Testing tongue swab samples by Cepheid Xpert MTB/RIF Ultra: comparison of two protocols applied to samples from persons with low-bacillary load TB

Tongue swabs (TS) are non-sputum specimens for molecular diagnosis of tuberculosis (TB). Analysis of swabs by Cepheid Xpert MTB/RIF Ultra (Xpert Ultra) is less sensitive than the use of certain manual quantitative polymerase chain reaction methods, but is desirable given the widespread use and familiarity of Xpert Ultra. This study evaluated an easy-to-use protocol for analyzing TS by Xpert Ultra. TS samples from symptomatic South African patients were previously collected and tested by Xpert Ultra using a protocol that requires a heating block (termed Heat + TE). Replicate, paired samples from the same patients were tested by a newly reported method that does not require heating (termed 2:1 SR). The diagnostic accuracy of the two methods was compared. This paired comparison prioritized samples from participants with low sputum bacillary loads, a population in whom TS sensitivity is lowest. Eighty-eight were TB-positive by sputum microbiological reference standard (MRS) and 20 were TB-negative (total <i>N</i> = 180). Within this sample set, the Heat + TE method was 42.5% (38/88; 95% confidence interval [CI]: 33-54%) sensitive, and the 2:1 SR method was not significantly different at 52.3% (46/88; 95% CI: 41-63%) sensitive relative to sputum MRS. Both methods were 100% (20/20; 95% CI: 83-100%) specific. A secondary analysis compared the sensitivities of single-sample versus dual-sample testing within a cohort (<i>N</i> = 241) that included both high- and low-bacillary load participants. Testing of a single sample was 75.5% (182/241; 95% CI: 70-81%) sensitive relative to sputum MRS, whereas dual sampling was 81.3% (196/241; 95% CI: 76-86%) sensitive; the difference was not significant.IMPORTANCETongue swab (TS) samples are novel, non-invasive, easy-to-collect diagnostic specimens for tuberculosis testing. This study compared two methods for processing TS samples in preparation for analysis using Xpert Ultra, a popular commercial platform for molecular detection of <i>Mycobacterium tuberculosis</i> DNA in human specimens. A newly described method has logistical advantages over a previously described method, in that it does not require additional equipment and is less prone to errors. The newly described method was found to be at least as sensitive and specific as the previous method. Therefore, the logistical advantages of the new method come at no cost in terms of diagnostic accuracy, and its adoption is recommended. A secondary analysis indicated that dual-sample testing can modestly boost diagnostic yield relative to testing a single sample.