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

Abstract

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.