GWAMAR: Genome-wide assessment of mutations associated with drug resistance in bacteriaReport as inadecuate




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BMC Genomics

, 15:S10

First Online: 12 December 2014DOI: 10.1186-1471-2164-15-S10-S10

Cite this article as: Wozniak, M., Tiuryn, J. & Wong, L. BMC Genomics 2014 15Suppl 10: S10. doi:10.1186-1471-2164-15-S10-S10

Abstract

BackgroundDevelopment of drug resistance in bacteria causes antibiotic therapies to be less effective and more costly. Moreover, our understanding of the process remains incomplete. One promising approach to improve our understanding of how resistance is being acquired is to use whole-genome comparative approaches for detection of drug resistance-associated mutations.

ResultsWe present GWAMAR, a tool we have developed for detecting of drug resistance-associated mutations in bacteria through comparative analysis of whole-genome sequences. The pipeline of GWAMAR comprises several steps. First, for a set of closely related bacterial genomes, it employs eCAMBer to identify homologous gene families. Second, based on multiple alignments of the gene families, it identifies mutations among the strains of interest. Third, it calculates several statistics to identify which mutations are the most associated with drug resistance.

ConclusionsBased on our analysis of two large datasets retrieved from publicly available data for M. tuberculosis, we identified a set of novel putative drug resistance-associated mutations. As a part of this work, we present also an application of our tool to detect putative compensatory mutations.

Keywordsdrug resistance bacteria Mycobacterium tuberculosis comparative genomics compensatory mutations Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-S10-S10 contains supplementary material, which is available to authorized users.

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Author: Michal Wozniak - Jerzy Tiuryn - Limsoon Wong

Source: https://link.springer.com/



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