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

BMC Bioinformatics

Jean-Pierre Flandrois¹  Gérard Lina²  Oana Dumitrescu² 

[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] Hospices Civils de Lyon, 69002 Lyon, France

关键词: Web;    Sequence database;    Mutation database;    Antibiotics;    Tuberculosis;   

Others  :  818669
DOI  :  10.1186/1471-2105-15-107

 received in 2013-12-09, accepted in 2014-04-07,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Flandrois et al.; licensee BioMed Central Ltd.

【 图 表 】

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