Nucleic Acid–Based Rapid Detection of Tuberculosis and Rifampicin Resistance in a Resource-Limited Setting

Abstract BackgroundThe GeneXpert MTB/RIF assay for the diagnosis of tuberculosis (TB) and its uptake has been limited in most developing countries. This may lead to under-diagnosis, ineffective treatment and high mortality. We determine the prevalence of Mycobacterium tuberculosis (MTB) and Rifampicin-resistant TB using a nucleic acid–based test and AFB-smear in a Nigerian population.MethodsWe analyzed a single early morning sputum and extrapulmonary specimen from suspected cases of TB. Smear microscopic and real-time PCR for the detection of MTB and mutation on the rpoB gene using a molecular beacon was performed. ResultsThe median age of the participants was 40 years (range: 6 weeks to 120 years). The incidence of MTB and RR-TB determined using GeneXpert were 620 (16.6%) and 59(1.6%), respectively. Acid-fast bacilli (AFB) smear identified AFB only in 2 out of 59(3.4%) cases with RR-TB. The agreement between the paired test of GeneXpert and AFB smear was poor (Kappa = 0.009, p = 0.01; McNemar’s p < 0.0001). AFB sensitivity, specificity positive and negative predictive value were 2.4%, 98.2%, 1.9 and 98.1 respectively. The distribution of the RR-TB are more prominent among new TB-AFB-negative cases, those residing in densely populated semi urban communities and migrants at border towns. Conclusion The GeneXpert test shows a high detection for MTB in the paediatric population but a lower RR-TB than the national average. There is a need for aggressive escalation of the nuclei acid based test in low middle-income-countries in order to achieve the end TB strategy in a global village.