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BioMed Research International
Volume 2015, Article ID 139580, 17 pages
Research Article

Pan-Genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets

1Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
2Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil
3Department of Bioinformatics, Mohammad Ali Jinnah University (MAJU), Sehala Road, Islamabad 44000, Pakistan
4KIMS, Khyber Medical University, Peshawar 25000, Pakistan
5Federal University of Pará, 66075-110 Belém, PA, Brazil
6Laboratory of Aquatic Animal Diseases (AQUAVET), Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, 31907-270 Belo Horizonte, MG, Brazil
7Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172, India
8Centre for Biological Sequence Analysis (CBS), Technical University of Denmark, 2800 Kongens Lyngby, Denmark

Received 3 February 2014; Revised 11 July 2014; Accepted 11 July 2014

Academic Editor: Angel Cataldi

Copyright © 2015 Amjad Ali et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.