title: 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.
abstract: 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.
authors.affiliation: Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan ; Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Amjad
authors.initials: A
authors.lastname: Ali
authors.affiliation: Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan.
authors.forename: Anam
authors.initials: A
authors.lastname: Naz
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Siomar C
authors.initials: SC
authors.lastname: Soares
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil ; Department of Bioinformatics, Mohammad Ali Jinnah University (MAJU), Sehala Road, Islamabad 44000, Pakistan.
authors.forename: Marriam
authors.initials: M
authors.lastname: Bakhtiar
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Sandeep
authors.initials: S
authors.lastname: Tiwari
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Syed S
authors.initials: SS
authors.lastname: Hassan
authors.affiliation: KIMS, Khyber Medical University, Peshawar 25000, Pakistan.
authors.forename: Fazal
authors.initials: F
authors.lastname: Hanan
authors.affiliation: Federal University of Pará, 66075-110 Belém, PA, Brazil.
authors.forename: Rommel
authors.initials: R
authors.lastname: Ramos
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil ; Laboratory of Aquatic Animal Diseases (AQUAVET), Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Ulisses
authors.initials: U
authors.lastname: Pereira
authors.affiliation: Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal 721172, India.
authors.forename: Debmalya
authors.initials: D
authors.lastname: Barh
authors.affiliation: Laboratory of Aquatic Animal Diseases (AQUAVET), Department of Preventive Veterinary Medicine, Federal University of Minas Gerais, 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Henrique César Pereira
authors.initials: HC
authors.lastname: Figueiredo
authors.affiliation: Centre for Biological Sequence Analysis (CBS), Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Anderson
authors.initials: A
authors.lastname: Miyoshi
authors.affiliation: Federal University of Pará, 66075-110 Belém, PA, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais (UFMG), 31907-270 Belo Horizonte, MG, Brazil.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics*; D023281:Genomics / Q000379:methods; D016481:Helicobacter Infections / Q000382:microbiology / Q000473:pathology; D016480:Helicobacter pylori / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D013270:Stomach / Q000382:microbiology* / Q000473:pathology; D013274:Stomach Neoplasms / Q000382:microbiology / Q000473:pathology; D014774:Virulence / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial