Diagnosis of Multi-drug Resistant Tuberculosis Mutations Using Hain Line Probe Assay and GeneXpert: A Study Done in Zimbabwe

Background and Aims: Tuberculosis (TB) is a global public health problem and one of the leading causes of death. Worldwide, 31% of all estimated new TB cases are from Africa. Zimbabwe is one of the 22 high TB burden countries. Multi-drug resistant TB (MDR-TB) poses challenges in TB control, hence the need for rapid laboratory diagnosis of MDR-TB for optimal treatment and reducing spread. The study aim was to investigate genetic mutations associated with MDR-TB isolates from various Harare clinics using the GeneXpert MTB/RIF® by Cepheid and Genotype MTBDRplus, to improve the diagnosis and management of MDR-TB.
Methods: Samples from adults aged 16 years and older, recruited from several polyclinics in the southern suburbs of Harare were used for our study. All laboratory tests prior to this study had been carried out at Biomedical research and training institute’s level three bio-safety TB laboratory from January 2008-August 2012. Ethical approval was sought from BRTI Institutional review board. A total of 69 (37 MDR-TB and 32 non MDR-TB) archived isolates processed on Genotype MTBDRplus (Hains) and corresponding 39 sputum were processed on the GeneXpert. Mutations on rpoB, katG and inhA genes were observed. The gold standard was culture. Diagnostic accuracy of both methods and their level of agreement were calculated.
Results: Of the 37/69 isolates screened by culture for MDR-TB, 88.4% were confirmed by MTBDR® plus line probe assay (Hains). Within the 39 isolates tested using the Xpert MTB/RIF (GeneXpert) assay 12 were true MDR-TB. Over 8 single nucleotide polymorphisms were observed on the three genes conferring Rifampicin and Isoniazide drug resistance. The Hains and GeneXpert had an almost perfect agreement with a kappa value of 0.82.
Conclusion: Genetic markers can be used in the diagnosis of MDR-TB, to complement phenotypic methods such as culture. Using the commercial methods, Hains and GeneXpert, 88.4-94.2% of drug resistance maybe detected. Furthermore, we recommend sequencing so as to identify novel mutations and to design a kit that is custom made for the population.