Nationwide analysis of Mycobacterium chimaera and Mycobacterium intracellulare isolates: Frequency, clinical importance, and molecular and phenotypic resistance profiles.

The burden of tuberculosis (TB) in Slovenia is low due to good ongoing preventive measures. However, analysis of data obtained from the Registry for Tuberculosis and National Reference Laboratory for Mycobacteria at University Clinic of Respiratory and Allergic Diseases Golnik from January 2000 to December 2017 revealed that the number of nontuberculous mycobacterial (NTM) isolates is increasing. A group of slowly growing NTM and a common cause of NTM disease among humans is the Mycobacterium avium complex, the taxonomy of which is rapidly changing. M. intracellulare and M. chimaera are part of the Mycobacterium avium complex, and together represent 19.6% of all isolated NTM species in Slovenia. Due to the high genotypic and phenotypic similarity between M. intracellulare and M. chimaera species, both species are difficult to differentiate. A method that can be used to successfully distinguish between M. intracellulare and M. chimaera is the molecular assay GenoType NTM-DR. Mutations in the rrl and rrs genes that are associated with macrolide and aminoglycoside resistance, respectively, can also be detected with this method. Overall, 222 clinical isolates were tested, and the nationwide study showed that 44.6% of the previously identified M. intracellulare species were actually M. chimaera. Further, this study showed that none of the tested M. intracellulare and M. chimaera isolates harboured mutations in the rrl and rrs genes. The genotyping result that no isolates were resistant to macrolides or aminoglycosides was also confirmed phenotypically with the broth microdilution method. Among isolates from the Slovenian Mycobacterial Isolates Collection all these tested strains (n = 222) were sensitive to macrolides and aminoglycosides.