Diagnosis of extrapulmonary tuberculosis by GeneXpert MTB/RIF Ultra assay

ABSTRACT Introduction Diagnosis of extrapulmonary tuberculosis (EPTB) is an arduous task owing to different anatomical locations, unusual clinical presentations, and sparse bacillary load in clinical specimens. Although GeneXpert® MTB/RIF is a windfall in TB diagnostics including EPTB, it yields low sensitivities but high specificities in many EPTB specimens. To further improve the sensitivity of GeneXpert®, GeneXpert® Ultra, a fully nested real-time PCR targeting IS6110, IS1081 and rpoB (Rv0664) has been endorsed by the WHO (2017), wherein melt curve analysis is utilized to detect rifampicin-resistance (RIF-R). Area covered We described the assay chemistry/work design of Xpert Ultra and evaluated its performance in several EPTB types, that is, TB lymphadenitis, TB pleuritis, TB meningitis, and so on, against the microbiological reference standard or composite reference standard. Notably, Xpert Ultra exhibited better sensitivities than Xpert, but mostly at the compensation of specificity values. Moreover, Xpert Ultra exhibited low false-negative and false-positive RIF-R results, compared with Xpert. We also detailed other molecular tests, that is, Truenat MTBTM/TruPlus, commercial real-time PCR, line probe assay, and so on, for EPTB diagnosis. Expert opinion A combination of clinical features, imaging, histopathological findings, and Xpert Ultra are adequate for definite EPTB diagnosis so as to initiate an early anti-tubercular therapy. Plain Language Summary We discussed the assay chemistry and evaluated performance of GeneXpert®MTB/RIF Ultra to identify the TB germs and resistance to one of the potent bactericidal drugs, that is, rifampicin in different types of extrapulmonary TB (EPTB, TB in organs other than lungs) and compared its performance with its ancestor, that is, GeneXpert. We briefly outlined the other molecular tests, such as Truenat MTBTM/Truenat MTBTM Plus, commercial real-time PCR, line probe assay, and so on for EPTB diagnosis. While evaluating Xpert Ultra results, the ‘trace call’ has been introduced, whose interpretation is important. By and large, Xpert Ultra assay outperformed in TB lymphadenitis, TB pleuritis, and TB meningitis when compared with Xpert, though limited information is available on other EPTB forms. Overall, the sensitivity of Xpert Ultra has been increased in most of EPTB cases, but mostly at the cost of specificity values. SUMMARY We detailed the assay chemistry and efficiency of GeneXpert® MTB/RIF Ultra to detect Mtb and RIF-R in different clinical forms of EPTB, against culture or composite reference standard. We compared the pros and cons of Xpert Ultra with its predecessor, that is, Xpert and also outlined the other molecular tests, that is, Truenat MTBTM/TruenatMTBTM Plus, commercial real-time PCR (e.g. Cobas TaqMan Mtb), line probe assay, and so on, to diagnose EPTB. While interpreting Xpert Ultra results, the ‘trace call’ has been incorporated, its interpretation is crucial that needs consideration of previous TB history, HIV status and whether the individual has childhood/adult TB. Overall, Xpert Ultra performed well in TB lymphadenitis, TB pleuritis, and TB meningitis, while limited information is available on other EPTB types, for which more studies are needed to ensure the authenticity of assay.