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Open Access Highly Accessed Database

MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis

Jean-Pierre Flandrois1*, Gérard Lina23 and Oana Dumitrescu23

Author Affiliations

1 Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Claude Bernard – Lyon 1, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France

2 CIRI, International Center for Infectiology Research, LabEx Ecofect, Université Lyon1; Inserm, U1111, Ecole Normale Supérieure de Lyon; CNRS, UMR5308, 69000 Lyon, France

3 Hospices Civils de Lyon, 69002 Lyon, France

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BMC Bioinformatics 2014, 15:107  doi:10.1186/1471-2105-15-107

Published: 14 April 2014

Abstract

Background

Tuberculosis is an infectious bacterial disease caused by Mycobacterium tuberculosis. It remains a major health threat, killing over one million people every year worldwide. An early antibiotic therapy is the basis of the treatment, and the emergence and spread of multidrug and extensively drug-resistant mutant strains raise significant challenges. As these bacteria grow very slowly, drug resistance mutations are currently detected using molecular biology techniques. Resistance mutations are identified by sequencing the resistance-linked genes followed by a comparison with the literature data. The only online database is the TB Drug Resistance Mutation database (TBDReaM database); however, it requires mutation detection before use, and its interrogation is complex due to its loose syntax and grammar.

Description

The MUBII-TB-DB database is a simple, highly structured text-based database that contains a set of Mycobacterium tuberculosis mutations (DNA and proteins) occurring at seven loci: rpoB, pncA, katG; mabA(fabG1)-inhA, gyrA, gyrB, and rrs. Resistance mutation data were extracted after the systematic review of MEDLINE referenced publications before March 2013. MUBII analyzes the query sequence obtained by PCR-sequencing using two parallel strategies: i) a BLAST search against a set of previously reconstructed mutated sequences and ii) the alignment of the query sequences (DNA and its protein translation) with the wild-type sequences. The post-treatment includes the extraction of the aligned sequences together with their descriptors (position and nature of mutations). The whole procedure is performed using the internet. The results are graphs (alignments) and text (description of the mutation, therapeutic significance). The system is quick and easy to use, even for technicians without bioinformatics training.

Conclusion

MUBII-TB-DB is a structured database of the mutations occurring at seven loci of major therapeutic value in tuberculosis management. Moreover, the system provides interpretation of the mutations in biological and therapeutic terms and can evolve by the addition of newly described mutations. Its goal is to provide easy and comprehensive access through a client–server model over the Web to an up-to-date database of mutations that lead to the resistance of M. tuberculosis to antibiotics.

Keywords:
Tuberculosis; Antibiotics; Mutation database; Sequence database; Web