top of page


Deeplex® Myc-TB assay: Informing genotypic/phenotypic associations in Mycobacterium tuberculosis isolates

J Steyn(1) M Grobbelaar(1) J Williams(1) Y Ghebrekristos(4) C J Opperman(1,4) S Singh(1,4) N Ismail(1) T C Rodwell(5,6) R Colman(5,6) F Naufal(2) J Limberis(2) R M Warren(1) J Metcalfe(2,3)

1:Faculty of Medicine and Health Sciences, Stellenbosch University; 2:Division of Experimental Medicine, University of California; 3:Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California; 4:National Health Laboratory Service, Green Point TB Laboratory; 5:FIND, Geneva, Switzerland; 6:Department of Medicine, University of California

The World Health Organization (WHO) endorsed the Deeplex Myc-TB assay (GenoScreen), which utilizes targeted next-generation sequencing (tNGS) to predict Mycobacterium tuberculosis antibiotic resistance, including drugs in the BPaLM regimen (bedaquiline [BDQ], linezolid, and moxifloxacin).

We initiated a pilot study (TS ELiOT) in collaboration with the National Health Laboratory Services to determine the feasibility of implementing tNGS into the routine standard of care for rifampicin resistant (RR-)TB. We successfully sequenced 343 clinical specimens (consecutive sampling) using the Deeplex assay between April and August 2023.

Resistance-associated or uncharacterized variants we identified from sequence data using the automated Deeplex web app. Phenotypic drug susceptibility testing was done on isolates with variants in the mmR5 gene to confirm BDQ resistance.

A total of 29/343 (8.5%) isolates harboured variants in mmR5 of which 18/29 (62%) were deemed resistant to BDQ by tNGS, while 11/29 (38%) harboured uncharacterised variants. pDST confirmed BDQ resistance to 9/11 (82%) uncharacterised variants. 5 of the 11 uncharacterised variants were listed as uncertain significance in the WHO catalogue while 6 were not listed. Out of the 18/29 isolates deemed resistant to BDQ by tNGS, pDST confirmed resistance to 15 isolates.

We document a relatively high proportion of BDQ resistance in an unselected sample of patients with RR-TB before the formal roll-out of BPaLM. Scale-up of tNGS may be critical to inform clinical decision-making and preserve the utility of keystone drugs like BDQ. tNGS data must contribute to the WHO catalogue to ensure the utility of genetic drug susceptibility testing.

bottom of page