title: Diagnostic accuracy of Xpert MTB/RIF for extrapulmonary tuberculosis specimens: establishing a laboratory testing algorithm for South Africa.
abstract: 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 = 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-acetyl-l-cysteine-sodium hydroxide) decontamination prior to liquid culture. Residual specimens (volumes > 1 ml) after inoculation of culture (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.
authors.affiliation: Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa lesley.scott@nhls.ac.za.
authors.forename: Lesley Erica
authors.initials: LE
authors.lastname: Scott
authors.affiliation: National Health Laboratory Service, South Africa Division of Clinical Microbiology and Infectious Diseases; University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Natalie
authors.initials: N
authors.lastname: Beylis
authors.affiliation: 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 National Health Laboratory Service, South Africa.
authors.forename: Mark
authors.initials: M
authors.lastname: Nicol
authors.affiliation: Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Gloria
authors.initials: G
authors.lastname: Nkuna
authors.affiliation: National Health Laboratory Service, National Priority Program, Johannesburg, South Africa.
authors.forename: Sebaka
authors.initials: S
authors.lastname: Molapo
authors.affiliation: National Health Laboratory Service, National Priority Program, Johannesburg, South Africa.
authors.forename: Leigh
authors.initials: L
authors.lastname: Berrie
authors.affiliation: National Health Laboratory Service, South Africa Division of Clinical Microbiology and Infectious Diseases; University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Adriano
authors.initials: A
authors.lastname: Duse
authors.affiliation: Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa National Health Laboratory Service, National Priority Program, Johannesburg, South Africa.
authors.forename: Wendy Susan
authors.initials: WS
authors.lastname: Stevens
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000465:Algorithms; D000995:Antitubercular Agents / Q000494:pharmacology; D001431:Bacteriological Techniques / Q000379:methods*; D001826:Body Fluids / Q000382:microbiology; D002648:Child; D002675:Child, Preschool; D024881:Drug Resistance, Bacterial; D005260:Female; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008198:Lymph Nodes / Q000382:microbiology; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D012293:Rifampin / Q000494:pharmacology; D012680:Sensitivity and Specificity; D013019:South Africa; D014376:Tuberculosis / Q000175:diagnosis*; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents; D012293:Rifampin