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A person infected with drug-resistant tuberculosis (DR-TB) is the one who does not respond to typical TB treatment. DR-TB necessitates a longer treatment period and a more difficult treatment protocol. In addition, it can spread and infect individuals in the same manner as regular TB, despite the fact that early detection of DR-TB could reduce the cost and length of TB treatment. This study provided a fast and effective classification scheme for the four subtypes of TB: Drug-sensitive tuberculosis (DS-TB), drug-resistant tuberculosis (DR-TB), multidrug-resistant tuberculosis (MDR-TB), and extensively drug-resistant tuberculosis (XDR-TB). The drug response classification system (DRCS) has been developed as a classification tool for DR-TB subtypes. As a classification method, ensemble deep learning (EDL) with two types of image preprocessing methods, four convolutional neural network (CNN) architectures, and three decision fusion methods have been created. Later, the model developed by EDL will be included in the dialog-based object query system (DBOQS), in order to enable the use of DRCS as the classification tool for DR-TB in assisting medical professionals with diagnosing DR-TB. EDL yields an improvement of 1.17–43.43% over the existing methods for classifying DR-TB, while compared with classic deep learning, it generates 31.25% more accuracy. DRCS was able to increase accuracy to 95.8% and user trust to 95.1%, and after the trial period, 99.70% of users were interested in continuing the utilization of the system as a supportive diagnostic tool.