Whole-Genome Sequencing for Predicting Clarithromycin Resistance in Mycobacterium abscessus

Abstract

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 characterize the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance-determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there were paired genotype/phenotype data. A search for novel resistance-determining mutations was conducted using a heuristic algorithm. The sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% confidence interval [CI], 89 to 98%), and the specificity was 66% (95% CI, 54 to 76%). The subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance-conferring single nucleotide polymorphisms (SNPs) were identified. WGS demonstrated probable resistance-determining SNPs in regions that the NTM-DR line probe cannot detect. These mutations are potentially clinically important, as they all occurred in samples that were 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.

Antibiograms and Molecular Characterization of Drug Resistance ofMycobacterium abscessuscomplex from Patients with Multidrug-Resistant Pulmonary Tuberculosis (MDR TB) Infection

“…On the other hand, three M. massiliense isolates (MAS04: >16μg/ml, MAS06: >16μg/ml, MAS10: >16μg/ml) exhibited inducible resistance to CLR and AZM on the 14 th day. This is contrast with previous studies (Kim et al , 2015; Koh et al , 2010) which demonstrated that inducible resistance to CLR was only present in M. abscessus and not in M. massiliense. Nevertheless, our results support the findings of Li et al .…”

“…Susceptibility rates of M. abscessus complex isolates in the present study showed that MXF has better in vitro activity against M. abscessus (81.8% susceptible) and M. massiliense (60% susceptible) compared to CIP against M. abscessus (9.1% susceptible) and M. massiliense (20% susceptible). This is consistent with other studies showing that MXF has better in vitro activity against M. abscessus and M. massiliense compared to CIP (Kim et al , 2015; Lee et al , 2014; Koh et al , 2010). On the other hand, DOX was found to be more potent against M. abscessus (72.7% susceptible) isolates compared to its activity against M. massiliense (10% susceptible).…”

“…The results are comparable to those of Nie et al (2014) that showed 0% resistant M. abscessus isolates, while 53% were moderately susceptible. Koh et al (2010) likewise showed no resistant isolates of M. abscessus and only 1% resistance rate in M. massiliense against FOX. Lee et al (2015) reported resistance rate of 1.3% in M. abscessus subsp.…”

“…Mycobacterium abscessus isolate MAB09 showed inducible resistance to both CLR (>16μg/ml) and AZM (>16μg/ml) on the 14 th day of incubation. Inducible resistance in M. abscessus was expected since they have a functional erm(41) gene (Kim et al , 2015; Koh et al , 2010; Nash et al , 2009). On the other hand, three M. massiliense isolates (MAS04: >16μg/ml, MAS06: >16μg/ml, MAS10: >16μg/ml) exhibited inducible resistance to CLR and AZM on the 14 th day.…”

Improved Performance Predicting Clarithromycin Resistance in Mycobacterium abscessus on an Independent Data Set

“…I n our recent study of 203 sequential isolates evaluating the ability of whole-genome sequencing (WGS) to predict clarithromycin resistance in Mycobacterium abscessus (1), we demonstrated high sensitivity but poor specificity of mutations identified in a literature search. Most of the discrepancies occurred in isolates predicted to be inducibly resistant (they showed early time point susceptibility but became resistant after prolonged incubation).…”