Reflex Xpert MTB/XDR Testing of Residual Rifampicin-Resistant Specimens: A Clinical Laboratory-Based Diagnostic Accuracy and Feasibility Study in South Africa

C M Centner; R Munir; E Tagliani; F Rieß; P Brown; C Hayes; T Dolby; W Zemanay; D M Cirillo; A David; S G Schumacher; C M Denkinger; M Ruhwald; V N Leukes; M P Nicol; I Van der Walt; G Kisten; M Gumede; A Mace; A Brink; W Stevens; L Scott; A Penn-Nicholson; H Cox; TB-CAPT Consortium

doi:10.1093/ofid/ofae437

Reflex Xpert MTB/XDR Testing of Residual Rifampicin-Resistant Specimens: A Clinical Laboratory-Based Diagnostic Accuracy and Feasibility Study in South Africa

Open Forum Infect Dis. 2024 Jul 31;11(8):ofae437. doi: 10.1093/ofid/ofae437. eCollection 2024 Aug.

Authors

C M Centner^{1

2}, R Munir³, E Tagliani⁴, F Rieß⁵, P Brown¹, C Hayes⁶, T Dolby⁷, W Zemanay¹, D M Cirillo⁴, A David³, S G Schumacher⁸, C M Denkinger^{8

9}, M Ruhwald⁸, V N Leukes⁸, M P Nicol¹⁰, I Van der Walt⁶, G Kisten⁷, M Gumede⁷, A Mace⁸, A Brink^{1

2

11}, W Stevens^{3

12}, L Scott^{3

12}, A Penn-Nicholson⁸, H Cox^{1

11}; TB-CAPT Consortium

Collaborators

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

Affiliations

¹ Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
² National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa.
³ Wits Diagnostic Innovation Hub, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁴ Emerging Bacterial Pathogens Unit, IRCCS Ospedale San Raffaele, Milan, Italy.
⁵ Division of Infectious Diseases and Tropical Medicine, LMU University Hospital, LMU Munich, Munich, Germany.
⁶ National Health Laboratory Service, Gqeberha, South Africa.
⁷ National Health Laboratory Service, Cape Town, South Africa.
⁸ Tuberculosis Programme, FIND, Geneva, Switzerland.
⁹ Division of Infectious Disease and Tropical Medicine, Center for Infectious Diseases, Heidelberg University Hospital, and German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.
¹⁰ Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.
¹¹ Welcome Centre for Infectious Disease Research in Africa and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
¹² National Priority Program, National Health Laboratory Service, Johannesburg, South Africa.

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.

Keywords: Xpert MTB/XDR; diagnostic accuracy; drug resistance; feasibility; tuberculosis.