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. 2023 Oct 19;13(20):3253.
doi: 10.3390/diagnostics13203253.

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

Manuel Pedro da Silva  1   2 , Naseem Cassim  1   2 , Silence Ndlovu  1 , Puleng Shiela Marokane  1 , Mbuti Radebe  1 , Anne Shapiro  3 , Lesley Erica Scott  2 , Wendy Susan Stevens  1   2
Affiliations

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

Manuel Pedro da Silva et al. Diagnostics (Basel). .

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.

Keywords: GeneXpert MTB/RIF; GeneXpert MTB/RIF Ultra; extra-pulmonary tuberculosis; implementation; molecular diagnostics; pulmonary tuberculosis; specimen types; tuberculosis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Decentralised footprint of 173 GeneXpert testing laboratories supporting molecular tuberculosis testing by the National Health Laboratory Service, South Africa. The laboratories that offer mycobacteriology culture testing are also depicted. The number of testing laboratories varies by province based on the respective provincial population.
Figure 2
Figure 2
GeneXpert testing in South Africa with number of specimens and Mycobacterium tuberculosis complex detection rate (indicated on the secondary y-axis), by month. Transition from Xpert MTB/RIF to Xpert MTB/RIF Ultra was phased commencing October 2017 and fully completed by April 2018. MTBC: Mycobacterium tuberculosis complex.
Figure 3
Figure 3
Number of specimens tested on GeneXpert platforms by anatomical origin (pulmonary and extra-pulmonary) by calendar year. Specimens that could not be categorised as either of pulmonary or extra-pulmonary origin (n = 1,103,728) were excluded. COVID-19 lockdown and restrictive containment measures were introduced in March 2020. EPTB: extra-pulmonary tuberculosis; PTB: pulmonary tuberculosis.
See this image and copyright information in PMC

References

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