{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:09:12Z","timestamp":1784246952179,"version":"3.55.0"},"reference-count":25,"publisher":"American Society for Microbiology","issue":"6","license":[{"start":{"date-parts":[[2014,6,1]],"date-time":"2014-06-01T00:00:00Z","timestamp":1401580800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2014,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            South Africa implemented Xpert MTB\/RIF as the initial diagnostic test for pulmonary tuberculosis (TB). Xpert MTB\/RIF's accuracy for diagnosing extrapulmonary tuberculosis (EPTB) was investigated. EPTB specimens (\n            <jats:italic>n<\/jats:italic>\n            = 7,916) from hospitalized patients received over a 6-month period at a high-throughput TB referral laboratory in Johannesburg were investigated. Large-volume specimens were centrifuged, tissue biopsy specimens homogenized, and all specimens checked for growth of contaminating bacteria on blood agar. Contaminated samples received NALC-NaOH (\n            <jats:italic>N<\/jats:italic>\n            -acetyl-\n            <jats:sc>l<\/jats:sc>\n            -cysteine\u2013sodium hydroxide) decontamination prior to liquid culture. Residual specimens (volumes &gt; 1 ml) after inoculation of culture (\n            <jats:italic>n<\/jats:italic>\n            = 1,175) were tested using the Xpert MTB\/RIF sputum protocol. Using culture as the reference, Xpert MTB\/RIF's overall sensitivity was 59% (95% confidence interval [95% CI], 53% to 65%) and specificity was 92% (CI, 90% to 94%), with the highest sensitivities of 91% (95% CI, 78% to 97%) for pus, 80% (95% CI, 56% to 94%) for lymph node aspirates, and 51% (95% CI, 44% to 58%) for fluids (ascitic, 59%; pleural, 47%). A difference in sensitivities was noticed between specimens classified as having a thick (87% [95% CI, 76% to 94%]) versus clear (watery) (48% [95% CI, 36% to 61%]) appearance. This was unchanged with traces of blood (52% [95% CI, 44% to 60%]) or precentrifugation (57% [95% CI, 28% to 82%]) among clear specimens. Xpert MTB\/RIF generated an additional 124 specimen results that were contaminated by Mycobacterial Growth Indicator Tubes (MGIT; 10.5%) and diagnosed rifampin (RIF) resistance earlier (9.6% [25\/260]). Xpert MTB\/RIF's performance on EPTB specimens provides very promising results and should be considered for incorporation into national TB guidelines. Xpert MTB\/RIF is less affected by contaminating bacteria and reduces laboratory labor and diagnostic delay compared to traditional methods.\n          <\/jats:p>","DOI":"10.1128\/jcm.03553-13","type":"journal-article","created":{"date-parts":[[2014,3,13]],"date-time":"2014-03-13T01:02:55Z","timestamp":1394672575000},"page":"1818-1823","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":94,"title":["Diagnostic Accuracy of Xpert MTB\/RIF for Extrapulmonary Tuberculosis Specimens: Establishing a Laboratory Testing Algorithm for South Africa"],"prefix":"10.1128","volume":"52","author":[{"given":"Lesley Erica","family":"Scott","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalie","family":"Beylis","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, South Africa"},{"name":"Division of Clinical Microbiology and Infectious Diseases; University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Nicol","sequence":"additional","affiliation":[{"name":"Division of Medical Microbiology, Department of Clinical Laboratory Sciences and Institute for Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa"},{"name":"National Health Laboratory Service, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gloria","family":"Nkuna","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebaka","family":"Molapo","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, National Priority Program, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leigh","family":"Berrie","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, National Priority Program, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriano","family":"Duse","sequence":"additional","affiliation":[{"name":"National Health Laboratory Service, South Africa"},{"name":"Division of Clinical Microbiology and Infectious Diseases; University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wendy Susan","family":"Stevens","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa"},{"name":"National Health Laboratory Service, National Priority Program, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.2217\/17460913.3.1.1"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0907847"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1002\/14651858.CD009593.pub3"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1586\/eri.12.43"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1183\/09031936.00176311"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02157-10"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00491-11"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05454-11"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02268-10"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01310-11"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.06467-11"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02319-10"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.5588\/ijtld.10.0497"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00211-11"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2012.02.012"},{"key":"e_1_3_2_17_2","volume-title":"Global tuberculosis report 2013","author":"World Health Organization","year":"2013","unstructured":"World Health Organization. 2013. Global tuberculosis report 2013. World Health Organization, Geneva, Switzerland. http:\/\/www.who.int\/tb\/country\/en\/."},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.7196\/SAMJ.7156"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01310-11"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-013-1890-0"},{"key":"e_1_3_2_21_2","volume-title":"Abstr. 43rd Union World Conf. Lung Health","author":"Stevens W","year":"2011","unstructured":"StevensWErasmusLOlsenFPotgieterMCandySMvusiLMolapoSMametjaDScottLE. 2011. Reporting Xeprt MTB\/RIF resistance data from South Africa's National TB programme, IUATLD. Abstr. 43rd Union World Conf. Lung Health, Kuala Lumpur, Malaysia, poster PC-687-16."},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1155\/2013\/650561"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00332-13"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01463-09"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00128-10"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01053-10"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.03553-13","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.03553-13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T11:55:45Z","timestamp":1646481345000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.03553-13"}},"subtitle":[],"editor":[{"given":"G. 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