Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance inMycobacterium tuberculosis

Synopsis Fluoroquinolone resistance poses a threat to the successful treatment of tuberculosis. Whole genome sequencing (WGS), and the subsequent detection of catalogued resistance-associated mutations, offers an attractive solution to fluoroquinolone susceptibility testing. However, the bioinformatic pipelines used often mask the recognition of minor alleles which are implicated in fluoroquinolone resistance. Using the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium’s (CRyPTIC) dataset of globally diverse WGS Mycobacterium tuberculosis isolates, with matched minimum inhibitory concentrations for two fluoroquinolone drugs, we show that detecting minor alleles increased the sensitivity of WGS for moxifloxacin resistance prediction from 85.4% to 94.0%, without significantly reducing specificity. We also found no correlation between the proportion of an M. tuberculosis population containing a resistance-conferring allele and the magnitude of resistance. Together our results highlight the importance of detecting minor resistance conferring alleles when using WGS, or indeed any sequencing-based approach, to diagnose fluoroquinolone resistance.