Objectives:Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases with concern regarding patient to patient transmission. The recent introduction of routine whole genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterise the genetic determinants of resistance.
Methods:A systematic review was performed to catalogue all known resistance determining mutations. This knowledge was used to construct a predictive algorithm which was tested on a collection of 209 sequentially acquired clinical isolates for which there was paired genotype/phenotype data. Predictions were made for those drugs for which genetic loci involved in drug resistance were identified in the literature search. A search for novel resistance determining mutations was conducted using an heuristic algorithm.
Results:The literature search identified two genes of interest for Clarithromycin (rrl and erm (41)) and Ciprofloxacin (gyrA and gyrB) and one for Amikacin (rrs). After excluding isolates predicted to be inducibly resistant and those for which there were null calls in key positions, the sensitivity of existing knowledge for clarithromycin was 76.19% (95% CI 52.8 -91.8%) and the specificity was 100%. Subspecies alone was a poor predictor of resistance to macrolides. For Ciprofloxacin the sensitivity was 0% and for Amikacin it was 5.0% (95% CI 2.0 -10.0). Seven potential new resistance conferring SNPs were identified for clarithromycin, four for ciprofloxacin and three for amikacin.
Conclusion:We demonstrate that WGS demonstrates probable resistance determining SNPs in regions the NTM-DR line probe cannot detect. These mutations are potentially clinically important as they all occurred in samples predicted to be inducibly resistant, and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.