Background Factors associated with long-term TB treatment outcomes are not well understood. The aim of our study was to determine the association of mycobacterial lineage and HIV co-infection on mortality and TB recurrence five years after first-line TB treatment in Bamako, Mali.

Methods Between 2015–2022, we conducted a longitudinal cohort study enrolling adults with smear-positive rifampicin-susceptible pulmonary TB. After diagnosis, patients were followed at 1 month (M), 2M, 5M and 6M to determine treatment outcome. Spoligotyping was used to determine baseline lineage classification (M. tuberculosis (L4), and M. africanum (L6)). After treatment completion, patients were evaluated every 6 months for five years to determine their clinical status. Univariate and multivariate logistic regression was used to identify factors associated with treatment outcome.

Results Of the 1,283 patients enrolled, 911 (71%) were male and 116 (9%) were co-infected with HIV. BMI <18.5 (aOR: 1.4, 95% CI: 1.1–1.9) and HIV co-infection (aOR: 2.9, 95% CI: (1.8–4.8) were associated with initial treatment failure. Among the 684 patients maintained for the entire 5-year follow-up, 72 (11%) died and 35 (5%) developed recurrent TB. Baseline L4-infected patients were not more likely to die than L6-infected patients (51% vs 26%, p=0.79) or develop recurrent TB (54% vs. 31%, p=0.58). HIV was not associated with death (p=0.58) or TB recurrence (p=0.32). Among all recurrences, 8 (23%) recurred within 1 year after treatment completion, 25 (71%) within 18 months, and 28 (80%) within 2 years. We were not able to obtain a recurrent TB sputum sample.

Conclusion Neither HIV co-infection nor mycobacterial lineage was associated with 5-year mortality or TB recurrence. Only half of the patients completed follow up and we were limited by the inability to differentiate TB relapse from reinfection. Future analyses that can differentiate relapse from reinfection may be helpful.