Whole-genome sequencing and machine learning reveal key drivers of delayed sputum conversion in rifampicin-resistant tuberculosis

Abstract

Rifampicin-resistant tuberculosis (RR-TB) remains a major global health challenge, with delayed sputum culture conversion (SCC) predicting poor treatment outcomes. This study integrated whole-genome sequencing (WGS) and machine learning to identify clinical and genomic determinants of SCC failure in 150 RR-TB patients (2019–2023). Phenotypic and genotypic analysis revealed high rates of isoniazid resistance (74.0%) and rpoB mutations (97.3%, predominantly Ser450Leu), with 90% of strains belonging to Lineage 2 (Beijing family). While 64.7% achieved 2-month SCC, 18.0% remained culture-positive at 6 months. Univariate analysis linked 2-month SCC failure to smear positivity, resistance to isoniazid, amikacin, capreomycin, and levofloxacin, and pre-XDR-TB status, though only smear positivity (aOR=2.41, P=0.008) and levofloxacin resistance (aOR=2.83, P=0.003) persisted as independent predictors in multivariable analysis. A Random Forest model achieved robust prediction of SCC failure (AUC: 0.86 ± 0.06 at 2 months; 0.76 ± 0.10 at 6 months), identifying levofloxacin resistance (feature importance: 6.37), embB_p.Met306Ile (5.94), and smear positivity (5.12) as top 2-month predictors, while katG_p.Ser315Thr (4.85) and gyrA_p.Asp94Gly (3.43) dominated 6-month predictions. These findings underscore smear positivity, levofloxacin resistance, and specific resistance mutations as critical drivers of SCC failure, guiding targeted RR-TB treatment strategies.