Drug Exposure Dictates Evolutionary Dynamics of Drug-Resistant Tuberculosis: A Longitudinal Cohort Study in Beijing, China

Shufang Wen,1,* Haoran Li,2,* Yiheng Shi,3 Rongrong Wei,1 Fei Ge,1 Yu Pang,2 Yi Liu1 1Department of Biobank, Beijing Chest Hospital, Capital Medical University / Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, People’s Republic of China; 2Department of Bacteriology and Immunology, Beijing Key Laboratory for Key Technologies in Tuberculosis Prevention and Control, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, People’s Republic of China; 3Department of Clinical Laboratory, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Yi Liu, Department of Biobank, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, No. 9 Beiguan Street, Tongzhou District, Beijing, 101149, People’s Republic of China, Tel +86-10-8950 9534, Email [email protected] Yu Pang, Department of Bacteriology and Immunology, Beijing Key Laboratory for Key Technologies in Tuberculosis Prevention and Control, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Postal No. 9, Beiguan Street, Tongzhou District, Beijing, 101149, People’s Republic of China, Email [email protected]: Despite global efforts to combat drug-resistant tuberculosis (DR-TB), key gaps remain in understanding how resistance amplifies during treatment and the role of collateral drug effects in this process. Resistance amplification complicates management and undermines outcomes. This study aimed to identify the risk factors and collateral drug effects contributing to resistance amplification.Methods: We conducted a retrospective, longitudinal cohort study of 133 DR-TB patients with paired phenotypic drug susceptibility tests (pDSTs) at Beijing Chest Hospital in Beijing, China, from January 2018 to January 2023. Patients were classified into “progression” and “non-progression” groups based on acquisition of new drug resistance. Multivariable logistic regression identified risk factors, and a restrictive cohort analysis assessed collateral drug effects.Results: The median number of resistances per isolate increased significantly from 7.0 (IQR 5– 9) to 8.0 (IQR 6– 10) (P < 0.05), with 76 patients (57.1%) exhibiting resistance progression. A dominant trajectory was identified from isoniazid monoresistance (INH-Mono) to multidrug-/rifampicin-resistant TB (MDR/RR-TB) (9/14, 64.3%). In univariate analysis, bedaquiline (BDQ) use was associated with reduced progression (P=0.032), while pyrazinamide (PZA) use correlated with increased progression (P=0.035), though neither remained significant in multivariable models. Importantly, collateral effect analysis revealed that PZA exposure was strongly associated with acquired rifabutin (Rfb) resistance (OR, 5.94; 95% CI, 1.90– 18.53; P=0.001).Conclusion: Resistance amplification during DR-TB treatment is frequent, with INH-Mono representing a high-risk transitional state. While BDQ may offer a protective effect, the strong collateral association between PZA and Rfb resistance highlights the need for careful regimen design. These findings underscore the importance of individualized, resistance-informed therapy to mitigate further resistance amplification in DR-TB patients.Keywords: drug-resistant tuberculosis, acquired resistance, bedaquiline, pyrazinamide, collateral drug association