India accounts for about one-fourth of the global burden of MDR-TB. This study aims to assess  the prevalence and factors associated with tuberculosis drug resistance among patients from South India. MTBDRplus assay and MGIT liquid culture performed on 20,245 sputum specimens obtained from presumptive MDR-TB cases during a six-year period from 2013 to 2018 were analyzed retrospectively. Univariate and multivariate logistic regression analysis was carried out to evaluate factors associated with MDR, Rifampicin mono-resistance, and Isoniazid mono-resistance. MDR, Rifampicin mono- resistant and Isoniazid mono-resistant TB were  found in 5.4%, 2.5%, and 11.4% cases of presumptive MDR-TB, respectively. Based on the rpoB gene, true resistance, hetero-resistance, and inferred resistance to Rifampicin was found in 38%, 29.3%, and 32.7% of the 1582 MDR cases, respectively. S450L (MUT3) was the most common rpoB mutation present in 59.4% of the Rifampicin resistant cases. Of the 3390 Isoniazid resistant cases, 72.5% had mutations in the katG gene, and 27.5% had mutations in the inhA gene. True resistance, heteroresistance, and inferred resistance accounted for 42.9%, 22.2%, and 17.3% of the 2459 katG resistant cases, respectively. True resistance, heteroresistance, and inferred resistance for the inhA gene were found in 54.5%, 40.7%, and 4.7% cases, respectively. MDR-contact (AOR 3.171 95% CI: 1.747–5.754, p-0.000) treatment failure (AOR 2.17595% CI: 1.703–2.777, p-0.000) and female gender (AOR 1.315 95% CI: 1.117–1.548, p-0.001), were positively associated with MDR-TB. Previous TB treatment did not show a significant positive association with MDR (AOR 1.113 95% CI: 0.801–1.546, p-0.523). Old age (AOR 0.994 95% CI: 0.990–0.999, p-0.023) and HIV seropositivity (AOR 0.580 95% CI: 0.369–0.911, p-0.018) were negatively associated with MDR-TB. Although Rifampicin mono-resistance had a positive association with treatment failure (AOR 2.509 95% CI: 1.804–3.490, p < .001), it did not show any association with previous TB treatment (AOR 1.286 95% CI: 0.765–2.164, p-0.342) or with history of contact with MDR-TB (AOR 1.813 95% CI: 0.591–5.560, p-0.298). However, INH mono-resistance showed a small positive association with the previous history of treatment for TB (AOR 1.303 95% CI: 1.021–1.662, p-0.033). It was also positively associated (AOR 2.094 95% CI: 1.236–3.548, p-0.006) with MDR-TB contacts. Thus INH resistance may develop during treatment if compliance has not adhered too and may be easily passed on to the contacts while Rifampicin resistance is probably due to factors other than treatment compliance. MDR-TB, i.e. resistance to both Rifampicin and Isoniazid, is strongly correlated with treatment failure, spread through contact, and not to treatment compliance. The temporal trend in this region shows a decrease in MDR prevalence from 8.4% in 2015 to 1.3% in 2018. A similar trend is observed for Rifampicin mono-resistance and Isoniazid mono-resistance, pointing to the effectiveness of the TB control program. The higher proportion of inferred resistance observed for Rifampicin compared with INH may indicate a surfeit of mechanisms that enable rifampicin resistance. Association of MDR-TB with age, gender, and HIV status suggest the role of the immune system in the emergence of the MDR phenotype.

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The diagnostic challenges in extra-pulmonary tuberculosis remain to be addressed even though remarkable progress has been made in the diagnostics of pulmonary tuberculosis during the last decade. Methods: This study was conducted to evaluate the use of polymerase chain reaction (PCR) in diagnosis of definitive extra pulmonary tuberculosis patients, and to assess the performance of insertion sequence (IS)6110 based PCR assay as compared to conventional liquid culture by Microbial growth Indicator Tube (MGIT) 960 system. Results: A total of 792 clinical specimens were collected from clinically suspected extra pulmonary tuberculosis patients. The specimens included 22 ascitic fluids, 69 pleural fluids, 240 Cerebrospinal fluids (CSF), 386 endometrial tissues, 47 lymph nodes, 22 pus, one synovial fluid, one fallopian tube, two brain abscess and two ovarian cyst samples. All these clinical samples were subjected to Auromine O staining (FM) for acid fast bacilli (AFB) and culture on MGIT 960 tubes containing Modified Middlebrooks 7H9 broth medium. PCR was performed by targeting 123bp fragment of insertion sequence IS6110 of Mycobacterium tuberculosis. Our study of 792 specimens, revealed their 87.5% sensitivity to endometrial samples, 92.31% sensitivity for cerebrospinal fluid, and 66.66% sensitivity in Pleural fluid and 60% sensitivity in Lymph node samples. The combined sensitivity and specificity of the PCR IS6110 was calculated to be 85.71% and 82.91%, respectively. Conclusion: PCR using IS6110 primer was able to pick up more positivity in extra pulmonary samples as compared to conventional culture method for the detection of M. tuberculosis.

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