Tran Buu Minh, Larsson Jimmy, Grip Anastasia, Karempudi Praneeth, Elf Johan
Department of Cell and Molecular Biology, SciLifeLab, Uppsala University, Uppsala, Sweden.
Nat Commun. 2025 May 10;16(1):4366. doi: 10.1038/s41467-025-59736-9.
Drug-resistant tuberculosis (DR-TB) kills ~200,000 people every year. A contributing factor is the slow turnaround time (TAT) associated with drug susceptibility diagnostics. The prevailing gold standard for phenotypic drug susceptibility testing (pDST) takes at least two weeks. Here we show that growth-based pDST for slow-growing mycobacteria can be conducted in 12 h. We use Mycobacterium tuberculosis variant bovis Bacillus Calmette-Guérin (BCG) and Mycobacterium smegmatis as the mycobacterial pathogen models and expose them to antibiotics used in (multidrug-resistant) tuberculosis (TB) treatment regimens - i.e., rifampicin (RIF), isoniazid (INH), ethambutol (EMB), linezolid (LZD), streptomycin (STR), bedaquiline (BDQ), and levofloxacin (LFX). The bacterial growth in a microfluidic chip is tracked by time-lapse phase-contrast microscopy. A deep neural network-based segmentation algorithm is used to quantify the growth rate and to determine how the strains responded to drug treatments. Most importantly, a panel of susceptible and resistant M. bovis BCG are tested at critical concentrations for INH, RIF, STR, and LFX. The susceptible strains could be identified in less than 12 h. These findings are comparable to what we expect for pathogenic M. tuberculosis as they share 99.96% genetic identity.
耐多药结核病（DR-TB）每年导致约20万人死亡。一个促成因素是与药物敏感性诊断相关的周转时间（TAT）缓慢。目前用于表型药物敏感性测试（pDST）的金标准至少需要两周时间。在此，我们表明针对生长缓慢的分枝杆菌的基于生长的pDST可以在12小时内完成。我们使用结核分枝杆菌牛型卡介苗（BCG）变种和耻垢分枝杆菌作为分枝杆菌病原体模型，并将它们暴露于（耐多药）结核病（TB）治疗方案中使用的抗生素——即利福平（RIF）、异烟肼（INH）、乙胺丁醇（EMB）、利奈唑胺（LZD）、链霉素（STR）、贝达喹啉（BDQ）和左氧氟沙星（LFX）。通过延时相差显微镜跟踪微流控芯片中的细菌生长。使用基于深度神经网络的分割算法来量化生长速率，并确定菌株对药物治疗的反应。最重要的是，在INH、RIF、STR和LFX的临界浓度下测试了一组敏感和耐药的牛型卡介苗。敏感菌株可在不到12小时内被鉴定出来。这些发现与我们对致病性结核分枝杆菌的预期相当，因为它们具有99.96%的基因同一性。
