Deciphering Rifampicin resistance among Tuberculosis patients who have trace and indeterminate results on Xpert MTB/RIF ultra assay

Abstract

Although WHO endorsed the GeneXpert test as the first initial test for Tuberculosis diagnosis, some of the GeneXpert Ultra results include MTB detected trace, RIF resistance indeterminate which necessitates a sample rerun, increasing the time necessary for treatment initiation. This study aimed to decipher Rifampicin resistance among tuberculosis patients who have trace and indeterminate results. 403 Sample results with MTB detected and Rifampicinn resistance indeterminate on Xpert MTB/RIF Ultra assay stored at the Mycobacteriology BSL-3 Laboratory from 2018 to 2023 were retrieved, thawed, sub-cultured using BACTECTM MGITTM960 System and subjected to a first line Drug susceptibility test, first line Line-Probe assay and a repeat GeneXpert to decipher Rifampicin resistance. Results: 403 sample results were retrieved from the database of which 31 (7.7%) were MGIT culture positive and 372 (92.3%) were culture negative. Of the 31 culture-positive isolates, 24/31 (77.4%) were confirmed MTBc positive, with sputum samples being the predominant sample type (87.5%) followed by stool samples at 4.7% and nasal swabs at 2.7%. Notably, 4/24 (16.7%) of samples turning MGIT culture positive were baseline samples. Of the 24 MTBc positive isolates, 19 stored isolates were successfully found and retested, revealing a complex pattern with no detected rifampicin resistance. The prevalence of rifampicin resistance was determined as nil based on phenotypic DST. No mutations were detected among cases with rifampicin resistance indeterminate results, and only one mutation related to isoniazid (INH) resistance was identified using LPA. Our study revealed no missed rifampicin resistance among patients with GeneXpert ultra-trace and rifampicin indeterminate results with both first line DST and LPA.