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

被引：79

作者：

Coll, Francesc ^{[1
]}

Mallard, Kim ^{[1
]}

Preston, Mark D. ^{[1
]}

Bentley, Stephen ^{[2
]}

Parkhill, Julian ^{[2
]}

McNerney, Ruth ^{[1
]}

Martin, Nigel ^{[3
]}

Clark, Taane G. ^{[1
]}

机构：

[1] Univ London London Sch Hyg & Trop Med, Fac Infect & Trop Dis, London WC1E 7HT, England

[2] Wellcome Trust Sanger Inst, Hinxton, England

[3] Birkbeck Coll, Dept Comp Sci & Informat Syst, Wellcome Trust Sanger Inst, London, England

来源：

BIOINFORMATICS | 2012年 / 28卷 / 22期

基金：

英国惠康基金;

关键词：

COMPLEX; EPIDEMIOLOGY; BACTERIA; SPACER; LOCUS;

D O I：

10.1093/bioinformatics/bts544

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：2991 / 2993

页数：3

共 9 条

[1]

The use of microbead-based spoligotyping for Mycobacterium tuberculosis complex to evaluate the quality of the conventional method: Providing guidelines for Quality Assurance when working on membranes [J].