{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T04:32:28Z","timestamp":1791952348919,"version":"4.3.4"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T00:00:00Z","timestamp":1478649600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["OPP1083118"],"award-info":[{"award-number":["OPP1083118"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0166158","type":"journal-article","created":{"date-parts":[[2016,11,9]],"date-time":"2016-11-09T18:36:44Z","timestamp":1478716604000},"page":"e0166158","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":48,"title":["Autopsy Prevalence of Tuberculosis and Other Potentially Treatable Infections among Adults with Advanced HIV Enrolled in Out-Patient Care in South Africa"],"prefix":"10.1371","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9643-664X","authenticated-orcid":true,"given":"Aaron S.","family":"Karat","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tanvier","family":"Omar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"von Gottberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mpho","family":"Tlali","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Violet N.","family":"Chihota","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gavin J.","family":"Churchyard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine L.","family":"Fielding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neil A.","family":"Martinson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kerrigan","family":"McCarthy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Wolter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily B.","family":"Wong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salome","family":"Charalambous","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alison D.","family":"Grant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,11,9]]},"reference":[{"key":"ref1","article-title":"Early mortality among adults accessing antiretroviral treatment programmes in sub-Saharan Africa","volume":"22","author":"SD Lawn","year":"2008","journal-title":"AIDS"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"e28691","DOI":"10.1371\/journal.pone.0028691","article-title":"Early mortality in adults initiating antiretroviral therapy (ART) in low- and middle-income countries (LMIC): a systematic review and meta-analysis","volume":"6","author":"A Gupta","year":"2011","journal-title":"PLoS One"},{"key":"ref3","article-title":"Sizanani: A randomized trial of health system navigators to improve linkage to HIV and TB care in South Africa","author":"I V Bassett","year":"2016","journal-title":"JAIDS J Acquir Immune Defic Syndr"},{"key":"ref4","first-page":"1","article-title":"Burden of tuberculosis at post mortem in inpatients at a tertiary referral centre in sub-Saharan Africa: a prospective descriptive autopsy study","volume":"3099","author":"M Bates","year":"2015","journal-title":"Lancet Infect Dis"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.5588\/ijtld.15.0222","article-title":"Undiagnosed TB in adults dying at home from natural causes in a high TB burden setting: a post-mortem study","volume":"19","author":"T Omar","year":"2015","journal-title":"Int J Tuberc Lung Dis"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1987","DOI":"10.1097\/QAD.0000000000000802","article-title":"Prevalence of tuberculosis in post-mortem studies of HIV-infected adults and children in resource-limited settings","volume":"29","author":"RK Gupta","year":"2015","journal-title":"AIDS"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"20714","DOI":"10.7448\/IAS.19.1.20714","article-title":"TB as a cause of hospitalization and in-hospital mortality among people living with HIV worldwide: a systematic review and meta-analysis","volume":"19","author":"N Ford","year":"2016","journal-title":"J Int AIDS Soc"},{"key":"ref8","unstructured":"World Health Organization. The End TB strategy: Global strategy and targets for tuberculosis prevention, care and control after 2015. 2015 [cited 5 May 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/tb\/post2015_strategy\/en\/\" xlink:type=\"simple\">http:\/\/www.who.int\/tb\/post2015_strategy\/en\/<\/ext-link>"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.5588\/ijtld.15.0782","article-title":"(Not) measuring in the dark","volume":"19","author":"KP Cain","year":"2015","journal-title":"Int J Tuberc Lung Dis"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/j.jclinepi.2011.08.007","article-title":"Validation study of cause of death statistics in Cape Town, South Africa, found poor agreement","volume":"65","author":"EH Burger","year":"2012","journal-title":"J Clin Epidemiol"},{"key":"ref11","first-page":"937013","article-title":"Inaccuracy of death certificate diagnosis of tuberculosis and potential underdiagnosis of TB in a region of high HIV prevalence","volume":"2012","author":"TT Liu","year":"2012","journal-title":"Clin Dev Immunol"},{"key":"ref12","unstructured":"Karat A, Tlali M, Charalambous S, McCarthy K, Chihota V, Churchyard GJ, et al. Needle autopsies highlight challenges in defining HIV+ TB deaths using verbal autopsy. 22nd Conference on Retroviruses and Opportunistic Infections. 2015. Abstract #825."},{"key":"ref13","unstructured":"Murithi S, Sitienei J, Mitchell E, Kipruto H, Amukoye E, Muturi C, et al. TB mortality measurement: comparing verbal autopsy methods to necropsy in a setting of high HIV prevalence in Siaya County, Kenya. The 46th Union World Conference on Lung Health. 2015. Abstract SOA-625-06."},{"key":"ref14","first-page":"1","article-title":"HIV\/AIDS-related mortality in Africa and Asia: evidence from INDEPTH health and demographic surveillance system sites","volume":"25370","author":"PK Streatfield","year":"2014","journal-title":"Glob Health Action"},{"key":"ref15","unstructured":"Statistics South Africa. Mortality and causes of death in South Africa, 2014: Findings from death notification. 2015 [cited 5 May 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.statssa.gov.za\/?page_id=1854&PPN=P0309.3\" xlink:type=\"simple\">www.statssa.gov.za\/?page_id=1854&amp;PPN=P0309.3<\/ext-link>"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"S340","DOI":"10.1093\/infdis\/jir859","article-title":"Tuberculosis and Tuberculosis\/HIV\/AIDS\u2013Associated Mortality in Africa: The Urgent Need to Expand and Invest in Routine and Research Autopsies","volume":"205","author":"V Mudenda","year":"2012","journal-title":"J Infect Dis"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1148\/radiol.2503080421","article-title":"Minimally Invasive Autopsy: An alternative to conventional autopsy?","volume":"250","author":"AC Weustink","year":"2009","journal-title":"Radiology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1097\/QAI.0000000000000290","article-title":"Needle Autopsy to Establish the Cause of Death in HIV-Infected Hospitalized Adults in Uganda: A Comparison to Complete Autopsy","volume":"67","author":"JA Cox","year":"2014","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1111\/j.1365-3156.2011.02798.x","article-title":"Autopsy acceptance rate and reasons for decline in Mulago Hospital, Kampala, Uganda","volume":"16","author":"JA Cox","year":"2011","journal-title":"Trop Med Int Heal"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.diagmicrobio.2015.10.002","article-title":"Infectious cause of death determination using minimally invasive autopsies in developing countries","volume":"84","author":"MJ Mart\u00ednez","year":"2016","journal-title":"Diagn Microbiol Infect Dis"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"20703","DOI":"10.1038\/srep20703","article-title":"The role of Xpert MTB\/RIF in diagnosing pulmonary tuberculosis in post-mortem tissues","author":"AL Garc\u00eda-Basteiro","year":"2016","journal-title":"Sci Rep"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"2043","DOI":"10.1097\/QAD.0b013e3282eea47f","article-title":"Causes of death in hospitalized adults with a premortem diagnosis of tuberculosis: an autopsy study","volume":"21","author":"NA Martinson","year":"2007","journal-title":"AIDS"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1078\/0344-0338-00028","article-title":"Value of Limited Necropsy in HIV-positive Patients","volume":"197","author":"I Guerra","year":"2001","journal-title":"Pathol Res Pract"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1186\/s13063-015-0650-0","article-title":"Evaluation of a point-of-care tuberculosis test-and-treat algorithm on early mortality in people with HIV accessing antiretroviral therapy (TB Fast Track study): study protocol for a cluster randomised controlled trial","volume":"16","author":"KL Fielding","year":"2015","journal-title":"Trials"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1128\/JCM.06087-11","article-title":"Clinical validation of multiplex real-time PCR assays for detection of bacterial meningitis pathogens","volume":"50","author":"X Wang","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref26","article-title":"Laboratory manual for the diagnosis of meningitis caused by Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae","volume":"71","author":"T Popovic","year":"2011","journal-title":"Int J Epidemiol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.diagmicrobio.2010.11.014","article-title":"Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay","volume":"70","author":"KA Thurman","year":"2011","journal-title":"Diagn Microbiol Infect Dis"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1128\/JCM.00601-11","article-title":"Novel multitarget real-time PCR assay for rapid detection of Bordetella species in clinical specimens","volume":"49","author":"KM Tatti","year":"2011","journal-title":"J Clin Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1093\/infdis\/jis538","article-title":"Respiratory viral coinfections identified by a 10-Plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness-South Africa, 2009\u20132010","volume":"206","author":"MA Pretorius","year":"2012","journal-title":"J Infect Dis"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.5588\/ijtld.11.0733","article-title":"Tuberculosis among adults starting antiretroviral therapy in South Africa: the need for routine case finding","volume":"16","author":"Y Hanifa","year":"2012","journal-title":"Int J Tuberc Lung Dis"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e22","DOI":"10.1097\/QAI.0b013e318251ae0b","article-title":"Undiagnosed tuberculosis among HIV clinic attendees: association with antiretroviral therapy and implications for intensified case finding, isoniazid preventive therapy, and infection control","volume":"60","author":"T Kufa","year":"2012","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref32","unstructured":"World Health Organization. Improving the diagnosis and treatment of smear-negative pulmonary and extrapulmonary tuberculosis among adults and adolescents: Recommendations for HIV-prevalent and resource-constrained settings. 2007 [cited 5 May 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/tb\/publications\/2006\/tbhiv_recommendations.pdf\" xlink:type=\"simple\">http:\/\/www.who.int\/tb\/publications\/2006\/tbhiv_recommendations.pdf<\/ext-link>"},{"key":"ref33","unstructured":"South Africa National Department of Health. National Tuberculosis Management Guidelines. 2014 [cited 5 May 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.health-e.org.za\/wp-content\/uploads\/2014\/06\/NTCP_Adult_TB-Guidelines-27.5.2014.pdf\" xlink:type=\"simple\">http:\/\/www.health-e.org.za\/wp-content\/uploads\/2014\/06\/NTCP_Adult_TB-Guidelines-27.5.2014.pdf<\/ext-link>"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1186\/s12916-015-0432-2","article-title":"Rapid microbiological screening for tuberculosis in HIV-positive patients on the first day of acute hospital admission by systematic testing of urine samples using Xpert MTB\/RIF: a prospective cohort in South Africa","volume":"13","author":"SD Lawn","year":"2015","journal-title":"BMC Med"},{"key":"ref35","unstructured":"World Health Organization. Implementing tuberculosis diagnostics: A policy framework. 2015 [cited 5 May 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/tb\/publications\/implementing_TB_diagnostics\/en\/\" xlink:type=\"simple\">http:\/\/www.who.int\/tb\/publications\/implementing_TB_diagnostics\/en\/<\/ext-link>"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e47542","DOI":"10.1371\/journal.pone.0047542","article-title":"Causes of Death on Antiretroviral Therapy: A Post- Mortem Study from South Africa","volume":"7","author":"EB Wong","year":"2012","journal-title":"PLoS One"},{"key":"ref37","unstructured":"World Health Organization. Consolidated guidelines on the use of antiretroviral drugs for treating and preventing HIV infection: Recommendations for a public health approach (Second edition). 2016 [cited 1 Sep 2016]. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.who.int\/hiv\/pub\/guidelines\/keypopulations-2016\/en\/\" xlink:type=\"simple\">http:\/\/www.who.int\/hiv\/pub\/guidelines\/keypopulations-2016\/en\/<\/ext-link>"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.tube.2003.08.003","article-title":"M. tuberculosis persistence, latency, and drug tolerance","volume":"84","author":"JE Gomez","year":"2004","journal-title":"Tuberculosis"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/j.humpath.2004.01.009","article-title":"Viability of mycobacteria in formalin-fixed lungs","volume":"35","author":"KF Gerston","year":"2004","journal-title":"Hum Pathol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S1344-6223(01)00002-5","article-title":"Postmortem bacteriology in forensic pathology: Diagnostic value and interpretation","volume":"3","author":"M Tsokos","year":"2001","journal-title":"Leg Med"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.cdip.2006.07.005","article-title":"Practical and theoretical aspects of postmortem bacteriology","volume":"13","author":"JA Morris","year":"2007","journal-title":"Curr Diagnostic Pathol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.cdip.2007.06.001","article-title":"The autopsy pathology of sepsis-related death","volume":"13","author":"S Lucas","year":"2007","journal-title":"Curr Diagnostic Pathol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1136\/jcp.2005.028183","article-title":"Postmortem bacteriology: a re-evaluation","volume":"59","author":"J Morris","year":"2006","journal-title":"J Clin Pathol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.forsciint.2015.02.020","article-title":"The importance of microbiological testing for establishing cause of death in 42 forensic autopsies","volume":"250","author":"S Christoffersen","year":"2015","journal-title":"Forensic Sci Int"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.forsciint.2010.02.002","article-title":"Post-mortem interval and bacteriological culture yield in sudden unexpected death in infancy (SUDI)","volume":"198","author":"MA Weber","year":"2010","journal-title":"Forensic Sci Int"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1111\/1556-4029.12155","article-title":"The Interest of Postmortem Bacteriology in Putrefied Bodies","volume":"58","author":"G Maujean","year":"2013","journal-title":"J Forensic Sci"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/j.jflm.2014.12.012","article-title":"Cerebrospinal fluid PCR analysis and biochemistry in bodies with severe decomposition","volume":"30","author":"C Palmiere","year":"2015","journal-title":"J Forensic Leg Med"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0166158","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T19:50:42Z","timestamp":1588967442000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0166158"}},"subtitle":[],"editor":[{"given":"Pere-Joan","family":"Cardona","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,11,9]]},"references-count":47,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2016,11,9]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0166158","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,9]]}}}