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In resource-limited settings, including Kenya, this empirical TB treatment is routine practice however limited data exist on patient clinical outcomes when comparing the method of diagnosis. We evaluated TB treatment outcomes comparing clinically diagnosed and bacteriologically confirmed TB, 6 months after starting treatment of TB in a rural county in Kenya. Our analysis compared patients with a clinical versus a bacteriologically confirmed TB diagnosis. In this retrospective analysis, we included all adults (\u2265\u200918\u00a0years) starting treatment of TB and followed up for 6 months, within the County TB surveillance database from 2012 to 2018. Patients included from both public and private facilities. The TB treatment outcomes assessed included treatment success, treatment failure, death, defaulted and transferred out. We used survival regression models to assess effect of type of diagnosis on TB treatment outcome defining time at risk from date of starting treatment to experiencing one of the treatment outcomes or completing 6-months of treatment. A total of 12,856 patients; median age 37 [IQR 28\u2009\u2212\u200950] years were included. 7639 (59%) were male while 11,339 (88%) were pulmonary TB cases. Overall, 11,633 (90%) were given first-line TB treatment and 3791 (29%) were HIV infected. 6472 (50%) of the patients were clinically diagnosed of whom 4521\/6472 (70%) had a negative sputum\/GeneXpert test. During the study 5565 person-years (PYs) observed, treatment success was 82% and 83% amongst clinically and bacteriologically diagnosed patients (P\u2009=\u20090.05). There were no significant differences in defaulting (P\u2009=\u20090.70) or transfer out (P\u2009=\u20090.19) between clinically and bacteriologically diagnosed patients. Mortality was significantly higher among clinically diagnosed patients: 639 (9.9%) deaths compared to 285 (4.5%) amongst the bacteriologically diagnosed patients; aHR 5.16 (95%CI 2.17\u2009\u2212\u200912.3) P\u2009&lt;\u20090.001. Our study suggests survival during empirical TB treatment is significantly lower compared to patients with laboratory evidence, irrespective of HIV status and age. To improve TB treatment outcomes amongst clinically diagnosed patients, we recommend systematic screening for comorbidities, prompt diagnosis and management of other infections.<\/jats:p>","DOI":"10.1038\/s41598-021-94153-0","type":"journal-article","created":{"date-parts":[[2021,7,21]],"date-time":"2021-07-21T06:07:53Z","timestamp":1626847673000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":28,"title":["The effect of empirical and laboratory-confirmed tuberculosis\u00a0on treatment outcomes"],"prefix":"10.1038","volume":"11","author":[{"given":"Osman","family":"Abdullahi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ngari","family":"Moses","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deche","family":"Sanga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Willetts","family":"Annie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,7,21]]},"reference":[{"key":"94153_CR1","unstructured":"World Health Organization. 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