What constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics.
BACKGROUND
Helicobacter pylori, the human gastric pathogen, causes a variety of gastric diseases ranging from mild gastritis to gastric cancer. While the studies on H. pylori are dominated by those based on either East Asian or Western strains, information regarding H. pylori strains prevalent in the Middle East remains scarce. Therefore, we carried out whole-genome sequencing and comparative analysis of three H. pylori strains isolated from three native Arab, Kuwaiti patients.


METHODS
H. pylori strains were sequenced using Illumina platform. The sequence reads were filtered and draft genomes were assembled and annotated. Various pathogenicity-associated regions and phages present within the genomes were identified. Phylogenetic analysis was carried out to determine the genetic relatedness of Kuwaiti strains to various lineages of H. pylori. The core genome content and virulence-related genes were analyzed to assess the pathogenic potential.


RESULTS
The three genomes clustered along with HpEurope strains in the phylogenetic tree comprising various H. pylori lineages. A total of 1187 genes spread among various functional classes were identified in the core genome analysis. The three genomes possessed a complete cagPAI and also retained most of the known outer membrane proteins as well as virulence-related genes. The cagA gene in all three strains consisted of an AB-C type EPIYA motif.


CONCLUSIONS
The comparative genomic analysis of Kuwaiti H. pylori strains revealed a European ancestry and a high pathogenic potential.
Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana, India.
Narender
N
Kumar
Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait.
M John
MJ
Albert
Department of Microbiology, Faculty of Medicine, Kuwait University, Jabriya, Kuwait.
Hanan
H
Al Abkal
Department of Medicine, Faculty of Medicine, Kuwait University, Jabriya, Kuwait.
Iqbal
I
Siddique
Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, Telangana, India.
Niyaz
N
Ahmed
D000328:Adult; D000368:Aged; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D016481:Helicobacter Infections / Q000453:epidemiology / Q000382:microbiology*; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007730:Kuwait / Q000453:epidemiology; D008297:Male; D017720:Molecular Epidemiology; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics; D055815:Young Adult
D037521:Virulence Factors

Helicobacter pylori
; genome sequencing; outer membrane proteins; phylogeny; virulence