Key operational challenges at a programmatic level to achieve optimal use of the GeneXpert platform

Background Although Xpert MTB/RIF Ultra (Ultra) has revolutionised TB diagnosis, operational challenges can significantly undermine its benefits. This study examined operational experiences and challenges associated with Ultra use across Rwanda's health care settings. Methods We conducted a cross-sectional survey across 53 GeneXpert testing centres between October and December 2024. The survey addressed machine usage, sample processing timelines, and technical challenges through structured interviews with laboratory managers and operators. Results While 41% of sites processed samples within 5 h, 55% experienced delays exceeding 24 h due to high volumes and limited capacity. Four labs (8%) reported significant delays (>8 h) processing sputum with sample reagent. Modules failures occurred in 81% of facilities within the preceding year, with most experiencing infrequent failures and one site experiencing more than six annually. Connectivity issues with internet and/or 'DataToCare' affected 17% of sites, causing workflow delays. Equipment capacity constraints were identified in 30% of sites, particularly affecting facilities managing dual TB and HIV/hepatitis testing, while 9% reported staffing shortages. Conclusion Despite successful nationwide deployment, operational challenges limit Ultra's full potential. Strategic machine allocation, upgraded connectivity, and improved preventive maintenance represent key intervention areas. These findings offer valuable insights optimising rapid molecular diagnostic use in similar settings.