Although a few inflammatory cells infiltrating the meninges were detected in some of the mice as early as day 7 after infection (Fig.2A) the mean neuropathology score [mean ± SE (0.400 ± 0.245)] for this group of mice was not significantly different [p = 0.382, 95% CI for the difference in mean score (95% CI) = −0.254, 1.054] to the uninfected group (0.00 ± 0.00). However, a progressive increase in the severity of the neuroinflammatory reaction was seen in the mice as the disease developed (Fig.3A) and by 14 days -post-infection the neuroinflammatory reaction, characterised by the presence of a mild meningitis (Fig.2B) (0.800 ± 0.122), was significantly (p = 0.012, 95% CI = 0.146, 1.454) higher than in uninfected mice (Fig.3A). A further significant increase (p < 0.05) in the severity of the neuropathological response was found in mice killed at days 21 (1.500 ± 0.158) and 28 (2.000 ± 0.000) post-infection compared to earlier time points (Fig.3A). In both of these groups the main features of the neuroinflammatory reaction were the presence of moderate inflammatory cell infiltration of the meninges and the perivascular space surround some of the blood vessels. The presence of perivascular cuffs was most often associated with the vessels situated in the hippocampal fissure (Fig.2C and D). Summary statistics for the neuroinflammatory score data are detailed in Supplementary Table 1.Fig. 2The neuroinflammatory reaction. Coronal brain sections, prepared at the level of the hippocampus, and stained with haematoxylin and eosin were employed to assess the neuroinflammatory reaction in uninfected mice (A) and mice infected with T.b.brucei. Inflammatory cells can be seen infiltrating the meninges (blue arrows) of the cerebral cortex on day 14 post-infection (B) and are most abundant at day 21 (C) and 28 (D) post-infection. Inserts show the development of mild perivascular cuffing of the vessels in the hippocampal fissure (black arrows) on days 21 (C) and 28 (D) post-infection. (magnification; ×200, calibration bar (20 µm) shown in panel D).Fig. 3Assessing the neuroinflammatory response and brain parasite burden. A. The neuroinflammatory response scores were analysed in uninfected animals (n = 4) and animals killed at 7, 14, 21 and 28 days post-infection (n = 5 per group). An increase in the severity of the reaction can be seen as the infection progresses. B. The number of copies of the parasite specific PFR-2 gene in a 100 ng sample of DNA extracted from the brains animals killed at 7, 14, 21 and 28 days post-infection (n = 5 per group) was measured by Taqman PCR. The trypanosome burden within the CNS increases as the disease progresses with a significant increase in parasite load detected at 14 days post-infection compared to the earlier time-point. A and B. Dots represent the group mean, bars represent one standard error of the mean. The means of groups that do not share a letter are significantly different (p < 0.05) from each other.