phSGM2 detected the presence of 10% RIFr cells in an otherwise drug-susceptible population. H37Rv cells, RIFr cells, or mixtures of both containing 0.1, 1, or 10% RIFr cells were either left untreated or exposed to RIF, STR, or PNB and then infected with phSGM2. A >10-fold increase in cSML generation above STR or PNB samples was detected in mixtures containing at least 10% RIFr cells and exposed to RIF.