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Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

Kumar N 1 , Mariappan V 2 , Baddam R 1 , Lankapalli AK 1 , Shaik S 1 , Goh KL 3 Show all authors , Loke MF 2 , Perkins T 4 , Benghezal M 4 , Hasnain SE 5 , Vadivelu J 2 , Marshall BJ 4 , Ahmed N 6

Affiliations 

  • 1 Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
  • 2 Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
  • 3 Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
  • 4 School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia
  • 5 Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
  • 6 Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia niyaz.ahmed@uohyd.ac.in ahmed.nizi@gmail.com
Nucleic Acids Res, 2015 Jan;43(1):324-35.
PMID: 25452339 DOI: 10.1093/nar/gku1271

Abstract

The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host-pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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