Multiscale Model of Mycobacterium tuberculosis Infection Maps Metabolite and Gene Perturbations to Granuloma Sterilization Predictions

Abstract

cGranulomas are a hallmark of tuberculosis. Inside granulomas, the pathogen Mycobacterium tuberculosis may enter a metabolically inactive state that is less susceptible to antibiotics. Understanding M. tuberculosis metabolism within granulomas could contribute to reducing the lengthy treatment required for tuberculosis and provide additional targets for new drugs. Two key adaptations of M. tuberculosis are a nonreplicating phenotype and accumulation of lipid inclusions in response to hypoxic conditions. To explore how these adaptations influence granuloma-scale outcomes in vivo, we present a multiscale in silico model of granuloma formation in tuberculosis. The model comprises host immunity, M. tuberculosis metabolism, M. tuberculosis growth adaptation to hypoxia, and nutrient diffusion. We calibrated our model to in vivo data from nonhuman primates and rabbits and apply the model to predict M. tuberculosis population dynamics and heterogeneity within granulomas. We found that bacterial populations are highly dynamic throughout infection in response to changing oxygen levels and host immunity pressures. Our results indicate that a nonreplicating phenotype, but not lipid inclusion formation, is important for long-term M. tuberculosis survival in granulomas. We used virtual M. tuberculosis knockouts to predict the impact of both metabolic enzyme inhibitors and metabolic pathways exploited to overcome inhibition. Results indicate that knockouts whose growth rates are below ϳ66% of the wild-type growth rate in a culture medium featuring lipid as the only carbon source are unable to sustain infections in granulomas. By mapping metabolite-and gene-scale perturbations to granuloma-scale outcomes and predicting mechanisms of sterilization, our method provides a powerful tool for hypothesis testing and guiding experimental searches for novel antituberculosis interventions.T uberculosis (TB), caused by inhalation of the pathogen Mycobacterium tuberculosis, is a leading cause of death worldwide (1, 2). The main sites of infection during TB are lung granulomas, dense collections of immune cells and bacteria that develop following infection (3). Understanding M. tuberculosis dynamics within granulomas could aid in development of new antibiotic therapies, since M. tuberculosis growth rates, heterogeneity, and dynamics can affect antibiotic efficacy (3-7).Two in vitro-observed adaptations of M. tuberculosis, suspected to be important in the ability of M. tuberculosis to persist in the host lung, are (i) the adoption of a nonreplicating phenotype and (ii) the accumulation of lipid inclusions, aggregates of neutral lipids inside bacteria (8-13). Hypoxia is known to be a trigger for the transition to a nonreplicating phenotype and the formation of lipid inclusions (9,12,14,15).The in vivo role of the nonreplicating phenotype remains controversial. It has been suggested that M. tuberculosis acquires the nonreplicating phenotype in response to stresses present in the host (such as hypoxia) and that this phenotype allows M. tubercul...

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