1 SCIENTIFIC REPORTS | (2019) 9:16587 | https://doi.org/10.1038/s41598-019-53086-5 www.nature.com/scientificreports A Comparative Evaluation of the New Genexpert MTB/RIF Ultra and other Rapid Diagnostic Assays for Detecting Tuberculosis in Pulmonary and Extra Pulmonary Specimens John Osei Sekyere 1 , Nontobeko Maphalala 1 , Lesibana A. Malinga 3,4 , Nontombi M. Mbelle 1,2 & Nontuthuko E. Maningi 1* Studies evaluating the new GeneXpert Ultra with other rapid diagnostic assays are limited, particularly in diferent geographical settings. The performance of the GeneXpert Ultra, the GeneXpert G4, the Line probe assays (LPA) and auramine smear microscopy in detecting TB in pulmonary and extra- pulmonary samples were thus evaluated. Remnants (n = 205 samples) of pulmonary (n = 125 samples) and extra-pulmonary (n = 80 samples) specimens from TB suspects were prospectively collected. Each sample was divided for diagnosis using microscopy, GeneXpert MTB/RIF assays, and LPA; these were all comparatively evaluated, using the MGIT 960 culture as a gold standard. The sensitivity and specifcity of microscopy, Xpert Ultra, Xpert G4 and MTBDRplus (ver 2) in pulmonary samples were respectively: 82.00% and 90.28%; 88.00% and 58.57%; 79.59% and 90.28%; 80.00% and 11.11%. For extra- pulmonary specimen, the sensitivity and specifcity were respectively: 53.85% and 98.51%; 69.23% and 49.25%; 50.00% and 97.01%; 69.23% and 25.37%. The new and improved GeneXpert Ultra assay was more sensitive than GeneXpert G4 and LPA in both pulmonary and extra pulmonary samples, albeit with lower specifcity than the GeneXpert G4. The auramine and LPA tests were also highly sensitive, although the LPA was less specifc. Although curable, tuberculosis (TB) remains the deadliest infectious disease caused by a single aetiological agent, Mycobacterium tuberculosis (M. tb), among all infectious diseases. In 2017, 1.5 million people died of TB glob- ally. In South Africa, HIV-negative TB deaths were estimated to be ~23000 (17000–29000) while HIV-positive mortalities totalled 101 000 (67 000-142 000) in 2017 1,2 . Te WHO has reported a decline in TB incidence and mortality rates, and this has been due to the introduction of rapid diagnostic assays and efective TB treatment. Despite the global decline in new infections, the emergence of multidrug-resistant TB (MDR-TB) is worsening the burden of TB. In 2017, 558 000 people had MDR-TB, an increase from 490 000 people in 2016 while in South Africa, a decline from 19 000 cases in 2016 to 15 000 cases in 2017 was reported 1 . In South Africa, this decline was due to major eforts by the government to manage the problem, including the rolling out of GeneXpert machines throughout the country for quick diagnosis, screening high-risk groups (HIV infected individuals) to prevent transmission, treating latent TB, and using quality M. tb drugs for treatment 3 . In 2010, the WHO recommended the use of the GeneXpert MTB/RIF G4 (hereafer referred to as Xpert G4), which is an automated cartridge-based molecular test, as a primary test to increase TB detection and improve diagnosis of rifampicin (RIF) resistance in pulmonary and extra-pulmonary TB (EPTB) specimens 4 . However, 1 Department of Medical Microbiology, University of Pretoria, 0084, Pretoria, South Africa. 2 National Health Laboratory Services, Tshwane Academic Division, 0084, Pretoria, South Africa. 3 South African Medical Research Council, TB Platform Unit, 0084, Pretoria, South Africa. 4 Department of Internal Medicine, University of Pretoria, 0084, Pretoria, South Africa. *email: nontuthuko.maningi@up.ac.za OPEN