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

Christoffel Opperman; Chaldene Johannes; Sarishna Singh; Yonas Ghebrekristos; Rob Warren; Aliasgar Esmail; Wynand Goosen

doi:10.1016/j.diagmicrobio.2024.116531

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

Diagn Microbiol Infect Dis. 2024 Dec;110(4):116531. doi: 10.1016/j.diagmicrobio.2024.116531. Epub 2024 Sep 10.

Authors

Christoffel Opperman¹, Chaldene Johannes², Sarishna Singh³, Yonas Ghebrekristos³, Rob Warren⁴, Aliasgar Esmail⁵, Wynand Goosen⁴

Affiliations

¹ National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa; Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa. Electronic address: christoffel.opperman@nhls.ac.za.
² National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa.
³ National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa.
⁴ DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa.
⁵ UCT Lung Institute, Centre for Lung Infection and Immunity. Division of Pulmonology, Department of Medicine, University of Cape Town, & Groote Schuur Hospital, Cape Town, South Africa.

PMID: 39293319
DOI: 10.1016/j.diagmicrobio.2024.116531

Abstract

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.

Keywords: GenoType CMdirect; GenoType Mycobacterium CM; Molecular assay; Nontuberculous mycobacteria; Prevalence; South Africa; Sputum.

MeSH terms

Genotype*
Humans
Molecular Diagnostic Techniques / methods
Mycobacterium Infections, Nontuberculous* / diagnosis
Mycobacterium Infections, Nontuberculous* / epidemiology
Mycobacterium Infections, Nontuberculous* / microbiology
Nontuberculous Mycobacteria* / classification
Nontuberculous Mycobacteria* / genetics
Nontuberculous Mycobacteria* / isolation & purification
Prevalence
Sensitivity and Specificity*
South Africa / epidemiology
Sputum* / microbiology