Mgit sire

All sputum samples were digested-decontaminated following Kubica–Krasnow method^{17 (link)}. Decontaminated samples were stained with auramine–thiazine red technique and examined with a fluorescence microscope by well-trained staff. Smears were graded according to the International Union Against Tuberculosis and Lung Disease (IUATLD) scale¹⁸ .
Liquid cultures were performed by inoculation of 500 μL of decontaminated samples in mycobacteria growth indicator tubes (MGIT). MGIT tubes were incubated at 37 °C in an automated Bactec MGIT 960 instrument (Becton Dickinson, Sparks, MD, USA) for a maximum of 42 days. All positive cultures were confirmed to be MTB complex by detection of antigen MPT64 with a commercial immunochromatographic assay (BD MGIT™ TBc Identification Test, Becton Dickinson; Sparks, MD, USA). After identification of MTB complex strains, DST was performed using MGIT SIRE (Becton Dickinson; Sparks, MD, USA) according to the manufacturer's recommendations.

All the isolates were subjected to identification with the commercial line probe assay-Genotype Mycobacterium MTBC (Hain Lifescience, Nehren, Germany) as M. tuberculosis complex following manufacturer’s instructions. All the extrapulmonary isolates collected during the study period were subjected to first line drug susceptibility testing by using the commercial kit MGIT SIRE (Becton Dickinson, MD, USA). The following drug concentrations were tested: 1 μg/ml for streptomycin,
0.1 μg/ml for isoniazid, 1μg/ml for rifampin, and 5 μg/ml for ethambutol.