OR26
Evaluation of NTM-Profiler for identification and drug resistance prediction in nontuberculous mycobacteria from whole genome sequencing data
S Mok(1,2) E Roycroft(1,2) J Phelan(3) P Flanagan(2) Á O'Halloran(1) J Wagener(1,2) B Boyle(1,2) M M Fitzgibbon(1,2)
1:Irish Mycobacteria Reference Laboratory, St. James’s Hospital, Dublin, Ireland; 2:Department of Clinical Microbiology, Trinity College Dublin, the University of Dublin, Ireland; 3:Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
Global trends of NTM infection and disease are increasing. Accurate identification of NTM to species level and drug susceptibility tests are essential to guide clinical treatment regimens. In this study, we evaluated the performance of NTM-Profiler v0.6.0, a bioinformatic tool for the identification of NTM and prediction of drug resistance from whole genome sequencing data. WGS was performed on 532 NTM isolates (over 40 species) that were collected in the Irish Mycobacteria Reference Laboratory. Species identification and molecular resistance detection was previously performed using Bruker-HAIN line-probe assays (LPA) (GenoType CM/AS/NTM-DR) and/or Sanger sequencing as part of routine diagnostics. Of the 532 NTM isolates analysed with NTM-Profiler, 82% (436/532) were correctly identified to species level. Minor discrepancies were observed in 11% (56/532) of isolates where NTM-profiler further identified the isolate to subspecies level. Major discrepancies were observed in 7% (40/532) of isolates where a different NTM species was identified. Drug resistance prediction for 87 M. abscessus isolates showed 100% concordance for macrolides and 99% (86/87) concordance for aminoglycosides when compared to GenoType NTM-DR results. In conclusion, NTM-Profiler is a rapid and robust tool for NTM identification and drug resistance prediction and could potentially be implemented for routine use. Discrepancies were observed mainly among isolates where NTM-profiler had identified a different species or subspecies that is not covered by the LPA. Phylogenetic analysis is required to confirm the species and subspecies identified by NTM-Profiler and further work to evaluate the drug resistance prediction in M. avium complex isolates will also be performed.