Identification of nontuberculous mycobacteria using the GenoType CMdirect and GenoType Mycobacterium CM line probe assays in GeneXpert MTB/RIF Ultra negative sputum: A South African prevalence study

•Prevalence of nontuberculous mycobacteria (NTM) among a GXP-negative cohort was 1.7 %.•CMdirect line probe assay showed a specificity of 100 % as a possible rule-in test.•Culture-independent molecular techniques on decontaminated sputum could aid in NTM identification. The GenoType CMdirect Ver 1.0 and GenoType Mycobacterium Common Mycobacteria Ver 2.0-line probe assays were utilized to identify nontuberculous mycobacteria (NTM) from decontaminated sputum in a GeneXpert MTB/RIF Ultra negative cohort. A preliminary NTM prevalence of 1.7 % was observed, with a 100 % specificity. The high specificity advocates the CMdirect as a possible rule-in test for NTM disease.