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

DOI: 10.1128/JCM.00717-19

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FIG 1
Presence/absence of Xpert Ultra wild-type and mutant melt probes detected for the rifampin-resistant (RR):rifampin-susceptible (RS) mixtures per mutation type at various proportions of the minority resistant variants at the limit of detection (LOD) reported as heteroresistant (shaded in yellow), below LOD reported as RS (shaded in pink), and at full RR reported as resistant (shaded in green).

TABLE 1
Proportions of minority resistant variants detected among the rifampin-resistant:rifampin-susceptible mixtures by targeted deep sequencing^a
↵a The values represent the percentage of sequence reads bearing the indicated rpoB mutation. Gray boxes represent proportions below the nominal threshold of 3% for calling minority resistant variants used in the Deeplex-MycTB application.

TABLE 2

Limits of detection for rifampin heteroresistance among triplicates^a

Strain ID	Rifampin resistance-conferring mutations		Values by RDT quantified by Deeplex
Strain ID	Rifampin resistance-conferring mutations		LPA-Hain (%LOD)¹	Deeplex (%QP)¹	LPA-Nipro (%LOD)¹	Deeplex (%QP)¹	Xpert (%LOD)¹	Deeplex (%QP)¹	Ultra (%LOD)²	Deeplex (%QP)²
TB-TDR-0036	H445D^b	H526D^c	5–10	7.5	5	7.5	40–60	55.9	40–60
TB-TDR-0090	S450L^b	S531L^c	5	5	1–5	5	20–40	21.7	20–30	21.7
TB-TDR-0100	D435V^b	D516V^c	5–10	6	5–10	6	70–80	69.6	40–50
TB-TDR-0131	H445Y^b	H526Y^c	5–10	4.3	10	8.7	70–80	66.7	60–70

↵a With quantification of the respective lowest proportion by targeted deep sequencing (Deeplex-MycTB). ID, identifier; Deeplex-MycTB, targeted deep sequencing; RDT, rapid diagnostic test; LPA-Hain, GenoTypeMTDBRplusv2.0; LPA-Nipro, GenoscholarNTM+MTBII; Xpert, classic XpertMTB/RIF; Ultra, Xpert MTB/RIF Ultra; 1, batch 1; 2, batch 2; %LOD, limit of detection (range) among triplicates for the RDTs; %QP, quantified proportion of minority resistant variants determined by Deeplex on replicate 3.
↵b In M. tuberculosis numbering.
↵c In E. coli numbering.