A single-cell atlas of mouse central nervous system immune cells reveals unique infection-stage immune signatures during the progression of meningitis caused by Streptococcus suis.

Meningitis caused by Streptococcus suis serotype 2 (SS2) in humans and pigs is an acute nervous disorder associated with serious sequelae. Bacterial meningitis is tightly associated with immune cell responses and the local immune microenvironment. However, the dynamic changes of the immune system during the disease progression in the brain remains unclear. Here, single-cell mass cytometry analyses are used to comprehensively profile the composition and phenotypes of female mouse brain immune cells at different stages of SS2 meningitis. Ten major immune cell lineages are identified among which T cells and dendritic cells significantly increased during meningitis, with B cells increasing in the late stage. Specifically, SS2(+)PD-L1(+) neutrophils with strong phagocytosis, bactericidal and apoptotic effects accumulate in the acute phase of SS2 infection. Microglia sequentially display the features of homeostasis, proliferation, and activation (enhanced MHCII and TLR2 signals and TNF-α secretion) during the process of meningitis. Both border-associated and monocyte-derived macrophages contribute to the process of SS2-induced meningitis, exhibiting upregulation of CD38 and MHCII. Interestingly, CD11c(+)CD8(+)T cells are the main contributor of IFN-γ and specifically appeared during SS2 infection. In addition, the appearance of other lymphocytes such as CCR6(+/lo) B cells, CX3CR1(+) NK and MHCII(+) ILC3 are related to the progression of meningitis. Moreover, correlation analysis between the composition of immune cell clusters and the SS2 infection process yield a dynamic immune landscape in which key immune clusters, including some previously unidentified, mark different stages of infection. Together, these data reveal the unique infection-stage immune microenvironment during the progression of meningitis caused by SS2 and provide resources for the analysis of immunological pathogenesis, potential diagnostic markers and therapeutic targets for bacterial meningitis.