Reflex Xpert MTB/XDR Testing of Residual Rifampicin-Resistant Specimens: A Clinical Laboratory-Based Diagnostic Accuracy and Feasibility Study in South Africa
Authors: Centner C M , Munir R , Tagliani E , Rieß F , Brown P , Hayes C , Dolby T , Zemanay W , Cirillo D M , David A , Schumacher S G , Denkinger C M , Ruhwald M , Leukes V N , Nicol M P , Van der Walt I , Kisten G , Gumede M , Mace A , Brink A , Stevens W , Scott L , Penn-Nicholson A , Cox H ,   TB-CAPT Consortium, Leukes Vinzeigh , Penn-Nicholson Adam , Ruhwald Morten , Erkosar Berra , Schumacher Samuel G , Singh Sunita , Kivuma Bernard , Nuru Muhuminu , Mlenge Judith , Shija Neema , Bulime Deogratias , Mnzava Dorcas , Sabuni Petro , Temba Hosiana , Siru Jamali , Hella Jerry , Msafiri Jonathan , Weisser Maja , Mbaruku Mohamed , Sasamalo Mohamed , Leonard Alice , Malango Ambilikile , Alexander Annastazia , Komakoma Faith , Msigala Gloria , Johaness Kasmir , Mhalu Grace , Hamis Mwajabu , Mlay Priscilla , Ndege Robert , Barasa Sera , Masoud Swalehe , Byakuzana Theonestina , Lwilla Anange , Kayombo Benedict , Mangu Chacha , Manyama Christina , Mbunda Theodora , Siyame Elimina , Sabi Issa , Mwaipopo Last , Ntinginya Nyanda Elias , Edom Raphael , Olomi Willyhelmina , Elisio Delio , Nguenha Dinis , Mambuque Edson , Cossa Joaquim , Cossa Marta , Gomes Neide , Manjate Patricia , Munguambe Shilzia , Acacio Sozinho , Saavedra Belen , Chiconela Helio , Ribeiro Katia , Machiana António , Meggi Bindiya , Junior Candido Azize , Madeira Carla , Khosa Celso , Bila Claudio , Floripes Denise , Malamule Diosdélio , Viegas Sofia , Saavedra Belén , Amroune Carole , Ehrlich Joanna , de la Torre Pérez Laura , Sanz Sergi , Garcia-Basteiro Albero , Riess Friedrich , Mutuku Sarah , Appalarowthu Tejaswi , Larson Leyla , Kranzer Katharina , Hoelscher Michael , Heinrich Norbert , del Mar Castro Noriega Maria , Denkinger Claudia M , Arif Saima , Cirillo Daniela Maria , Tagliani Elisa , Di Marco Federico , Batignani Virginia , Malhotra Akash , Dowdy David , Schacht Claudia , Buech Julia , Stöhr Caroline , Loembé Marguerite Massinga , Ondoa Pascale , Ndlovu Nqobile , Brown Fumbani , Ghebrekristos Yonas , Hayes Cindy , Van der Walt Ilse , Abrahams Shareef , Marokane Puleng , Radebe Mbuti , Martinson Neil , David Anura , Scott Lesley , Ngwenya Lucky , Da Silva Pedro , Solomon Reyhana , Stevens Wendy , Abongomera Charles , Reither Klaus , Stieger Leon , Brink Adrian , Centner Chad M , Cox Helen , van Heerden Judi , Nicol Mark P , Hapeela Nchimunya , Brown Parveen , Solomon Reyhana , Zemanay Widaad , Dolby Tania 
Published: August 2024

Abstract

Background
The World Health Organization–approved Xpert MTB/XDR test detects Mycobacterium tuberculosis and resistance to isoniazid, fluoroquinolones, ethionamide, and injectable drugs directly in specimens. This pragmatic, laboratory-based study assessed the diagnostic accuracy and feasibility of a reflex testing approach, where Xpert MTB/XDR was performed on residual specimens previously processed for Xpert MTB/RIF Ultra.

Methods
Routine respiratory specimens, processed for Xpert MTB/RIF Ultra, were stored in sample reagent buffer at 2°C–8°C. If rifampicin resistant, the residual specimen was assessed for adequate volume (≥2 mL) and tested with Xpert MTB/XDR, with storage time recorded. A second specimen was used for routine and reference standard testing (culture and sequencing).

Results
Specimens (99% sputum) from 763 participants submitted to 2 large routine laboratories were included. Xpert MTB/XDR yielded valid resistance detection results in 639 (84%), compared with 507 (66%) for routine testing (difference [95% CI], 18% [13%–22%]). The median turnaround time for results was 23 hours for Xpert MTB/XDR and 15 days for routine testing. While 748 specimens (98%) were ≥2 mL, only 102 (13%) were stored for ≤4 hours. By the reference standard, 284 of 394 (72%) were isoniazid resistant, and 57 of 380 (15%) were fluroquinolone resistant. The sensitivities of Xpert MTB/XDR were 94% (95% CI, 91%–97%) for isoniazid and 91% (81%–97%) for fluoroquinolone resistance detection. The specificities were 98% (94%–100%) and 100% (98%–100%), respectively.

Conclusions
Xpert MTB/XDR performed favorably compared with the reference, and the reflex testing approach increased results availability over routine testing, while dramatically decreasing turnaround time from weeks to hours. Laboratory workflow precluded testing within the manufacturer-recommended 4-hour storage time, but longer storage did not appear detrimental.