Rapid direct drug susceptibility testing of <i>Mycobacterium tuberculosis</i> based on culture droplet digital polymerase chain reaction

Setting Early diagnosis and drug susceptibility testing are important for anti-tuberculosis treatment. Objective To develop a rapid method for detecting Mycobacterium tuberculosis and drug susceptibility based on culture and droplet digital polymerase chain reaction (ddPCR). Design M. tuberculosis in 102 sputum samples was detected using ddPCR, Xpert, quantitative PCR (qPCR) and MGIT™ 960™. The susceptibility of ddPCR-positive samples to rifampicin (RMP), isoniazid (INH) and streptomycin (SM) was tested by measuring changes in DNA quantity over 4 days of culture. For comparison, susceptibility of MGIT 960-positive samples was tested using the standard agar proportion method. Results The sensitivity and specificity of M. tuberculosis detection using ddPCR and MGIT 960 were respectively 95.7% (95%CI 80.0-99.2) and 88.9% (95%CI 76.7-95.4). Compared with agar proportion, the susceptibility of 44 specimens positive on culture-ddPCR showed sensitivity and specificity for RMP, INH and SM of respectively 83.3% (95%CI 50.9-97.1) and 90.6% (95%CI 73.8-97.6); 79.0% (95%CI 53.9-93.0) and 92% (95%CI 72.5-98.6); 94.1% (95%CI 69.2-99.7) and 92.6% (95%CI 74.3-98.7). Conclusion Culture ddPCR could detect M. tuberculosis within 5 h and drug susceptibility within 4 days directly from sputum, which would greatly reduce the laboratory time needed for tuberculosis diagnosis.