Resilient TB Diagnostics During a Pandemic: Xpert MTB/RIF versus Culture in a Resource-Limited Setting in Taung, South Africa

INTRODUCTION  Tuberculosis (TB) is a major global health problem infecting millions of people every year. The COVID-19 pandemic has affected health care systems and greatly affected socioeconomic parameters with global focus on fighting this unpredictable pandemic Mycobacterium tuberculosis diagnosis was hugely affected. The study presented here investigated the performance of TB GeneXpert and TB culture results during this period to evaluate the effects of COVID-19 on the diagnosis of tuberculosis. METHODOLOGY This retrospective study performed using existing data was extracted and evaluated from the NHLS Laboratory Information System (LIS) for samples analysed using Cepheid TB GeneXpert instrument and MGIT for TB culture results during this period. Two consecutive expectorated morning sputum were collected on the same day from the enrolled patients. The minimum acceptable volume of sputum was 2ml in each collection cube. One of the sputum specimens was tested by Xpert MTB /RIF assay in Taung laboratory. The other pair of sputum specimen was tested for TB culture, the sputum specimen were placed on ice packs in a cool box and transported to NHLS Universitas Academic laboratory within 3 days of collection and analyzed. RESULTS AND DISCUSSION For TB culture a total of 2520  samples were received  for the period of study, 808 samples were received in 2020 and 18% tested positive, 82 %  tested negative. In 2021 a decrease of 0.9% was noted on the number of samples received, on diagnosis of TB 16% tested positive which is a 2% increase from 2020 and 84% tested negative which is a 2% increase from 2020. In 2020 the number of samples that tested positive decreased with 4% whereas the number of samples that tested negative for TB culture increased by 4%. Genexpert results for the period of study were a total of 2781 samples were received for analysis, in  2020 88% tested negative and 12% tested positive on the 12% that tested positive 71% was rifampicin sensitive, 21% was trace and 8% was rifampicin resistant. In 2021 a decrease of 6% was noted on the number of samples received for analysis, 84% were negative and 16% were positive of which 71% was rifampicin sensitive, 24% was trace and 5% was rifampicin resistant. A total number 1128 samples were received in 2022 85 % tested negative and 16% was positive of which 85% Was rifampicin sensitive, 16% was trace and 6% was rifampicin resistant.  CONCLUSION The GeneXpert results performed in NHLS Taung correlate with TB culture results performed in NHLS Univerisitas for the diagnosis of pulmonary tuberculosis during COVID-19 pandemic.