Deep learning-based framework for Mycobacterium tuberculosis bacterial growth detection for antimicrobial susceptibility testing

Tuberculosis (TB) kills more people annually than any other pathogen. Resistance is an ever-increasing global problem, not least because diagnostics remain challenging and access limited. 96-well broth microdilution plates offer one approach to high-throughput phenotypic testing, but they can be challenging to read. Automated Mycobacterial Growth Detection Algorithm (AMyGDA) is a software package that uses image processing techniques to read plates, but struggles with plates that exhibit low growth or images of low quality. We developed a new framework, TMAS (TB Microbial Analysis System), which leverages state-of-the-art deep learning models to detect <i>M. tuberculosis</i> growth in images of 96-well microtiter plates. TMAS is designed to measure Minimum Inhibitory Concentrations (MICs) rapidly and accurately while differentiating between true bacterial growth and artefacts. Using 4,018 plate images from the CRyPTIC (Comprehensive Resistance Prediction for Tuberculosis: An International Consortium) dataset to train models and refine the framework, TMAS achieved an essential agreement of 98.8%, significantly outperformed the 90% threshold established by the International Organization for Standardization (ISO). TMAS offers a reliable, automated and complementary evaluation to support expert interpretation, potentially improving accuracy and efficiency in tuberculosis drug susceptibility testing (DST).