{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T16:19:17Z","timestamp":1792685957444,"version":"4.5.0"},"reference-count":39,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-025-07705-9","type":"journal-article","created":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T02:12:33Z","timestamp":1739931153000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["TBtypeR: Sensitive detection and sublineage classification of Mycobacterium tuberculosis complex mixed-strain infections"],"prefix":"10.1038","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2751-0989","authenticated-orcid":false,"given":"Jacob E.","family":"Munro","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7086-2621","authenticated-orcid":false,"given":"Anna K.","family":"Coussens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5132-0774","authenticated-orcid":false,"given":"Melanie","family":"Bahlo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,2,19]]},"reference":[{"key":"7705_CR1","unstructured":"World Health Organization. Global Tuberculosis Report 2023 (World Health Organization, 2023)."},{"key":"7705_CR2","first-page":"537","volume":"3","author":"R. W Yeh","year":"1999","unstructured":"Yeh, R. W., Hopewell, P. C. & Daley, C. L. Simultaneous infection with two strains of Mycobacterium tuberculosis identified by restriction fragment length polymorphism analysis. Int. J. Tuberc. Lung Dis. 3, 537\u2013539 (1999).","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"7705_CR3","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1164\/rccm.200305-714OC","volume":"169","author":"R. M Warren","year":"2004","unstructured":"Warren, R. M. et al. Patients with active tuberculosis often have different strains in the same sputum specimen. Am. J. Respir. Crit. Care Med. 169, 610\u2013614 (2004).","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"7705_CR4","doi-asserted-by":"publisher","first-page":"469","DOI":"10.1016\/j.tube.2008.02.002","volume":"88","author":"R Fang","year":"2008","unstructured":"Fang, R. et al. Mixed infections of Mycobacterium tuberculosis in tuberculosis patients in Shanghai, China. Tuberculosis 88, 469\u2013473 (2008).","journal-title":"Tuberculosis"},{"key":"7705_CR5","doi-asserted-by":"publisher","first-page":"4512","DOI":"10.1128\/JCM.01683-10","volume":"48","author":"K Mallard","year":"2010","unstructured":"Mallard, K. et al. Molecular detection of mixed infections of Mycobacterium tuberculosis strains in sputum samples from patients in Karonga District, Malawi. J. Clin. Microbiol. 48, 4512\u20134518 (2010).","journal-title":"J. Clin. Microbiol."},{"key":"7705_CR6","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1128\/CMR.00021-12","volume":"25","author":"T Cohen","year":"2012","unstructured":"Cohen, T. et al. Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clin. Microbiol. Rev. 25, 708\u2013719 (2012).","journal-title":"Clin. Microbiol. Rev."},{"key":"7705_CR7","first-page":"1974","volume":"218","author":"S. S Shin","year":"2018","unstructured":"Shin, S. S. et al. Mixed Mycobacterium tuberculosis\u2013Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance. J. Infect. Dis. 218, 1974\u20131982 (2018).","journal-title":"J. Infect. Dis."},{"key":"7705_CR8","doi-asserted-by":"crossref","unstructured":"McIvor, A., Koornhof, H. & Kana, B. D. Relapse, re-infection and mixed infections in tuberculosis disease. Pathog. Dis. 75, (2017).","DOI":"10.1093\/femspd\/ftx020"},{"key":"7705_CR9","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1038\/nrmicro.2018.8","volume":"16","author":"S Gagneux","year":"2018","unstructured":"Gagneux, S. Ecology and evolution of Mycobacterium tuberculosis. Nat. Rev. Microbiol. 16, 202\u2013213 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"7705_CR10","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-020-00817-3","volume":"12","author":"G Napier","year":"2020","unstructured":"Napier, G. et al. Robust barcoding and identification of Mycobacterium tuberculosis lineages for epidemiological and clinical studies. Genome Med. 12, 114 (2020).","journal-title":"Genome Med."},{"key":"7705_CR11","doi-asserted-by":"crossref","unstructured":"Coscolla, M. et al. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microb. Genom. 7, 000477 (2021).","DOI":"10.1099\/mgen.0.000477"},{"key":"7705_CR12","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16626-6","volume":"11","author":"J. C. S Ngabonziza","year":"2020","unstructured":"Ngabonziza, J. C. S. et al. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat. Commun. 11, 2917 (2020).","journal-title":"Nat. Commun."},{"key":"7705_CR13","doi-asserted-by":"publisher","first-page":"560","DOI":"10.3201\/eid3003.231466","volume":"30","author":"C Guyeux","year":"2024","unstructured":"Guyeux, C. et al. Newly Identified Mycobacterium africanum Lineage 10, Central Africa. Emerg. Infect. Dis. 30, 560\u2013563 (2024).","journal-title":"Emerg. Infect. Dis."},{"key":"7705_CR14","doi-asserted-by":"publisher","first-page":"100","DOI":"10.12688\/openreseurope.14029.2","volume":"1","author":"M Zwyer","year":"2021","unstructured":"Zwyer, M. et al. A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics. Open Res Eur. 1, 100 (2021).","journal-title":"Open Res Eur."},{"key":"7705_CR15","doi-asserted-by":"crossref","unstructured":"Thawornwattana, Y. et al. Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2. Microb. Genom. 7, 000697 (2021).","DOI":"10.1099\/mgen.0.000697"},{"key":"7705_CR16","doi-asserted-by":"publisher","first-page":"990","DOI":"10.3390\/genes13060990","volume":"13","author":"Y. A Shuaib","year":"2022","unstructured":"Shuaib, Y. A. et al. Origin and Global Expansion of Mycobacterium tuberculosis Complex Lineage 3. Genes 13, 990 (2022).","journal-title":"Genes"},{"key":"7705_CR17","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-4988-z","volume":"19","author":"B Sobkowiak","year":"2018","unstructured":"Sobkowiak, B. et al. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genom. 19, 613 (2018).","journal-title":"BMC Genom."},{"key":"7705_CR18","first-page":"000607","volume":"7","author":"E Gabbassov","year":"2021","unstructured":"Gabbassov, E., Moreno-Molina, M., Comas, I., Libbrecht, M. & Chindelevitch, L. SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data. Microb. Genom. 7, 000607 (2021).","journal-title":"Microb. Genom"},{"key":"7705_CR19","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).","journal-title":"Gigascience"},{"key":"7705_CR20","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-019-0650-x","volume":"11","author":"J. E Phelan","year":"2019","unstructured":"Phelan, J. E. et al. Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med. 11, 41 (2019).","journal-title":"Genome Med."},{"key":"7705_CR21","doi-asserted-by":"publisher","first-page":"btad648","DOI":"10.1093\/bioinformatics\/btad648","volume":"39","author":"R Derelle","year":"2023","unstructured":"Derelle, R. et al. fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing. Bioinformatics 39, btad648 (2023).","journal-title":"Bioinformatics"},{"key":"7705_CR22","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-6486-3","volume":"21","author":"C Anyansi","year":"2020","unstructured":"Anyansi, C. et al. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genom. 21, 80 (2020).","journal-title":"BMC Genom."},{"key":"7705_CR23","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. Preprint at https:\/\/www.R-project.org\/ (2023)."},{"key":"7705_CR24","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","volume":"27","author":"P Danecek","year":"2011","unstructured":"Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156\u20132158 (2011).","journal-title":"Bioinformatics"},{"key":"7705_CR25","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1038\/nbt.3820","volume":"35","author":"P Di Tommaso","year":"2017","unstructured":"Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316\u2013319 (2017).","journal-title":"Nat. Biotechnol."},{"key":"7705_CR26","doi-asserted-by":"publisher","first-page":"e107","DOI":"10.1002\/imt2.107","volume":"2","author":"S Chen","year":"2023","unstructured":"Chen, S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta 2, e107 (2023).","journal-title":"Imeta"},{"key":"7705_CR27","unstructured":"Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv [q-bio.GN] (2013)."},{"key":"7705_CR28","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1093\/bioinformatics\/btx699","volume":"34","author":"B. S Pedersen","year":"2018","unstructured":"Pedersen, B. S. & Quinlan, A. R. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics 34, 867\u2013868 (2018).","journal-title":"Bioinformatics"},{"key":"7705_CR29","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Magnusson, M., Lundin, S. & K\u00e4ller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047\u20133048 (2016).","journal-title":"Bioinformatics"},{"key":"7705_CR30","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1016\/0005-2795(75)90109-9","volume":"405","author":"B. W Matthews","year":"1975","unstructured":"Matthews, B. W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405, 442\u2013451 (1975).","journal-title":"Biochim. Biophys. Acta"},{"key":"7705_CR31","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-6413-7","volume":"21","author":"D Chicco","year":"2020","unstructured":"Chicco, D. & Jurman, G. The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation. BMC Genom. 21, 6 (2020).","journal-title":"BMC Genom."},{"key":"7705_CR32","doi-asserted-by":"publisher","first-page":"e265","DOI":"10.1016\/S2666-5247(21)00301-3","volume":"3","author":"T. M Walker","year":"2022","unstructured":"Walker, T. M. et al. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis. Lancet Microbe 3, e265\u2013e273 (2022).","journal-title":"Lancet Microbe"},{"key":"7705_CR33","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-44341-x","volume":"13","author":"L Wang","year":"2023","unstructured":"Wang, L., Campino, S., Phelan, J. & Clark, T. G. Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis. Sci. Rep. 13, 17100 (2023).","journal-title":"Sci. Rep."},{"key":"7705_CR34","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22705-z","volume":"12","author":"M Moreno-Molina","year":"2021","unstructured":"Moreno-Molina, M. et al. Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections. Nat. Commun. 12, 2716 (2021).","journal-title":"Nat. Commun."},{"key":"7705_CR35","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5782-2","volume":"20","author":"C Nimmo","year":"2019","unstructured":"Nimmo, C. et al. Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC Genom. 20, 389 (2019).","journal-title":"BMC Genom."},{"key":"7705_CR36","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1056\/NEJMoa1800474","volume":"379","author":"Consortium and the 100000, C","year":"2018","unstructured":"Consortium and the 100000, C. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N. Engl. J. Med. 379, 1403\u20131415 (2018).","journal-title":"N. Engl. J. Med."},{"key":"7705_CR37","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","volume":"11","author":"W Shen","year":"2016","unstructured":"Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA\/Q File Manipulation. PLoS One 11, e0163962 (2016).","journal-title":"PLoS One"},{"key":"7705_CR38","doi-asserted-by":"publisher","first-page":"1686","DOI":"10.21105\/joss.01686","volume":"4","author":"H Wickham","year":"2019","unstructured":"Wickham, H. et al. Welcome to the tidyverse. J. Open Source Softw. 4, 1686 (2019).","journal-title":"J. Open Source Softw."},{"key":"7705_CR39","doi-asserted-by":"publisher","unstructured":"Munro, J. E. TBtypeR Release-25.01.1. Zenodo https:\/\/doi.org\/10.5281\/zenodo.14769077 (2025).","DOI":"10.5281\/zenodo.14769077"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07705-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07705-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07705-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T02:12:39Z","timestamp":1739931159000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-025-07705-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,19]]},"references-count":39,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["7705"],"URL":"https:\/\/doi.org\/10.1038\/s42003-025-07705-9","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,19]]},"assertion":[{"value":"23 August 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 February 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 February 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"260"}}