Sample collection and processing
The samples were collected between March and November 2017. For the analysis of social and demographical factors subjective information was also collected with the help of questionnaire.
Blood, urine, fluid and sputum specimen were collected in sterile leak proof container, while tissue specimen were placed in sterile saline to protect from dehydration. All specimen were initially screened for presence of mycobacteria. The respiratory specimen were based on sputum, broncho alveolar lavage fluid and bronchial aspirates while specimens from tissue included blood, sterile body fluids and urine. Non respiratory specimens were also collected for the testing of Mycobacterium tuberculosis complex (MTBC) and other mycobacteria. Most common specimen for pulmonary infection was sputum. To enhance sensitivity through smear, sputum samples were taken early morning. Three sputum samples were collected from each patient at different time intervals (before breakfast, after breakfast and at laboratory by lab staff). All specimens were processed through Acid-Fast Bacillus (AFB) smear microscopy, GeneXpert assay and inoculate on the day of collection [13].