B cells in perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell signatures identify asymptomatic lung infection in Diversity Outbred mice.

Because most humans resist infection, there is a paucity of lung samples to study. To address this gap, we infected Diversity Outbred mice with and studied the lungs of mice in different disease states. After a low-dose aerosol infection, progressors succumbed to acute, inflammatory lung disease within 60 days, while controllers maintained asymptomatic infection for at least 60 days, and then developed chronic pulmonary tuberculosis (TB) lasting months to more than 1 year. Here, we identified features of asymptomatic infection by applying computational and statistical approaches to multimodal data sets. Cytokines and anti-. cell wall antibodies discriminated progressors vs controllers with chronic pulmonary TB but could not classify mice with asymptomatic infection. However, a novel deep-learning neural network trained on lung granuloma images was able to accurately classify asymptomatically infected lungs vs acute pulmonary TB in progressors vs chronic pulmonary TB in controllers, and discrimination was based on perivascular and peribronchiolar lymphocytes. Because the discriminatory lesion was rich in lymphocytes and CD4 T cell-mediated immunity is required for resistance, we expected CD4 T-cell genes would be elevated in asymptomatic infection. However, the significantly different, highly expressed genes were from B-cell pathways (e.g., , , , , , , and ), and CD20+ B cells were enriched in the perivascular and peribronchiolar regions of mice with asymptomatic infection. Together, these results indicate that genetically controlled B-cell responses are important for establishing asymptomatic lung infection.