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Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains

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Abstract

The occurrence of drug resistance in Mycobacterium tuberculosis, the aetiological agent of tuberculosis (TB), is hampering the management and control of TB in the world. Here we present a computational analysis of recently sequenced drug-sensitive (DS), multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of M. tuberculosis. Single-nucleotide variations (SNVs) were identified in a pair-wise manner using the anchor-based whole genome comparison (ABWGC) tool and its modified version. For this analysis, four fully sequenced genomes of different strains of M. tuberculosis were taken along with three KwaZulu-Natal (KZN) strains isolated from South Africa including one XDR and one MDR strain. KZN strains were compared with other fully sequenced strains and also among each other. The variations were analysed with respect to their biological influence as a result of either altered structure or synthesis. The results suggest that the DR phenotype may be due to changes in a number of genes. The database on KZN strains can be accessed through the website http://mirna.jnu.ac.in/mgdd.

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Abbreviations

ABWGC:

anchor-based whole genome comparison

AFLP:

amplified fragment length polymorphism

COG:

Clusters of Orthologous Groups

DS:

drug sensitive

KZN:

KwaZulu-Natal

MDR:

multidrug-resistant

SNV:

single-nucleotide variation

TB:

tuberculosis

XDR:

extensively drug-resistant

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Authors and Affiliations

  1. Center for Computational Biology and Bioinformatics, School of Information Technology, Jawaharlal Nehru University, New Delhi, 110 067, India

    Sarbashis Das, Ragothaman M. Yennamalli, Anchal Vishnoi, Parul Gupta & Alok Bhattacharya

  2. School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110 067, India

    Alok Bhattacharya

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  1. Sarbashis Das
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  2. Ragothaman M. Yennamalli
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  3. Anchal Vishnoi
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  4. Parul Gupta
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  5. Alok Bhattacharya
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Correspondence to Alok Bhattacharya.

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These authors contributed equally to this work.

Supplementary tables pertaining to this article are available on the Journal of Biosciences Website at http://www.ias.ac.in/jbiosci/sept09/pp397-404-suppl.pdf

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Das, S., Yennamalli, R.M., Vishnoi, A. et al. Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains. J Biosci 34, 397–404 (2009). https://doi.org/10.1007/s12038-009-0046-y

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  • DOI: https://doi.org/10.1007/s12038-009-0046-y

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