NPP Implementation of GeneXpert for TB testing


To read about the success of the implementation of the GeneXpert system for TB testing, click here


The GeneXpertTM MTB/Rif (GX) cassette-based molecular test was introduced in the National Health Laboratory Service (NHLS) to improve M. tuberculosis (MTB). The GeneXpert assay provides an automated molecular platform for TB case detection and rifampicin resistance testing for high‐endemic countries. It was designed to extract, amplify and identify targeted rpoB nucleic acid sequences. With dedicated staff and sufficient instrument capacity, results are available from raw sputum in about 2 hours, without the requirement of highly trained personnel.

The GeneXpert assay was found to be highly specific (99.2%) while the sensitivity of the assay for detecting M. tuberculosis (MTB) DNA was 98,2% in smear‐positive patients and 72,5% in smear‐negative culture‐positive patients. Sensitivity on smear‐negative culture‐positive patients increased by 12.6% by performing a second GX investigation on the same patient (different sputum).

At the request of the National Department of Health (NDOH), a roll-out of this technology is being undertaken in various phases. This roll out will enhance sensitivity of TB detection in smear negative, culture positive patients, as well as early recognition of a substantial additional pool of DR-TB cases, with significant medical and public health impacts in programmatic settings. The various phases for the GeneXpert rollout are described in the table below:

Table 1: GeneXpert phase descriptions
Phase Description Phase Details
1 World TB Day Placement (24 March 2011) Placement of instruments at 25 sites in the nine high burden districts (HBD) identified (one per province) for partial capacitation.
2a Full Capacitation of Phase 1 All 25 Phase 1 sites will be fully capacitated and will stop using smear microscopy
2b Full Capacitation of High Burden Districts Full capacitation of all laboratories in the nine high burden districts.
3a Gates Xpert Full capacitation of laboratories in Gates Foundation trial Xpert clusters, i.e. high prevalence sites
3b Gates Control Full capacitation of laboratories in Gates Foundation trial Control clusters, i.e. low prevalence sites
3c Minister Capacitation of one high test volume laboratory in the remaining health districts
3d All remaining Full capacitation of all health districts


The total scale-up (all phases) will lead to the placement of 65 GX4, 169 GX16, and 4 GX48 (“Infinity”) instruments, with a total national test capacity at full GeneXpert coverage in 2013 of 11,428 tests per day.

Testing officially started on 1st October 2011. The launch included a presentation by Dr Sibongiseni Dlomo, MEC for Health, KwaZulu Natal, talks by representatitives from WHO and PEPFAR, as well as presentations by Prof. Wendy Stevens and Prof. Harry Hausler, Director TB/HIV Care Association. 

To facilitate the training of laboratory staff across the country, the National Priority Program has developed the GeneXpert training manual to ensure standardization. The training has been centralized at regional level, as well as on-site and includes both clinical and technical training. The centralized GeneXpert training is an intensive one and half days course that concentrates on the background to the GeneXpert assay and testing algorithm, overview of quantitative real time PCR, good laboratory practice for molecular laboratories, GeneXpert operation, data entry, maintenance and troubleshooting, result interpretation and frequently asked questions. The on-site course is hands on and concentrates on navigating around the GeneXpert software and competency assessment of users. During 2011, training was conducted in all nine provinces for 129 technologists who are first cadre microscopists.

GeneXpert Senior Project Manager- Mr Sebaka Molapo (sebaka.molapo@nhls.ac.za)

Pholela Media event launching the GX4 instrument in the Sisonke District, 27 September 2011