{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T19:21:19Z","timestamp":1791660079507,"version":"4.3.4"},"reference-count":18,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:00:00Z","timestamp":1763683200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["R01AI137527"],"award-info":[{"award-number":["R01AI137527"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["1K01TW011482-01A1"],"award-info":[{"award-number":["1K01TW011482-01A1"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006279","name":"St. Jude Medical","doi-asserted-by":"publisher","award":["St. Judes\/PIDS Award in Basic and Translational Sciences"],"award-info":[{"award-number":["St. Judes\/PIDS Award in Basic and Translational Sciences"]}],"id":[{"id":"10.13039\/100006279","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005627","name":"Thrasher Research Fund","doi-asserted-by":"publisher","award":["14323"],"award-info":[{"award-number":["14323"]}],"id":[{"id":"10.13039\/100005627","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005627","name":"Thrasher Research Fund","doi-asserted-by":"publisher","award":["01098"],"award-info":[{"award-number":["01098"]}],"id":[{"id":"10.13039\/100005627","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009139","name":"DZIF","doi-asserted-by":"crossref","award":["TTU-TB 02.709"],"award-info":[{"award-number":["TTU-TB 02.709"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plosglobalpublichealth.org"],"crossmark-restriction":false},"short-container-title":["PLOS Glob Public Health"],"abstract":"<jats:p>\n                    In 2023, an estimated 10.8 million people developed tuberculosis, and 1.25 million people died from this disease, including 161,000 deaths in people with HIV (PWH) in whom tuberculosis remains the leading cause of death. Detecting\n                    <jats:italic>Mycobacterium tuberculosis<\/jats:italic>\n                    drug resistance remains a challenge among patients with paucibacillary tuberculosis; since there is such low bacterial load in their sputum it\u2019s unable to be detected via microscopy, there is also not enough bacteria for other sputum-based tests which could provide resistance testing. At an outpatient clinic in Eswatini from 2020-2023, stool and sputum samples were provided by a subset of children, adolescents, and adults prospectively enrolled in a tuberculosis diagnostic study. In addition to standard diagnostic testing available in country (direct sputum Xpert, stool Xpert, and phenotypic drug susceptibility testing of sputum culture), stool samples underwent extraction and sequencing using targeted next generation sequencing (tNGS), using both the Oxford Nanopore Technologies (ONT) TB Custom Kit (on an ONT MinION Mk1b) and the Deeplex Myc-TB kit (on an Illumina iSeq 100). From 250 participants with pulmonary tuberculosis diagnosed in Eswatini during our study period, 85 (34%) were smear negative on sputum microscopy. Of these, 21\/85 (24.7%) participants had adequate\n                    <jats:italic>M. tuberculosis<\/jats:italic>\n                    DNA shed in their stool for attempting tNGS. Targeted sequencing on stool detected\n                    <jats:italic>M. tuberculosis<\/jats:italic>\n                    DNA in 14\u201319% (n\u2009=\u200912\/85\u201316\/85) and provided a full report of mutations associated with drug resistance in 12\u201314% (n\u2009=\u200910\/85\u201312\/85) of patients with paucibacillary (smear-negative) tuberculosis, expanding drug resistance detection beyond other methods. Targeted sequencing of stool, even when applied to patients with paucibacillary disease, can provide case confirmation and expanded drug resistance information.\n                  <\/jats:p>","DOI":"10.1371\/journal.pgph.0005243","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T18:25:23Z","timestamp":1763749523000},"page":"e0005243","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgph.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Screening and targeted sequencing of stool for microbiologic confirmation and drug resistance determination in paucibacillary tuberculosis"],"prefix":"10.1371","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4425-418X","authenticated-orcid":true,"given":"Tara E.","family":"Ness","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mangaliso","family":"Ziyane","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nontobeko","family":"Maphalala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail","family":"Seeger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5336-7859","authenticated-orcid":true,"given":"Anca","family":"Vasiliu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wethusonke","family":"Khumalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mdigo","family":"Thunzini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sindisiwe","family":"Dlamini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3635-8405","authenticated-orcid":true,"given":"Gugu","family":"Maphalala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3190-9343","authenticated-orcid":true,"given":"Clement","family":"Gascua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christoph","family":"Lange","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha","family":"Meyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4085-4543","authenticated-orcid":true,"given":"Bryce","family":"Inman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2997-3693","authenticated-orcid":true,"given":"Viola","family":"Dreyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Utpatel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanja","family":"Niemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"DiNardo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Kay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Niemann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8091-3509","authenticated-orcid":true,"given":"Anna","family":"Mandalakas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,11,21]]},"reference":[{"key":"pgph.0005243.ref001","volume-title":"Global Tuberculosis Report 2024.","author":"WHO","year":"2024"},{"issue":"11","key":"pgph.0005243.ref002","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.3390\/pathogens11111343","article-title":"High Throughput Sequencing for Clinical Tuberculosis: An Overview","volume":"11","author":"TE Ness","year":"2022","journal-title":"Pathogens"},{"key":"pgph.0005243.ref003","volume-title":"WHO consolidated guidelines on tuberculosis. Module 3: diagnosis - rapid diagnostics for tuberculosis detection","author":"WHO","year":"2024"},{"issue":"1","key":"pgph.0005243.ref004","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s13073-022-01054-6","article-title":"Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing","volume":"14","author":"DB Sibandze","year":"2022","journal-title":"Genome Med"},{"key":"pgph.0005243.ref005","volume-title":"Improving the Diagnosis and Treatment of Smear-Negative Pulmonary and Extrapulmonary Tuberculosis Among Adults and Adolescents: Recommendations for HIV Prevalent and Resource-Constrained Settings","author":"WHO","year":"2007"},{"issue":"5","key":"pgph.0005243.ref006","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.04098-23","article-title":"Comparison of targeted next-generation sequencing and the Xpert MTB\/RIF assay for detection of Mycobacterium tuberculosis in clinical isolates and sputum specimens","volume":"12","author":"H Zhang","year":"2024","journal-title":"Microbiol Spectr"},{"issue":"3","key":"pgph.0005243.ref007","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1016\/S1473-3099(24)00586-3","article-title":"Evaluating culture-free targeted next-generation sequencing for diagnosing drug-resistant tuberculosis: a multicentre clinical study of two end-to-end commercial workflows","volume":"25","author":"RE Colman","year":"2025","journal-title":"Lancet Infect Dis"},{"key":"pgph.0005243.ref008","volume-title":"Use of targeted next-generation sequencing to detect drug-resistant tuberculosis: rapid communication","author":"WHO","year":"2024"},{"key":"pgph.0005243.ref009","volume-title":"The use of next-generation sequencing for the surveillance of drug-resistant tuberculosis: an implementation manual","author":"WHO","year":"2023"},{"key":"pgph.0005243.ref010","volume-title":"The use of next-generation sequencing technologies for the detection of mutations associated with drug resistance in Mycobacterium tuberculosis complex: technical guide. 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