Performance Evaluation of Xpert MTB/RIF Assay and Prevalence of rpoB Gene Mutation in <em> Mycobacterium Tuberculosis</em> in Clinical Isolates Quetta, Pakistan: A Cross Sectional Retrospective Cohort Study
DOI:
https://doi.org/10.24203/ajpnms.v9i1.6118Keywords:
RRDR, rpoB, MDR-TB, 81 bp, Xpert® MTB/RIF.Abstract
With the use of Xpert assay, the detection mechanism of tuberculosis has completely transformed. Concurrently detecting mycobacterium and its resistance to rifampin (rif) which is also one of the primary marker for MDR-TB in addition to its surrogate activity against MTB in first line drugs. At large, resistance of mycobacterium strains against rifampicin is caused by rpoB gene mutations about 96.1 % globally while these mutations are generally situated at a site of 507-533rd residuals of amino acid in the rpoB gene of Mycobacterium, this region is also termed as Rifampicin resistance determining region (RRDR). In this study, we determined the mutations of various rpoB genes in different probes of 81 bp of RRD Region. A total of 6353 different specimens obtained at provincial reference laboratory of Fatima Jinnah general and chest hospital, Quetta (FJHQ), between Jan 2016 and Apr 2018 were examined by Xpert MTB/RIF assay. Altogether positive and negative samples for MTB were further examined with the light emitting diode (LED) fluorescence microscope. Pearson Chi square test was used to find out the associations between probe type and gender, treatment history and age group of the patients. Out of 6353 specimens 1297 MTB positive cases were detected by Xpert assay including 184 samples having both mycobacterium and RIF-resistance advised by mutations in 81 bp-RRD Region of rpoB gene which is further divided into five different probes. Further LED fluorescence microscope detected and confirmed 327 positive MTB samples out of 1297 specimens of Xpert assay. The associated probes mutation for rifampicin resistance were as follow: E (98/184), D (23/184), B (15/184), C (5/184), A (3/184), two probe mutation (5/184) in D&E (3/184) and C&D (2/184) and all probe mutation (35/184). The percentage of rpoB gene mutation in the studied population was 14.187 %. The commonest mutation associated with rpoB gene was in Probe E (53.2608%) also termed as 531 and 533 codons, additionally two probe mutation (2.7173%) in D&E (1.6304%) and C&D (1.0869%) and all probe mutation (19.0217%) were also detected that has never been detected before globally.
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