{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T16:27:34Z","timestamp":1784824054863,"version":"3.55.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,7,27]],"date-time":"2022-07-27T00:00:00Z","timestamp":1658880000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Newton Institutional Links","award":["261868591"],"award-info":[{"award-number":["261868591"]}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/M01360X\/1"],"award-info":[{"award-number":["MR\/M01360X\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/N010469\/1"],"award-info":[{"award-number":["MR\/N010469\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/R025576\/1"],"award-info":[{"award-number":["MR\/R025576\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/R020973\/1"],"award-info":[{"award-number":["MR\/R020973\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/M01360X\/1"],"award-info":[{"award-number":["MR\/M01360X\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/R025576\/1"],"award-info":[{"award-number":["MR\/R025576\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council UK","doi-asserted-by":"crossref","award":["MR\/R020973\/1"],"award-info":[{"award-number":["MR\/R020973\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/R013063\/1"],"award-info":[{"award-number":["BB\/R013063\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>With &amp;gt;1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe\/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.<\/jats:p>","DOI":"10.1093\/bib\/bbac256","type":"journal-article","created":{"date-parts":[[2022,7,27]],"date-time":"2022-07-27T12:53:27Z","timestamp":1658926407000},"source":"Crossref","is-referenced-by-count":26,"title":["Portable sequencing of <i>Mycobacterium tuberculosis<\/i> for clinical and epidemiological applications"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3670-8786","authenticated-orcid":false,"given":"Paula J","family":"G\u00f3mez-Gonz\u00e1lez","sequence":"first","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine , WC1E 7HT London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1403-6138","authenticated-orcid":false,"given":"Susana","family":"Campino","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine , WC1E 7HT London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody E","family":"Phelan","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine , WC1E 7HT London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-9265","authenticated-orcid":false,"given":"Taane G","family":"Clark","sequence":"additional","affiliation":[{"name":"Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine , WC1E 7HT London, UK"},{"name":"Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine , WC1E 7HT London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,7,27]]},"reference":[{"key":"2022092013212419300_ref1","volume-title":"Global tuberculosis report, 2021","author":"World Health Organization (WHO)","year":"2021"},{"key":"2022092013212419300_ref2","doi-asserted-by":"crossref","first-page":"784","DOI":"10.1038\/ng.2656","article-title":"Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis","volume":"45","author":"Ford","year":"2013","journal-title":"Nat Genet"},{"key":"2022092013212419300_ref3","doi-asserted-by":"crossref","first-page":"e00250","DOI":"10.1128\/mBio.00250-13","article-title":"Clade-specific virulence patterns of Mycobacterium tuberculosis complex strains in human primary macrophages and aerogenically infected mice","volume":"4","author":"Reiling","year":"2013","journal-title":"mBio"},{"key":"2022092013212419300_ref4","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.smim.2014.09.012","article-title":"Consequences of genomic diversity in Mycobacterium tuberculosis","volume":"26","author":"Coscolla","year":"2014","journal-title":"Semin Immunol"},{"key":"2022092013212419300_ref5","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/s41588-017-0029-0","article-title":"Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis","volume":"50","author":"Coll","year":"2018","journal-title":"Nat Genet"},{"key":"2022092013212419300_ref6","doi-asserted-by":"crossref","first-page":"dkw502","DOI":"10.1093\/jac\/dkw502","article-title":"Unexpected high prevalence of resistance-associated Rv0678 variants in MDR-TB patients without documented prior use of clofazimine or bedaquiline","volume":"72","author":"Villellas","year":"2016","journal-title":"J Antimicrob Chemother"},{"key":"2022092013212419300_ref7","doi-asserted-by":"crossref","first-page":"e000361","DOI":"10.1099\/mgen.0.000361","article-title":"Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants","volume":"6","author":"Sobkowiak","year":"2020","journal-title":"Microb Genomics."},{"key":"2022092013212419300_ref8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/JCM.00666-18","article-title":"Direct whole-genome sequencing of sputum accurately identifies drug-resistant mycobacterium tuberculosis faster than MGIT culture sequencing","volume":"56","author":"Doyle","year":"2018","journal-title":"J Clin Microbiol"},{"key":"2022092013212419300_ref9","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s13073-015-0164-0","article-title":"Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences","volume":"7","author":"Coll","year":"2015","journal-title":"Genome Med"},{"key":"2022092013212419300_ref10","doi-asserted-by":"crossref","first-page":"19431","DOI":"10.1038\/s41598-021-98862-4","article-title":"Genetic diversity of candidate loci linked to Mycobacterium tuberculosis resistance to bedaquiline, delamanid and pretomanid","volume":"11","author":"G\u00f3mez-Gonz\u00e1lez","year":"2021","journal-title":"Sci Rep"},{"key":"2022092013212419300_ref11","doi-asserted-by":"crossref","first-page":"4812","DOI":"10.1038\/ncomms5812","article-title":"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains","volume":"5","author":"Coll","year":"2014","journal-title":"Nat Commun"},{"key":"2022092013212419300_ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.05166","article-title":"Large-scale whole genome sequencing of M. tuberculosis provides insights into transmission in a high prevalence area","volume":"4","author":"Guerra-Assun\u00e7\u00e3o","year":"2015","journal-title":"Elife"},{"key":"2022092013212419300_ref13","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/s13073-019-0650-x","article-title":"Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs","volume":"11","author":"Phelan","year":"2019","journal-title":"Genome Med"},{"key":"2022092013212419300_ref14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13073-021-00934-7","article-title":"An implementation science approach to evaluating pathogen whole genome sequencing in public health","volume":"13","author":"Ferdinand","year":"2021","journal-title":"Genome Med"},{"key":"2022092013212419300_ref15","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13073-016-0385-x","article-title":"The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs","volume":"8","author":"Phelan","year":"2016","journal-title":"Genome Med"},{"key":"2022092013212419300_ref16","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1186\/s12864-016-2467-y","article-title":"Recombination in pe\/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages","volume":"17","author":"Phelan","year":"2016","journal-title":"BMC Genomics"},{"key":"2022092013212419300_ref17","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/s41579-019-0214-5","article-title":"Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues","volume":"17","author":"Meehan","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2022092013212419300_ref18","first-page":"mgen000465","article-title":"Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases. Microb","volume":"7","author":"Modlin","year":"2021","journal-title":"Genom"},{"key":"2022092013212419300_ref19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-41692-2","article-title":"An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome","volume":"9","author":"Gomez-Gonzalez","year":"2019","journal-title":"Sci Rep"},{"key":"2022092013212419300_ref20","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1186\/s12864-017-3687-5","article-title":"SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis","volume":"18","author":"Elghraoui","year":"2017","journal-title":"BMC Genomics"},{"key":"2022092013212419300_ref21","first-page":"e000188","article-title":"A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE\/PPE gene regions","volume":"4","author":"Bainomugisa","year":"2018","journal-title":"Microb Genom"},{"key":"2022092013212419300_ref22","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1093\/bioinformatics\/btac023","article-title":"Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome","volume":"38","author":"Marin","year":"2022","journal-title":"Bioinformatics"},{"key":"2022092013212419300_ref23","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1128\/JCM.02483-16","article-title":"Same-day diagnostic and surveillance data for tuberculosis via whole-genome sequencing of direct respiratory samples","volume":"55","author":"Votintseva","year":"2017","journal-title":"J Clin Microbiol"},{"key":"2022092013212419300_ref24","first-page":"143","volume-title":"Advances in Experimental Medicine and Biology","author":"Runtuwene","year":"2019"},{"key":"2022092013212419300_ref25","doi-asserted-by":"crossref","first-page":"000740","DOI":"10.1099\/mgen.0.000740","article-title":"Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance- associated genes","volume":"7","author":"Mariner-Llicer","year":"2021","journal-title":"Microb Genomics"},{"key":"2022092013212419300_ref26","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1093\/clinchem\/hvaa092","article-title":"Targeted-sequencing workflows for comprehensive drug resistance profiling of mycobacterium tuberculosis cultures using two commercial sequencing platforms: comparison of analytical and diagnostic performance, turnaround time, and cost","volume":"66","author":"Tafess","year":"2020","journal-title":"Clin Chem"},{"key":"2022092013212419300_ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13104-020-05287-9","article-title":"Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of mycobacterium tuberculosis","volume":"13","author":"Chan","year":"2020","journal-title":"BMC Res Notes"},{"key":"2022092013212419300_ref28","first-page":"1","article-title":"Assessing nanopore sequencing for clinical diagnostics: a comparison of next-generation sequencing (NGS) methods for Mycobacterium tuberculosis","volume":"59","author":"Smith","year":"2021","journal-title":"J Clin Microbiol"},{"key":"2022092013212419300_ref29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/Spectrum.00610-21","article-title":"A rapid drug resistance genotyping workflow for Mycobacterium tuberculosis, using targeted isothermal amplification and Nanopore sequencing","volume":"9","author":"Gliddon","year":"2021","journal-title":"Microbiol Spectr"},{"key":"2022092013212419300_ref30","doi-asserted-by":"crossref","first-page":"2996","DOI":"10.1128\/JCM.43.6.2996-2997.2005","article-title":"Extraction of Mycobacterium tuberculosis DNA: a question of containment","volume":"43","author":"Somerville","year":"2005","journal-title":"J Clin Microbiol"},{"key":"2022092013212419300_ref31","first-page":"100011","article-title":"Fast-bonito: a faster deep learning based basecaller for nanopore sequencing","volume":"1","author":"Xu","year":"2021","journal-title":"Artif Intell Life Sci"},{"key":"2022092013212419300_ref32","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2022092013212419300_ref33","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2022092013212419300_ref34","first-page":"1","article-title":"Haplotype-based variant detection from short-read sequencing","author":"Garrison","year":"2012","journal-title":"arXiv: Genomics"},{"key":"2022092013212419300_ref35","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1093\/bioinformatics\/bts378","article-title":"DELLY: structural variant discovery by integrated paired-end and split-read analysis","volume":"28","author":"Rausch","year":"2012","journal-title":"Bioinformatics"},{"key":"2022092013212419300_ref36","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac256\/45937263\/bbac256.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac256\/45937263\/bbac256.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T17:42:23Z","timestamp":1663695743000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac256\/6650479"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,27]]},"references-count":36,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac256","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,9]]},"published":{"date-parts":[[2022,7,27]]},"article-number":"bbac256"}}