resistance phenotypes. The strains from Eastern India showed higher resistance to metronidazole and clarithromycin, while lower resistance to amoxicillin and furazolidone. Moreover, more antimicrobial resistance genes were observed in the Eastern Indian strains compared to the Southern Indian strains. The study also revealed phylogenetic differences among the H. pylori strains based on their geographical locations, with conditionally beneficial functions, including antibiotic resistance phenotypes, being linked to faster evolution rates in the Indian isolates.