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SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
<span title="2012-09-26">2012</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a>
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TG (2012) SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. Bioinformatics (Oxford, England), 28 (22). pp. ...
To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. ...
INTRODUCTION Tuberculosis is an infectious disease caused by bacterium of the Mycobacterium tuberculosis (Mtb) complex. ...
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SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
<span title="2016-02-17">2016</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a>
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SpoTyping is a fast and accurate program for in silico spoligotyping of Mycobacterium tuberculosis isolates from nextgeneration sequencing reads. ...
This novel method achieves high accuracy for reads of both uniform and varying lengths, and is about 20 to 40 times faster than SpolPred. ...
and Beijing genotype Mtb isolates, and Christopher Wong, Min Gong, and Hui-Maan Seah from Genome Institute of Singapore for the whole genome sequencing of both H37Ra and Beijing genotype Mtb isolates. ...
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Spoligotyping and whole-genome sequencing analysis of lineage 1 strains of Mycobacterium tuberculosis in Da Nang, Vietnam
<span title="2017-10-19">2017</span>
<i title="Public Library of Science (PLoS)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a>
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Objectives We investigated the genomic features of Vietnamese lineage 1 strains, comparing spoligotype patterns using whole-genome sequencing (WGS) data. ...
De novo assembly of the entire DR region and in silico spoligotyping analysis suggested the absence of spacer 26, and direct sequencing revealed that the 17 th spacer sequence not used for conventional ...
Acknowledgments The authors would like to thank Akiko Miyabayashi and Keiko Wakabayashi (The Research Institute of Tuberculosis, JATA), Nguyen Thi Kieu Diem and Nguyen Thi Thanh Yen (Da Nang Lung Hospital ...
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A robust SNP barcode for typing Mycobacterium tuberculosis complex strains
<span title="2014-09-01">2014</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a>
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Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug ...
We identify B92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. ...
We also thank the tuberculosis research community, including the Wellcome Trust Sanger Institute and other sequencing centres, for making whole-genome data available in the public domain. ...
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In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer
<span title="2016-11-02">2016</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a>
</i>
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Whole-genome sequencing is increasingly used in clinical diagnosis of tuberculosis and study of Mycobacterium tuberculosis complex (MTC). ...
Conclusions: RD-Analyzer is a useful and accurate tool for species, lineage and sublineage prediction using known RDs of MTC from sequence reads and is extendable to accepting user-defined RDs for analysis ...
Mycobacterium tuberculosis complex (MTC) is the causal agent of TB, which comprises of several genetically homogenous mycobacteria species including human-adapted pathogens of Mycobacterium tuberculosis ...
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Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis
[article]
<span title="2019-12-13">2019</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes.We set up tailored ...
AbstractDiversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. ...
Acknowledgements Laura Morel, Valentin Pohyer, Matthieu Petrou, three previous undergraduates students who contribute to the start of the MTC CRISPR genome project are warmly acknowledged ...
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The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology
[article]
<span title="2018-04-16">2018</span>
<i title="Cold Spring Harbor Laboratory">
bioRxiv
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Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. ...
Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated. ...
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis 569 spoligotypes from short genomic sequences. ...
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Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies
<span title="2020-12-14">2020</span>
<i title="Springer Science and Business Media LLC">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a>
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Methods To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. ...
Background Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. ...
Acknowledgements The MRC eMedLab computing resource was used for bioinformatics and statistical analysis. ...
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Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study
<span title="2016-10-04">2016</span>
<i title="Public Library of Science (PLoS)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iznnn644szdwva7khyxqzc73bi" style="color: black;">PLoS Medicine</a>
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of isolating single colonies prior to sequencing is likely to lead to an overestimation of the number of SNPs between cases resulting from direct transmission; and (5) despite appreciable genomic diversity ...
The aim of this study was to investigate the power and value of whole genome sequencing (WGS) to resolve the transmission network compared to current molecular strain typing approaches, including analysis ...
Stone and Simon Warwick for VNTR-typing and Vladyslav Nikolayevskyy for spoligotyping. ...
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A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics
<span title="2015-03-25">2015</span>
<i title="American Society for Microbiology">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qhog6viejbhxzp457e5gjyus74" style="color: black;">Clinical Microbiology Reviews</a>
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ACKNOWLEDGMENTS We thank the British Columbia Centre for Disease Control Foundation, Genome British Columbia, and the British Columbia Lung Association for their support of our TB genomics research. ...
SpolPred calculates a spoligotyping pattern directly from short-read sequencing data (82) , and as sequencing platforms improve and are able to handle longer repetitive regions, generating in silico MIRU-VNTR ...
The rapid and accurate clinical laboratory diagnosis and characterization of M. tuberculosis are pivotal to battling TB (7) . ...
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Genomic Analysis of Mycobacterium tuberculosis Isolates and Construction of a Beijing Lineage Reference Genome
<span title="2020-02-01">2020</span>
<i title="Oxford University Press (OUP)">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/c3tk2qca4vdq5htca2effydqim" style="color: black;">Genome Biology and Evolution</a>
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rapid evolution of M. tuberculosis. ...
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis, kills over 1 million people worldwide annually. ...
Acknowledgments All the library construction and next-generation sequencing experiments were carried out by the High Throughput Genomics Core Facility of the Biodiversity Research Center in Academia Sinica ...
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Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance
<span title="2016-03-23">2016</span>
<i title="Springer Nature">
<a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ycxb7r3c2zg4jejs6bezyrefhe" style="color: black;">BMC Medicine</a>
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Methods: To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical ...
A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. ...
However, the direct sequencing of M. tuberculosis from sputum from suspected drug resistant patients [58] and the development of rapid strain profiling tools, suggests that culture-free approaches have ...
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