No hidden rifampicin resistance found in Xpert Ultra trace TB tests

When a modern molecular test flags tuberculosis with a “trace” signal but reports rifampicin resistance as indeterminate, clinicians face a frustrating gap: the result is usually non-actionable and prompts retesting. That dilemma is the focus of work led by Nelissa Juliet Nantumbwe and colleagues. The team set out to “decipher” rifampicin resistance among patients whose Xpert MTB/RIF Ultra assay results showed MTB detected trace and RIF resistance indeterminate. To do this they searched laboratory records from August 2018 to June 2023 at the Mycobacteriology (BSL-3) and Molecular Diagnostic laboratories in the College of Health Sciences, Makerere University. They identified 403 Xpert MTB/RIF Ultra assay records that met those criteria and that had matching culture results. Rather than relying solely on the initial molecular readout, the researchers retrieved isolates from those samples that were culture positive and prepared them for further testing. The aim was practical: determine whether the initial indeterminate rifampicin call hid any true rifampicin resistance that would affect patient care and treatment decisions.

From the 403 MTB detected trace, RIF resistance indeterminate results with culture data, the researchers focused on samples that yielded positive cultures. Isolates that turned out culture positive were retrieved and sub-cultured in liquid media to allow additional testing. The team performed phenotypic first line Drug Susceptibility tests, first line Line-Probe assays (LPA) and repeat GeneXpert ultra on those sub-cultured isolates. They also ran MTBDRplus assay as part of the molecular line-probe work. The key molecular finding reported was that MUT1 related to isoniazid (INH) resistance was identified using MTBDRplus assay. Crucially, across the MTBc culture positive samples that had initially been Xpert ultra-trace and rifampicin resistance indeterminate, the study did not identify any missed rifampicin resistance. In other words, repeat and supplementary testing in this group did not uncover hidden rifampicin-resistant strains.

The findings have a clear, cautious message. In this set of 403 trace Xpert MTB/RIF Ultra assay results with RIF resistance indeterminate, further testing of culture-positive isolates did not reveal missed rifampicin resistance. That suggests that, at least in this laboratory setting and time period, an indeterminate rifampicin result on a trace Xpert Ultra did not routinely mask rifampicin-resistant tuberculosis. At the same time, the identification of MUT1 related to isoniazid (INH) resistance by MTBDRplus assay highlights that other drug resistance signals can appear and may warrant attention. The authors emphasize limits: the study size and setting constrain broad conclusions. They call for more studies with bigger sample sizes, especially in high MDR-TB settings, before changing clinical practice about repeat testing or treatment decisions based solely on an Xpert ultra-trace, rifampicin resistance indeterminate result.