How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis ?

Kamela C. S. Ng (1, 2, 3) , Philip Supply (4) , Frank G. J. Cobelens (2) , Cyril Gaudin (5) , Julian Gonzalez-Martin (3) , Bouke C. de Jong (1) , Leen Rigouts (1, 6)

1 ITM - Institute of Tropical Medicine [Antwerp]
2 VU University Medical Center [Amsterdam]
3 UB - Universitat de Barcelona
4 CIIL - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
5 Genoscreen [Lille]
6 Universiteit Antwerpen = University of Antwerpen [Antwerpen]

Rifampin heteroresistance—where rifampin-resistant and -susceptible tuberculosis (TB) bacilli coexist—may result in failed standard TB treatment and potential spread of rifampin-resistant strains. The detection of rifampin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment and may improve rifampin-resistant TB control. The limit of detection (LOD) of rifampin heteroresistance for phenotypic drug susceptibility testing by the proportion method is 1% and, yet, is insufficiently documented for RDTs. We, therefore, aimed to determine, for the four RDTs (XpertMTB/RIF, XpertMTB/RIF Ultra, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII), the LOD per probe and mutation, validated by CFU counting and targeted deep sequencing (Deeplex-MycTB). We selected one rifampin-susceptible and four rifampin-resistant strains, with mutations D435V, H445D, H445Y, and S450L, respectively, mixed them in various proportions in triplicate, tested them with each RDT, and determined the LODs per mutation type. Deeplex-MycTB revealed concordant proportions of the minority resistant variants in the mixtures. The Deeplex-MycTB-validated LODs ranged from 20% to 80% for XpertMTB/RIF, 20% to 70% for Xpert Ultra, 5% to 10% for GenoTypeMTBDRplusv2.0, and 1% to 10% for GenoscholarNTM+MDRTBII for the different mutations. Deeplex-MycTB, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII provide explicit information on rifampin heteroresistance for the most frequently detected mutations. Classic Xpert and Ultra report rifampin heteroresistance as rifampin resistance, while Ultra may denote rifampin heteroresistance through “mixed patterns” of wild-type and mutant melt probe, melt peak temperatures. Overall, our findings inform end users that the threshold for reporting resistance in the case of rifampin heteroresistance is the highest for Classic Xpert and Ultra to resolve phenotypic and genotypic discordant rifampin-resistant TB results.

Mots clés: Deeplex-MycTB; GenoscholarNTM+MDRTBII; GenoTypeMTBDRplusv2.0; Mycobacterium tuberculosis; XpertMTB/RIF; XpertMTB/RIF Ultra; limit of detection; rifampin heteroresistance; rifampin-resistant tuberculosis

Domaines: Microbiologie et Parasitologie

Kamela C. S. Ng, Philip Supply, Frank G. J. Cobelens, Cyril Gaudin, Julian Gonzalez-Martin, et al.. How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis ?. Journal of Clinical Microbiology, 2019, 57 (11), pp.e00717-19. ⟨10.1128/JCM.00717-19⟩. ⟨hal-02347029⟩