Strengthening diagnostic pathways: Inside SA's TB programme transformation
4 August 2025
To address a significant operational challenge within SA’s National Tuberculosis Programme, Genesis was tasked with a pivotal mandate: to convert dormant public health data on sputum rejections into a potent instrument for change and embed data-led decision-making into the national TB response.
Sputum rejection refers to the inability to test a sputum sample (mucus coughed up from the lungs) for tuberculosis (TB) due to issues like insufficient quantity, poor quality of specimens, or improper collection and labelling.
When a sputum sample is rejected, it means a patient's TB diagnosis is delayed, leading to potential delays in treatment, continued transmission of TB, poorer patient outcomes, and increased patient costs, noting that 57% of TB patients experience catastrophic costs and a large proportion live below the poverty line. Reducing the sputum rejection rate is therefore crucial for effective TB control, as it ensures timely diagnosis and treatment, ultimately saving lives and curbing the spread of the disease.
The programme’s sophisticated TB diagnostic test called Nucleic Acid Amplification Testing (TB NAAT) was being undermined by an acute operational challenge: chronically high sputum sample rejections. Between August and November 2024, this inefficiency escalated, with up to 20,000 samples rejected monthly. This pushed the national rejection rate from an already concerning 4% to 6%, delaying treatment initiation for thousands and pointing to profound procedural weaknesses at healthcare facilities.
Genesis’s role was to dissect this inefficiency and help engineer a solution. Collaborating with provincial and district managers, our team conducted a granular analysis of laboratory data to pinpoint the specific facilities where the problem was most severe. We then designed the architecture for an electronic dashboard for real-time monitoring of the rejection trends and reasons for rejection.
Our analysis revealed that over 90% of rejections were due to clinical collection errors, allowing us to identify the top 20 facilities, primarily in KwaZulu-Natal, Gauteng and the Western Cape, that were the main contributors to the national sputum rejection rate. Based on this, we designed and delivered a suite of bespoke quality improvement (QI) instruments for intensive facility assessments and root cause analysis. A key innovation was the dashboard itself, which empowered local teams to self-monitor against a national 3% target and drive remedial action through their weekly technical meetings.
The impact of this intervention has been unequivocal. Between January and June of this year, the national sputum rejection rate fell from 6.30% to 3.94%.
The direct human and economic consequences of this Genesis-led intervention was that 28,332 more patients received a timely TB diagnosis and were initiated on treatment. This represents a substantial return on investment, realised through more efficient use of healthcare worker time and reduced patient costs. The project has marked a strategic shift in the National TB Programme towards a culture of continuous quality improvement and unwavering accountability.