Molecular analysis of rpoB gene mutation in MTB detected isolates in a tertiary care centre (AGMC) of North-East, India.

BACKGROUND: Rifampicin (RIF), one of the first line drug in treatment of tuberculosis. It acts on rpoB gene which encodes RNA polymerase ß subunit. In 95% of RIF resistant cases, mutations are present in rpoB gene. Most of them are within 81bp RIF-resistance determining region (RRDR).Xpert MTB/RIF assay has been tremendously revolutionalised the diagnosis of tuberculosis (TB).Also sequencially detect bacteria and resistance to rifampicin (rif).Approximately 96% of rif-resistant Mycobacterium tuberculosis (MTB) strains worldwide, showed mutations in a region at the 507-533rd amino acid residuals (81 bp) in the MTB rpoB gene. Here evaluation is made about frequent regions of amplification and mutation in various codons of 81bp of rpoB gene in rif sensitive and rif resistant cases. METHODS: A total of 4116 samples were received at Mycobacteriology laboratory, AGMC and processed in CBNAAT.Data of MTB detected samples were collected & statistically analysed to detect frequency of amplification & no amplification in various regions of 81bp of rpoB genes. RESULTS: Out of 4116 samples, MTB was detected in 1323 samples. Among them 1291 (97.58%) cases were Rif sensitive (RS) and 32 (2.41%) cases were rif resistance (RR).Most of the MTBC detected samples showed amplification in probe A then in probe C.78.12% rif resistant cases showed mutation in either of the probe, commonest is probe E. Study also showed low bacillary loads in most of the RR cases. CONCLUSION: Study highlighted variations in amplification of different regions of 81bp of rpoB gene in MTBC detected cases. North-east India, like other part of world, also showed highest frequency of mutation in probe E in rif resistant cases.

Comparison of SARS-CoV-2 diagnosis by rapid antigen detection kit with RT-qPCR in a tertiary care setup in North Eastern India.

PURPOSE: Real time reverse transcriptase polymerase chain reaction (RT-qPCR) is still considered a gold standard for the diagnosis of COVID-19. However, due to several limitations, use of RT-qPCR is limited in a resource poor setting like North East India. Rapid antigen detection testing kit has revolutionized the diagnosis and management of COVID-19 in India. However, conflicting reports exist regarding the efficacy of the kits for diagnosis of COVID-19. This study aims to highlight the performance of Standard Q COVID-19® Antigen detection kit (SD Biosensor) compared with RT-qPCR in the setup of North East India. METHODS: Nasopharyngeal and oropharyngeal swab samples were collected from consenting patients attending the flu clinic in the period from 1st July to December 31, 2020. Samples were transferred to Viral Research and Diagnostic Laboratory (VRDL) for RT-qPCR test. Antigen detection from the patient samples were undertaken using Standard Q ® COVID-19 antigen detection kit (SD Biosensor, Republic of Korea). Data were then analyzed for comparison between RT-qPCR and antigen kit results. RESULTS: During the study period, 189 samples were collected, out of which 119 were positive by RT-qPCR. Out of 119 positive samples, calculated sensitivity and specificity of the rapid antigen kit was 63% and 100% respectively. Sensitivity and diagnostic accuracy increases in symptomatic patients as compared to asymptomatic patients. Cohen's Kappa coefficient showed a moderate association (0.6) between the kit and RT-qPCR test. The kit performed optimally at a CT value of ≤32.5 for N gene with a predicted sensitivity of 77.3% and specificity of 93.3%. CONCLUSION: The study shows an overall acceptable sensitivity and specificity of the testing kit, with a better performance in symptomatic patients. The association of the kit result is moderate with the results obtained in RT-qPCR. In this study, the rapid antigen test kit performed optimally at N gene qRT PCR cut off value of ≤32.5.