More Than a Decade of GeneXpert® Mycobacterium tuberculosis/Rifampicin (Ultra) Testing in South Africa: Laboratory Insights from Twenty-Three Million Tests

Abstract

This study seeks to describe the rollout and current state of South Africa’s GeneXpert molecular diagnostic program for tuberculosis (TB). Xpert MTB/RIF was introduced in 2011 with a subsequent expansion to include extra-pulmonary and paediatric testing, followed by Xpert MTB/RIF Ultra in 2017. Through a centralised laboratory information system and the use of a standardised platform for more than a decade, over 23 million tests were analysed, describing the numbers tested, Mycobacterium tuberculosis complex detection, rifampin resistance, and the unsuccessful test rates. The stratification by province, specimen type, age, and sex identified significant heterogeneity across the program and highlighted testing gaps for men, low detection yield for paediatric pulmonary TB, and the effects of inadequate specimen quality on the detection rate. The insights gained from these data can aid in the monitoring of interventions in support of the national TB program beyond laboratory operational aspects.

The 10-year health impact, economic impact, and return on investment of the South African molecular diagnostics programme for HIV, Tuberculosis and SARS-CoV-2

“…Solely aggregate data from previously published manuscripts was used for this analysis. (10,19,24,25). The data are available open access in each publication.…”

“…The total number of TB tests conducted and number of positive diagnoses through the molecular diagnostics programme in South Africa was sourced from the literature (10). We compared the total net impact of the molecular TB programme as well as the incremental impact compared to if the sputum smear microscopy (SSM) programme had continued as it was in 2010.…”

“…The sensitivity and specificity of Xpert MTB/Rif (12) was assumed to be 85% and 98% respectively, and the sensitivity and specificity of Xpert MTB/Rif Ultra (13), was assumed to be 91% and 99% respectively(14). For the total impact of the programme, we multiplied the number of DALYs averted per correct positive TB diagnosis (assumed to be 1 DALY per diagnosis (15)) by the number of correct TB diagnoses reported over time (10) (adjusting for test specificity). The benefits of the molecular programme are results of the improved accuracy of molecular diagnostics compared to smear microscopy for TB diagnosis.…”

“…Return on investment was calculated as the total economic impact per diagnostic tool divided by the total cost of all diagnostic tests required to generate that impact (including both "positive" and "negative" tests). The total number of tests per programme, across the respective time periods considered, were taken from the literature for TB, HIV viral load, SARS-CoV-2, and EID (10,19,(24)(25)(26). To calculate the number of HIV EID tests conducted on average for 2020-2022, we used the number of live births to women living with HIV in 2021 (~275 527), the EID testing algorithm in South Africa and the coverage of testing at each part of the algorithm (averaged between NICD and DHIS sources).…”