Clinical Microbiology: Open Access

Abstract

Evaluation of the GenoType^® NTM DR for Subspecies Identification and Determination of Drug Resistance in Clinical M. abscessus Isolates

Nasstasja Wassilew, Doris Hillemann, Florian P. Maurer, Thomas A. Kohl, Matthias Merker, Folke Brinkmann, Marc Lipman and Katharina Kranzer

Introduction: A new line probe assay, the GenoType® NTM DR, has been developed for subspecies identification and detection of resistance to macrolides and aminoglycosides in clinical Mycobacterium abscessus isolates. We studied the performance of the test compared to DNA sequencing and phenotypic drug susceptibility testing (pDST).

Methods: 48 clinical M. abscessus isolates collected between 2015 and 2016 were identified to the subspecies level and analysed for erm (41) genotype, rrl and rrs gene mutations by Sanger sequencing. Broth micro dilution was performed for pDST of Clarithromycin and Amikacin. The results were compared to those of the GenoType® NTM DR assay. Discordant results were further analysed by repeat pDST and whole genome sequencing (WGS).

Results: 35 isolates were identified as M. abscessus subsp. abscessus , 6 as M. abscessus subsp. bolletii , and 7 as M. abscessus subsp. massiliense based on rpoB sequences. Concordance of GenoType® NTM DR results with Sanger sequencing was 92% for subspecies identification and 100% for erm (41), rrl, and rrs genotypes, respectively. GenoType® NTM DR and pDST results matched in 98% for Clarithromycin resistance and in 96% for Amikacin resistance when repeat pDST results were taken into account.

Conclusion: The new GenoType® NTM DR assay is a valuable test for subspecies identification of M. abscessus isolates and detection of defined mutations conferring resistance to Amikacin and Clarithromycin. Discrepancies between the line probe assay and pDST mainly relate to variations in phenotypic test results.