SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.


Coll, F; Mallard, K; Preston, MD; Bentley, S; Parkhill, J; McNerney, R; Martin, N; Clark, TG; (2012) SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics (Oxford, England), 28 (22). pp. 2991-3. ISSN 1367-4803 DOI: https://doi.org/10.1093/bioinformatics/bts544

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Abstract

SUMMARY: Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations.<br/> AVAILABILITY AND IMPLEMENTATION: SpolPred is written in C and is available from www.pathogenseq.org/spolpred.<br/> CONTACT: francesc.coll@lshtm.ac.uk.<br/> SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.<br/>

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Clinical Research
Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology
PubMed ID: 23014632
Web of Science ID: 311303500021
URI: http://researchonline.lshtm.ac.uk/id/eprint/375662

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