Department of Biotechnology and Bioinformatics

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Browsing Department of Biotechnology and Bioinformatics by Author "Ahmad, Naheed"
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    Comparing genomes of Helicobacter pylori strains from the high-altitude desert of Ladakh, India
    ( 2005-04-01) Kauser, Farhana ; Abid Hussain, M. ; Ahmed, Irshad ; Ahmad, Naheed ; Habeeb, Aejaz ; Khan, Aleem A. ; Ahmed, Niyaz
    The genomic diversity of Helicobacter pylori from the vast Indian subcontinent is largely unknown. We compared the genomes of 10 H. pylori strains from Ladakh, North India. Molecular analysis was carried out to identify rearrangements within and outside the cag pathogenicity island (cag PAI) and DNA sequence divergence in candidate genes. Analyses of virulence genes (such as the cag PAI as a whole, cagA, vacA, iceA, oipA, babB, and the plasticity cluster) revealed that H. pylori strains from Ladakh are genetically distinct and possibly less virulent than the isolates from East Asian countries, such as China and Japan. Phylogenetic analyses based on the cagA-glr motifs, enterobacterial repetitive intergenic consensus patterns, repetitive extragenic palindromic signatures, the glmM gene mutations, and several genomic markers representing fluorescent amplified fragment length polymorphisms revealed that Ladakhi strains share features of the Indo-European, as well as the East Asian, gene pools. However, the contribution of genetic features from the Indo-European gene pool was more prominent. Copyright © 2005, American Society for Microbiology. All Rights Reserved.
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    Erratum: Comparing genomes of Helicobacter pylori strains from the high-altitude desert of Ladakh, India (Journal of Clinical Microbiology (2005) 43, 4 (1538-1545))
    ( 2005-07-01) Kauser, Farhana ; Hussain, M. Abid ; Ahmed, Irshad ; Ahmad, Naheed ; Habeeb, Aejaz ; Khan, Aleem A. ; Ahmed, Niyaz
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    The cag pathogenicity island of Helicobacter pylori is disrupted in the majority of patient isolates from different human populations
    ( 2004-11-01) Kauser, Farhana ; Khan, Aleem A. ; Hussain, M. Abid ; Carroll, Ian M. ; Ahmad, Naheed ; Tiwari, Santosh ; Shouche, Yogesh ; Das, Bimal ; Alam, Mahfooz ; Ali, S. Mahaboob ; Habibullah, C. M. ; Sierra, Rafaela ; Megraud, Francis ; Sechi, Leonardo A. ; Ahmed, Niyaz
    The cag pathogenicity island (cag-PAI) is one of the major virulence determinants of Helicobacter pylori. The chromosomal integrity of this island or the lack thereof is speculated to play an important role in the progress of the gastroduodenal pathology caused by H. pylori. We determined the integrity of the cag-PAI by using specific flanking and internally anchored PCR primers to know the biogeographical distribution of strains carrying fully integral cag-PAI with proinflammatory behavior in vivo. Genotypes based on eight selected loci were studied in 335 isolates obtained from eight different geographic regions. The cag-PAI appeared to be disrupted in the majority of patient isolates throughout the world. Conservation of cag-PAI was highest in Japanese isolates (57.1%). However, only 18.6% of the Peruvian and 12% of the Indian isolates carried an intact cag-PAI. The integrity of cag-PAI in European and African strains was minimal. All 10 strains from Costa Rica had rearrangements. Overall, a majority of the strains of East Asian ancestry were found to have intact cag-PAI compared to strains of other descent. We also found that the cagE and cagT genes were less often rearranged (18%) than the cagA gene (27%). We attempted to relate cag-PAI rearrangement patterns to disease outcome. Deletion frequencies of cagA, cagE, and cagT genes were higher in benign cases than in isolates from severe ulcers and gastric cancer. Conversely, the cagA promoter and the left end of the cag-PAI were frequently rearranged or deleted in isolates linked to severe pathology. Analysis of the cag-PAI genotypes with a different biogeoclimatic history will contribute to our understanding of the pathogen-host interaction in health and disease.