ArticleBioinformatics (Oxford, England)2012
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Trial
- Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools.FEMS microbiology reviews · 2025Review
- Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data.Scientific reports · 2023Article
- Genomic changes underpinning the emergence of a successfulFrontiers in microbiology · 2023Article
- Investigating the Diversity of Tuberculosis Spoligotypes with Dimensionality Reduction and Graph Theory.Genes · 2022Article
- Bedaquiline Drug Resistance Emergence Assessment in Multidrug-Resistant Tuberculosis (MDR-TB): a 5-Year ProspectiveJournal of clinical microbiology · 2022Article
- Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid.Scientific reports · 2021Article
- A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods andJournal of clinical microbiology · 2021Article
- CRISPRbuilder-TB: "CRISPR-builder for tuberculosis". Exhaustive reconstruction of the CRISPR locus in mycobacterium tuberculosis complex using SRA.PLoS computational biology · 2021Article
- Genetic Diversity and Potential Paths of Transmission ofFrontiers in veterinary science · 2021Article
- Novel methods included in SpolLineages tool for fast and precise prediction of Mycobacterium tuberculosis complex spoligotype families.Database : the journal of biological databases and curation · 2020Article
- Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies.Genome medicine · 2020Article
- Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis.BMC genomics · 2020Article
- Bacterial and host determinants of cough aerosol culture positivity in patients with drug-resistant versus drug-susceptible tuberculosis.Nature medicine · 2020Article
- Review
- A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic.BMC medicine · 2020Article
- Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome.Genome biology and evolution · 2020Article
- Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan.Scientific reports · 2019Article
- Mycobacterium tuberculosis whole genome sequencing provides insights into the Manila strain and drug-resistance mutations in the Philippines.Scientific reports · 2019Article
- Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summarySpoligotyping 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. AVAILABILITY AND IMPLEMENTATION: SpolPred is written in C and is available from www.pathogenseq.org/spolpred. CONTACT: francesc.coll@lshtm.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
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