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

Francesc Coll, Kim Mallard, Mark D. Preston, Stephen Bentley, Julian Parkhill, Ruth McNerney, Nigel Martin, Taane G. Clark
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts544">doi:10.1093/bioinformatics/bts544</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23014632">pmid:23014632</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3496340/">pmcid:PMC3496340</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/idhagogi2bfobbbbzg5uxr6sju">fatcat:idhagogi2bfobbbbzg5uxr6sju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721232936/http://researchonline.lshtm.ac.uk/375662/1/bts544.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/ec/90ecd9972bdbbab64031b661e445dd0965c98b10.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts544"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496340" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads

Eryu Xia, Yik-Ying Teo, Rick Twee-Hee Ong
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-016-0270-7">doi:10.1186/s13073-016-0270-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26883915">pmid:26883915</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4756441/">pmcid:PMC4756441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q6wz7q772vfxpmcyrz4keyd5za">fatcat:q6wz7q772vfxpmcyrz4keyd5za</a> </span>
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Spoligotyping and whole-genome sequencing analysis of lineage 1 strains of Mycobacterium tuberculosis in Da Nang, Vietnam

Minako Hijikata, Naoto Keicho, Le Van Duc, Shinji Maeda, Nguyen Thi Le Hang, Ikumi Matsushita, Seiya Kato, Igor Mokrousov
<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> </i> &nbsp;
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0186800">doi:10.1371/journal.pone.0186800</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29049400">pmid:29049400</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5648229/">pmcid:PMC5648229</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kzoqymz22neo7plooihmsallly">fatcat:kzoqymz22neo7plooihmsallly</a> </span>
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A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Francesc Coll, Ruth McNerney, José Afonso Guerra-Assunção, Judith R. Glynn, João Perdigão, Miguel Viveiros, Isabel Portugal, Arnab Pain, Nigel Martin, Taane G. Clark
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms5812">doi:10.1038/ncomms5812</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25176035">pmid:25176035</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4166679/">pmcid:PMC4166679</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m4eqgignjrbv7ngv7c4gmwwora">fatcat:m4eqgignjrbv7ngv7c4gmwwora</a> </span>
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In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer

Kiatichai Faksri, Eryu Xia, Jun Hao Tan, Yik-Ying Teo, Rick Twee-Hee Ong
<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> &nbsp;
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-016-3213-1">doi:10.1186/s12864-016-3213-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27806686">pmid:27806686</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5093977/">pmcid:PMC5093977</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uv2hzir4qbgjfenmcvdms3ihcm">fatcat:uv2hzir4qbgjfenmcvdms3ihcm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171009035758/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/12c/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEyODY0LTAxNi0zMjEzLTEucGRm.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/05/c805b2515fc10c53fea0c2512afbf56bcb9b5e2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12864-016-3213-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093977" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis [article]

Guislaine Refrégier, Christophe Sola, Christophe Guyeux
<span title="2019-12-13">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2019.12.13.875765">doi:10.1101/2019.12.13.875765</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ism6fr4ldzgk5caays7ym7za5i">fatcat:ism6fr4ldzgk5caays7ym7za5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324130600/https://www.biorxiv.org/content/biorxiv/early/2019/12/13/2019.12.13.875765.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/57/01573c4ed3078d685a33b5709c93aa9c9f877dd0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2019.12.13.875765"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology [article]

Conor J Meehan, Pieter Moris, Thomas A Kohl, Julija Pecerska, Suriya Akter, Matthias Merker, Christian Utpatel, Patrick Beckert, Florian Gehre, Pauline Lempens, Tanja Stadler, Michel K Kaswa (+3 others)
<span title="2018-04-16">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/302232">doi:10.1101/302232</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sfnfrgnxivfuphoo7g65kznwje">fatcat:sfnfrgnxivfuphoo7g65kznwje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723184332/https://www.biorxiv.org/content/biorxiv/early/2018/04/19/302232.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c9/47/c947fcc45c6d07b3b56b7d8aacd89411f68de3f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/302232"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies

Gary Napier, Susana Campino, Yared Merid, Markos Abebe, Yimtubezinash Woldeamanuel, Abraham Aseffa, Martin L. Hibberd, Jody Phelan, Taane G. Clark
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-020-00817-3">doi:10.1186/s13073-020-00817-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33317631">pmid:33317631</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/66626q65x5gfbemuwrdqhaqocm">fatcat:66626q65x5gfbemuwrdqhaqocm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201218071942/https://genomemedicine.biomedcentral.com/track/pdf/10.1186/s13073-020-00817-3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d9/22/d922d0b67c70578e674762ff7b430b881c82aae7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-020-00817-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study

Nicola Casali, Agnieszka Broda, Simon R. Harris, Julian Parkhill, Timothy Brown, Francis Drobniewski, John Z Metcalfe
<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> </i> &nbsp;
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.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pmed.1002137">doi:10.1371/journal.pmed.1002137</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27701423">pmid:27701423</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5049847/">pmcid:PMC5049847</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2hmnnsxxsjeeddvq4zmsyf6dei">fatcat:2hmnnsxxsjeeddvq4zmsyf6dei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015000807/http://journals.plos.org/plosmedicine/article/file?id=10.1371/journal.pmed.1002137&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b5/15/b515e7509579f059709b6b881bfd6c26d471229b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pmed.1002137"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049847" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

Marta Wlodarska, James C. Johnston, Jennifer L. Gardy, Patrick Tang
<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> </i> &nbsp;
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) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/cmr.00124-14">doi:10.1128/cmr.00124-14</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25810419">pmid:25810419</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4402953/">pmcid:PMC4402953</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sijvfyhtczfnfeb7mglyrvheoi">fatcat:sijvfyhtczfnfeb7mglyrvheoi</a> </span>
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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> </i> &nbsp;
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

Jody Phelan, Francesc Coll, Ruth McNerney, David B. Ascher, Douglas E. V. Pires, Nick Furnham, Nele Coeck, Grant A. Hill-Cawthorne, Mridul B. Nair, Kim Mallard, Andrew Ramsay, Susana Campino (+4 others)
<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> </i> &nbsp;
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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