title: Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution.
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.
authors.affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India.
authors.forename: Narender
authors.initials: N
authors.lastname: Kumar
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Vanitha
authors.initials: V
authors.lastname: Mariappan
authors.affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India.
authors.forename: Ramani
authors.initials: R
authors.lastname: Baddam
authors.affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India.
authors.forename: Aditya K
authors.initials: AK
authors.lastname: Lankapalli
authors.affiliation: Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Gachibowli, Hyderabad, 500046, India.
authors.forename: Sabiha
authors.initials: S
authors.lastname: Shaik
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Khean-Lee
authors.initials: KL
authors.lastname: Goh
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Mun Fai
authors.initials: MF
authors.lastname: Loke
authors.affiliation: School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia.
authors.forename: Tim
authors.initials: T
authors.lastname: Perkins
authors.affiliation: School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Benghezal
authors.affiliation: Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
authors.forename: Seyed E
authors.initials: SE
authors.lastname: Hasnain
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
authors.forename: Jamuna
authors.initials: J
authors.lastname: Vadivelu
authors.affiliation: School of Pathology and Laboratory Medicine, University of Western Australia, Nedlands 6009, Western Australia, Australia.
authors.forename: Barry J
authors.initials: BJ
authors.lastname: Marshall
authors.affiliation: 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.
authors.forename: Niyaz
authors.initials: N
authors.lastname: Ahmed
mesh_terms: D015280:DNA Restriction-Modification Enzymes / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics; D016480:Helicobacter pylori / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D006801:Humans; D008296:Malaysia; D010802:Phylogeny; D058974:Phylogeography; D014774:Virulence
chemical_list: D015280:DNA Restriction-Modification Enzymes