{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:19:18Z","timestamp":1790835558864,"version":"4.1.0"},"reference-count":56,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T00:00:00Z","timestamp":1727395200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T00:00:00Z","timestamp":1727395200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["K43TW012302"],"award-info":[{"award-number":["K43TW012302"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI136894"],"award-info":[{"award-number":["R01AI136894"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["98948"],"award-info":[{"award-number":["98948"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001713","name":"European and Developing Countries Clinical Trials Partnership","doi-asserted-by":"publisher","award":["SF1041"],"award-info":[{"award-number":["SF1041"]}],"id":[{"id":"10.13039\/501100001713","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001322","name":"South African Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-024-73497-3","type":"journal-article","created":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T15:02:14Z","timestamp":1727449334000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Subtracting the background by reducing cell-free DNA\u2019s confounding effects on Mycobacterium tuberculosis quantitation and the sputum microbiome"],"prefix":"10.1038","volume":"14","author":[{"given":"Charissa C.","family":"Naidoo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rouxjeane","family":"Venter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesc","family":"Codony","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gemma","family":"Agust\u00ed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha","family":"Kitchin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selisha","family":"Naidoo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hilary","family":"Monaco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hridesh","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonghua","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose C.","family":"Clemente","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robin M.","family":"Warren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leopoldo N.","family":"Segal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grant","family":"Theron","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,9,27]]},"reference":[{"issue":"7221","key":"73497_CR1","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1038\/nature07450","volume":"456","author":"D Bouskra","year":"2008","unstructured":"Bouskra, D. et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature456 (7221), 507\u2013510 (2008).","journal-title":"Nature"},{"issue":"2","key":"73497_CR2","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/s41576-022-00529-x","volume":"24","author":"H VanEvery","year":"2023","unstructured":"VanEvery, H. et al. Microbiome epidemiology and association studies in human health. Nat. Rev. Genet.24 (2), 109\u2013124 (2023).","journal-title":"Nat. Rev. Genet."},{"issue":"11","key":"73497_CR3","doi-asserted-by":"publisher","first-page":"2535","DOI":"10.1007\/s40121-023-00880-4","volume":"12","author":"J Wen","year":"2023","unstructured":"Wen, J. & He, J. Q. The causal impact of the gut microbiota on respiratory tuberculosis susceptibility. Infect. Dis. Ther.12 (11), 2535\u20132544 (2023).","journal-title":"Infect. Dis. Ther."},{"issue":"1","key":"73497_CR4","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1038\/s41467-021-21475-y","volume":"12","author":"MF Wipperman","year":"2021","unstructured":"Wipperman, M. F. et al. Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. Nat. Commun.12 (1), 1141 (2021).","journal-title":"Nat. Commun."},{"issue":"11","key":"73497_CR5","doi-asserted-by":"publisher","first-page":"e913","DOI":"10.1016\/S2666-5247(23)00191-X","volume":"4","author":"E Musisi","year":"2023","unstructured":"Musisi, E. et al. Effect of seven anti-tuberculosis treatment regimens on sputum microbiome: a retrospective analysis of the HIGHRIF study 2 and PanACEA MAMS-TB clinical trials. Lancet Microbe4 (11), e913\u2013e922 (2023).","journal-title":"Lancet Microbe"},{"issue":"1","key":"73497_CR6","doi-asserted-by":"publisher","first-page":"10767","DOI":"10.1038\/s41598-017-10346-6","volume":"7","author":"MF Wipperman","year":"2017","unstructured":"Wipperman, M. F. et al. Antibiotic treatment for tuberculosis induces a profound dysbiosis of the microbiome that persists long after therapy is completed. Sci. Rep.7 (1), 10767 (2017).","journal-title":"Sci. Rep."},{"key":"73497_CR7","unstructured":"Global tuberculosis report 2023. Geneva: World Health Organization (2023)."},{"issue":"8","key":"73497_CR8","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1093\/cid\/civ1223","volume":"62","author":"G Theron","year":"2016","unstructured":"Theron, G. et al. Xpert MTB\/RIF results in patients with previous tuberculosis: can we distinguish true from false positive results? Clin. Infect. Dis.62 (8), 995\u20131001 (2016).","journal-title":"Clin. Infect. Dis."},{"issue":"4","key":"73497_CR9","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1016\/S2213-2600(19)30370-4","volume":"8","author":"H Mishra","year":"2020","unstructured":"Mishra, H. et al. Xpert MTB\/RIF Ultra and Xpert MTB\/RIF for diagnosis of tuberculosis in an HIV-endemic setting with a high burden of previous tuberculosis: a two-cohort diagnostic accuracy study. Lancet Respir. Med.8 (4), 368\u2013382 (2020).","journal-title":"Lancet Respir. Med."},{"key":"73497_CR10","doi-asserted-by":"crossref","unstructured":"Theron, G. et al. False-positive Xpert MTB\/RIF results in retested patients with previous tuberculosis: frequency, profile, and prospective clinical outcomes. J. Clin. Microbiol.56 (3) (2018).","DOI":"10.1128\/JCM.01696-17"},{"issue":"36","key":"73497_CR11","doi-asserted-by":"publisher","first-page":"57581","DOI":"10.18632\/oncotarget.11420","volume":"7","author":"R Jacobs","year":"2016","unstructured":"Jacobs, R. et al. Identification of novel host biomarkers in plasma as candidates for the immunodiagnosis of tuberculosis disease and monitoring of tuberculosis treatment response. Oncotarget7 (36), 57581 (2016).","journal-title":"Oncotarget"},{"key":"73497_CR12","doi-asserted-by":"crossref","unstructured":"Goletti, D. et al. Can we predict tuberculosis cure? What tools are available? Eur. Respir. J.52 (5) (2018).","DOI":"10.1183\/13993003.01089-2018"},{"issue":"1","key":"73497_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-017-0286-2","volume":"5","author":"S Namasivayam","year":"2017","unstructured":"Namasivayam, S. et al. Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy. Microbiome5 (1), 1\u201317 (2017).","journal-title":"Microbiome"},{"key":"73497_CR14","doi-asserted-by":"crossref","unstructured":"Burdet, C. et al. Impact of antibiotic gut exposure on the temporal changes in microbiome diversity. Antimicrob. Agents Chemother.63 (10) (2019).","DOI":"10.1128\/AAC.00820-19"},{"issue":"11","key":"73497_CR15","doi-asserted-by":"publisher","first-page":"1656","DOI":"10.1111\/j.1469-0691.2010.03189.x","volume":"16","author":"G Rogers","year":"2010","unstructured":"Rogers, G. et al. The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples. Clin. Microbiol. Infect.16 (11), 1656\u20131658 (2010).","journal-title":"Clin. Microbiol. Infect."},{"issue":"5","key":"73497_CR16","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1111\/j.1523-5378.2010.00794.x","volume":"15","author":"G Agust\u00ed","year":"2010","unstructured":"Agust\u00ed, G. et al. Viability determination of Helicobacter pylori using propidium monoazide quantitative PCR. Helicobacter15 (5), 473\u2013476 (2010).","journal-title":"Helicobacter"},{"issue":"9","key":"73497_CR17","doi-asserted-by":"publisher","first-page":"2936","DOI":"10.1128\/AEM.02524-08","volume":"75","author":"H Rawsthorne","year":"2009","unstructured":"Rawsthorne, H., Dock, C. & Jaykus, L. PCR-based method using propidium monoazide to distinguish viable from nonviable Bacillus subtilis spores. Appl. Environ. Microbiol.75 (9), 2936\u20132939 (2009).","journal-title":"Appl. Environ. Microbiol."},{"issue":"2","key":"73497_CR18","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1016\/j.mimet.2007.11.017","volume":"72","author":"S Vesper","year":"2008","unstructured":"Vesper, S. et al. Quantifying fungal viability in air and water samples using quantitative PCR after treatment with propidium monoazide (PMA). J. Microbiol. Methods72 (2), 180\u2013184 (2008).","journal-title":"J. Microbiol. Methods"},{"issue":"3","key":"73497_CR19","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1007\/s00284-016-1189-3","volume":"74","author":"G Agust\u00ed","year":"2017","unstructured":"Agust\u00ed, G., Fittipaldi, M. & Codony, F. False-positive viability PCR results: an association with microtubes. Curr. Microbiol.74 (3), 377\u2013380 (2017).","journal-title":"Curr. Microbiol."},{"issue":"8","key":"73497_CR20","doi-asserted-by":"publisher","first-page":"2537","DOI":"10.1128\/AEM.02288-07","volume":"74","author":"AO Wagner","year":"2008","unstructured":"Wagner, A. O. et al. Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Appl. Environ. Microbiol.74 (8), 2537\u20132539 (2008).","journal-title":"Appl. Environ. Microbiol."},{"key":"73497_CR21","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.foodcont.2017.09.013","volume":"85","author":"L Vondrakova","year":"2018","unstructured":"Vondrakova, L. et al. Impact of various killing methods on EMA\/PMA-qPCR efficacy. Food Control85, 23\u201328 (2018).","journal-title":"Food Control"},{"key":"73497_CR22","doi-asserted-by":"publisher","first-page":"103310","DOI":"10.1016\/j.fm.2019.103310","volume":"86","author":"ML Kragh","year":"2020","unstructured":"Kragh, M. L., Thykier, M. & Hansen, L. T. A long-amplicon quantitative PCR assay with propidium monoazide to enumerate viable Listeria monocytogenes after heat and desiccation treatments. Food Microbiol.86, 103310 (2020).","journal-title":"Food Microbiol."},{"issue":"4","key":"73497_CR23","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1016\/j.jcf.2014.10.004","volume":"14","author":"L Cuthbertson","year":"2015","unstructured":"Cuthbertson, L. et al. Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses. J. Cyst. Fibros.14 (4), 464\u2013467 (2015).","journal-title":"J. Cyst. Fibros."},{"issue":"16","key":"73497_CR24","doi-asserted-by":"publisher","first-page":"5111","DOI":"10.1128\/AEM.02987-06","volume":"73","author":"A Nocker","year":"2007","unstructured":"Nocker, A. et al. Use of propidium monoazide for live\/dead distinction in microbial ecology. Appl. Environ. Microbiol.73 (16), 5111\u20135117 (2007).","journal-title":"Appl. Environ. Microbiol."},{"issue":"2","key":"73497_CR25","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1016\/j.mimet.2006.04.015","volume":"67","author":"A Nocker","year":"2006","unstructured":"Nocker, A., Cheung, C. Y. & Camper, A. K. Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs. dead bacteria by selective removal of DNA from dead cells. J. Microbiol. Methods67 (2), 310\u2013320 (2006).","journal-title":"J. Microbiol. Methods"},{"key":"73497_CR26","doi-asserted-by":"publisher","first-page":"106223","DOI":"10.1016\/j.mimet.2021.106223","volume":"185","author":"I Hortelano","year":"2021","unstructured":"Hortelano, I. et al. Optimization of pre-treatments with Propidium Monoazide and PEMAX\u2122 before real-time quantitative PCR for detection and quantification of viable Helicobacter pylori cells. J. Microbiol. Methods185, 106223 (2021).","journal-title":"J. Microbiol. Methods"},{"key":"73497_CR27","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1016\/j.tube.2016.08.006","volume":"101","author":"XA Kayigire","year":"2016","unstructured":"Kayigire, X. A. et al. Propidium monoazide and Xpert MTB\/RIF to quantify Mycobacterium tuberculosis cells. Tuberculosis101, 79\u201384 (2016).","journal-title":"Tuberculosis"},{"issue":"2","key":"73497_CR28","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/j.tube.2014.11.005","volume":"95","author":"V Nikolayevskyy","year":"2015","unstructured":"Nikolayevskyy, V. et al. Utility of propidium monoazide viability assay as a biomarker for a tuberculosis disease. Tuberculosis95 (2), 179\u2013185 (2015).","journal-title":"Tuberculosis"},{"issue":"3","key":"73497_CR29","doi-asserted-by":"publisher","first-page":"203","DOI":"10.3343\/alm.2014.34.3.203","volume":"34","author":"YJ Kim","year":"2014","unstructured":"Kim, Y. J. et al. Evaluation of propidium monoazide real-time PCR for early detection of viable Mycobacterium tuberculosis in clinical respiratory specimens. Ann. Lab. Med.34 (3), 203 (2014).","journal-title":"Ann. Lab. Med."},{"issue":"4","key":"73497_CR30","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1016\/j.tube.2014.04.008","volume":"94","author":"TM de Assun\u00e7\u00e3o","year":"2014","unstructured":"de Assun\u00e7\u00e3o, T. M. et al. Real time PCR quantification of viable Mycobacterium tuberculosis from sputum samples treated with propidium monoazide. Tuberculosis94 (4), 421\u2013427 (2014).","journal-title":"Tuberculosis"},{"issue":"5","key":"73497_CR31","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1183\/09031936.00124711","volume":"39","author":"P Miotto","year":"2012","unstructured":"Miotto, P. et al. Early tuberculosis treatment monitoring by Xpert\u00ae MTB\/RIF. Eur. Respir. J.39 (5), 1269\u20131271 (2012).","journal-title":"Eur. Respir. J."},{"issue":"3","key":"73497_CR32","doi-asserted-by":"publisher","first-page":"e22716","DOI":"10.1002\/jcla.22716","volume":"33","author":"J Lu","year":"2019","unstructured":"Lu, J. et al. Direct detection from clinical sputum samples to differentiate live and dead Mycobacterium tuberculosis. J. Clin. Lab. Anal.33 (3), e22716 (2019).","journal-title":"J. Clin. Lab. Anal."},{"issue":"10","key":"73497_CR33","doi-asserted-by":"publisher","first-page":"1214","DOI":"10.1164\/rccm.202107-1779OC","volume":"205","author":"A Esmail","year":"2022","unstructured":"Esmail, A. et al. An all-oral 6-month regimen for multidrug-resistant tuberculosis: a multicenter, randomized controlled clinical trial (the NExT study). Am. J. Respir. Crit Care Med.205 (10), 1214\u20131227 (2022).","journal-title":"Am. J. Respir. Crit Care Med."},{"key":"73497_CR34","unstructured":"Invitrogen. PureLink\u2122 Microbiome DNA Purification Kit. Pub. No. MAN0014267 Rev. A.0."},{"issue":"Supplement 1","key":"73497_CR35","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","volume":"108","author":"JG Caporaso","year":"2011","unstructured":"Caporaso, J. G. et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci.108 (Supplement 1), 4516\u20134522 (2011).","journal-title":"Proc. Natl. Acad. Sci."},{"key":"73497_CR36","unstructured":"GenIUL PEMAX 25 Reagent Monodose (TBC-Biomarker kit) INSTRUCTIONS in Doc Code 450000075-00 (2015)."},{"issue":"5","key":"73497_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/nmicrobiol.2016.31","volume":"1","author":"LN Segal","year":"2016","unstructured":"Segal, L. N. et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat. Microbiol.1 (5), 1\u201311 (2016).","journal-title":"Nat. Microbiol."},{"key":"73497_CR38","doi-asserted-by":"crossref","unstructured":"Segal, L. N. et al. Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV Patients (Cell Host & Microbe, 2017).","DOI":"10.1016\/j.chom.2017.03.003"},{"issue":"9","key":"73497_CR39","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1164\/rccm.201710-2118OC","volume":"198","author":"JCJ Tsay","year":"2018","unstructured":"Tsay, J. C. J. et al. Airway Microbiota is associated with upregulation of the PI3K pathway in lung cancer. Am. J. Respir. Crit Care Med.198 (9), 1188\u20131198 (2018).","journal-title":"Am. J. Respir. Crit Care Med."},{"issue":"8","key":"73497_CR40","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","volume":"37","author":"E Bolyen","year":"2019","unstructured":"Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat. Biotechnol.37 (8), 852\u2013857 (2019).","journal-title":"Nat. Biotechnol."},{"issue":"7","key":"73497_CR41","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan, B. J. et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat. Methods13 (7), 581\u2013583 (2016).","journal-title":"Nat. Methods"},{"issue":"3","key":"73497_CR42","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/ismej.2011.139","volume":"6","author":"D McDonald","year":"2012","unstructured":"McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J.6 (3), 610\u2013618 (2012).","journal-title":"ISME J."},{"issue":"8","key":"73497_CR43","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","volume":"6","author":"JG Caporaso","year":"2012","unstructured":"Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J.6 (8), 1621\u20131624 (2012).","journal-title":"ISME J."},{"key":"73497_CR44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0605-2","volume":"6","author":"NM Davis","year":"2018","unstructured":"Davis, N. M. et al. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome6, 1\u201314 (2018).","journal-title":"Microbiome"},{"key":"73497_CR45","first-page":"631","volume":"10","author":"J Oksanen","year":"2007","unstructured":"Oksanen, J. et al. The vegan package. Community Ecol. Pack.10, 631\u2013637 (2007).","journal-title":"Community Ecol. Package"},{"issue":"12","key":"73497_CR46","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of Fold change and dispersion for RNA-seq data with DESeq2. Genome Biol.15 (12), 550 (2014).","journal-title":"Genome Biol."},{"issue":"1","key":"73497_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/jam.12365","volume":"116","author":"P Elizaqu\u00edvel","year":"2014","unstructured":"Elizaqu\u00edvel, P., Aznar, R. & S\u00e1nchez, G. Recent developments in the use of viability dyes and quantitative PCR in the food microbiology field. J. Appl. Microbiol.116 (1), 1\u201313 (2014).","journal-title":"J. Appl. Microbiol."},{"issue":"3","key":"73497_CR48","doi-asserted-by":"publisher","first-page":"203","DOI":"10.3343\/alm.2014.34.3.203","volume":"34","author":"YJ Kim","year":"2014","unstructured":"Kim, Y. J. et al. Evaluation of propidium monoazide real-time PCR for early detection of viable Mycobacterium tuberculosis in clinical respiratory specimens. Ann. Lab. Med.34 (3), 203\u2013209 (2014).","journal-title":"Ann. Lab. Med."},{"key":"73497_CR49","doi-asserted-by":"crossref","unstructured":"Sulaiman, I. et al. Evaluation of the airway microbiome in nontuberculous mycobacteria disease. Eur. Respir. J.52(4) (2018).","DOI":"10.1183\/13993003.00810-2018"},{"key":"73497_CR50","doi-asserted-by":"publisher","first-page":"103374","DOI":"10.1016\/j.ebiom.2021.103374","volume":"67","author":"CC Naidoo","year":"2021","unstructured":"Naidoo, C. C. et al. Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. EBioMedicine67, 103374 (2021).","journal-title":"EBioMedicine"},{"key":"73497_CR51","doi-asserted-by":"publisher","first-page":"633396","DOI":"10.3389\/fmicb.2021.633396","volume":"12","author":"MR Ticlla","year":"2021","unstructured":"Ticlla, M. R. et al. The sputum microbiome in pulmonary tuberculosis and its association with disease manifestations: a cross-sectional study. Front. Microbiol.12, 633396 (2021).","journal-title":"Front. Microbiol."},{"issue":"1","key":"73497_CR52","doi-asserted-by":"publisher","first-page":"24486","DOI":"10.1038\/s41598-021-04271-y","volume":"11","author":"DP Kateete","year":"2021","unstructured":"Kateete, D. P. et al. Sputum microbiota profiles of treatment-na\u00efve TB patients in Uganda before and during first-line therapy. Sci. Rep.11 (1), 24486 (2021).","journal-title":"Sci. Rep."},{"issue":"19","key":"73497_CR53","doi-asserted-by":"publisher","first-page":"5936","DOI":"10.1128\/AEM.01752-13","volume":"79","author":"AA Pezzulo","year":"2013","unstructured":"Pezzulo, A. A. et al. Abundant DNase I-sensitive bacterial DNA in healthy porcine lungs and its implications for the lung microbiome. Appl. Environ. Microbiol.79 (19), 5936\u20135941 (2013).","journal-title":"Appl. Environ. Microbiol."},{"issue":"2","key":"73497_CR54","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1016\/j.mimet.2007.04.014","volume":"70","author":"A Nocker","year":"2007","unstructured":"Nocker, A., Sossa, K. E. & Camper, A. K. Molecular monitoring of disinfection efficacy using propidium monoazide in combination with quantitative PCR. J. Microbiol. Methods70 (2), 252\u2013260 (2007).","journal-title":"J. Microbiol. Methods"},{"issue":"3","key":"73497_CR55","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.mcp.2015.03.003","volume":"29","author":"F Codony","year":"2015","unstructured":"Codony, F., Agust\u00ed, G. & Allu\u00e9-Guardia, A. Cell membrane integrity and distinguishing between metabolically active and inactive cells as a means of improving viability PCR. Mol. Cell Probes29 (3), 190\u2013192 (2015).","journal-title":"Mol. Cell Probes"},{"issue":"8","key":"73497_CR56","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/s41564-018-0202-y","volume":"3","author":"MC de Goffau","year":"2018","unstructured":"de Goffau, M. C. et al. Recognizing the reagent microbiome. Nat. Microbiol.3 (8), 851\u2013853 (2018).","journal-title":"Nat. Microbiol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-73497-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-73497-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-73497-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,27]],"date-time":"2024-09-27T16:04:11Z","timestamp":1727453051000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-024-73497-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,27]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["73497"],"URL":"https:\/\/doi.org\/10.1038\/s41598-024-73497-3","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,27]]},"assertion":[{"value":"14 June 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 September 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 September 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"GT acknowledges in-kind donations from Cepheid. GT declares no other competing interests. The other authors each declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"22350"}}