Genomic evidence for prisons as amplifiers of community tuberculosis epidemics

Prisons are high-incidence settings for tuberculosis around the world, yet the contribution of spillover from prisons in driving community epidemics has not been quantified. We whole genome sequenced 1,152 M. tuberculosis isolates from participants diagnosed with tuberculosis within prisons and in the community in Mato Grosso do Sul, Brazil from 2014 to 2019. By integrating timed phylogenies and detailed location data, we reconstructed probabilistic transmission histories. M. tuberculosis sequences from incarcerated and non-incarcerated people were closely phylogenetically related. We found that 57% of recent community-wide tuberculosis cases were attributable to transmission from individuals with an incarceration history, 2.6% of the population. Further, we find genomic evidence that the prison system disseminates M. tuberculosis genotypes through frequent transfers across the state. This population-wide genomic transmission reconstruction framework can be applied to identify key environments amplifying infectious disease transmission to prioritize public health interventions.