Performance of the G4 Xpert® MTB/RIF assay for the detection of Mycobacterium tuberculosis and rifampin resistance: a retrospective case-control study of analytical and clinical samples from high- and low-tuberculosis prevalence settings

Table 2 Sequence results for discrepant samples

a. Analytical study
DST Result	Xpert MTB/RIF assay result	Number	Sequence result^a
RIF-resistant	MTB not detected	3	MTB
RIF-susceptible	MTB not detected	1	MTB
RIF-resistant	RIF Resistance not detected	2	2 of 2 wild type rpoB core
RIF-susceptible	RIF Resistance detected	9	8 of 9 with resistance associated mutations in rpoB core: three with 531 ttg, three with 526 tgc, one with 516 gtc, one with 526 ctc 1 of 9 wild type rpoB core
b. Combined clinical studies
Culture/DST result	Xpert MTB/RIF assay result	Number	Bi-directional sequencing
Smear-positive specimens
MTB positive	MTB not detected	1	MTB
MTB negative^b	MTB detected	1	N/A
Smear-negative specimens
MTB positive	MTB not detected	28	MTB
MTB negative^c	MTB detected	7	N/A
Rifampin resistance results
MTB positive/RIF- resistant	MTB detected; RIF Resistance NOT detected	1	Resistance associated mutation in rpoB core: 531 ttg with evidence of wild type mixture
MTB positive/RIF- susceptible	MTB detected; RIF Resistance detected	4	2 of 4 with resistance associated mutations in rpoB core: both with 533 ccg
MTB positive/RIF- susceptible	MTB detected; RIF Resistance detected	4	2 of 4 with susceptible associated rpoB core: one wild-type and one 514 ttt (silent) mutation.

^aCulture negativity was based on only one sputum specimen for this subject
^bCulture negativity classification was based on one sputum specimen for three subjects, two sputum specimens for two subjects and three sputum specimens for two subjects
^cIt is noted that DST did not detect some common mutations associated with rifampin resistance that were identified by sequencing. Several studies have demonstrated that testing the same strains with varying DST methodology can result in different rifampin resistance results [12, 23–25]

ISSN: 1471-2334