Epidemiology of Molecular Probes in Xpert MTB/RIF Assay in AJK, Pakistan

Objective: This study aimed to detect rifampicin-resistant tuberculosis cases and assess the frequency of missing probes in different study populations in Azad Jammu and Kashmir (AJK), Pakistan. Methodology: The study was conducted at the State TB Reference Laboratory, District Headquarters Teaching Hospital, Mirpur, AJK. A total of 2,790 specimens collected between March 2016 to August 2019 were analyzed. Pulmonary TB (PTB) accounted for 94% of the cases, while 6% were classified as extra-pulmonary cases. All respiratory and non-respiratory samples underwent fluorescence smear microscopy (AFB) and a real-time PCR test (Xpert MTB/RIF assay) to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance. Results: Among the 2,790 suspected MTB patients, 734 (26%) were confirmed to have MTB using the Xpert MTB/RIF assay, while 564 (20%) tested positive by fluorescence microscopy. Of the MTB-positive patients, 720 (98%) were diagnosed with pulmonary TB, and 14 (2%) had extra-pulmonary TB. Rifampicin resistance (RR) was detected in 66 (9%) cases, with 97% of the resistant cases being pulmonary and 3% extra-pulmonary. The most frequently missing probe was E (Codon 529-533), accounting for 34% of the cases, followed by probe D (Codon 523-529) at 26%. The least frequently missing probe was C (Codon 523-529), observed in 3% of the cases. Probe B (Codon 512-518) was missing in 15.4% of cases, while probe A (Codon 518-523) was missing in 9.4% of cases. Conclusion: The utilization of molecular diagnostic techniques, such as the Xpert MTB/RIF assay, enables rapid identification of MTB and detection of rifampicin resistance. This study provides valuable baseline data on the prevalence of 81 bp mutations in the rpoB gene, highlighting the need for further evaluation of mutation patterns in AJK.