Abstract: Predicting viability and treatment of disease agents is described herein. In an example, a system accesses a disease agent transcriptome data of a disease agent. The system generates a disease agent viability score by applying a classifier to the disease agent transcriptome. The classifier defines a universal transcriptome signature for a viability of the disease agent in different host-relevant contexts. The system generates a viability state of the disease agent by determining a deviation of the disease agent viability score from a viability threshold of the universal transcriptome signature for viability and determines a treatment recommendation based on the viability state of the disease agent. The system outputs the treatment recommendation.