Figure 3. CFU and CEQ reflect viable and total bacterial burden in individual lesions.

(a) CFU in lesions from monkeys at 4 weeks (4 animals, 68 lesions) is significantly higher than at 11 weeks (3 animals, 98 lesions), in active disease (13 animals, 222 lesions) and in clinically latent infection (11 animals, 145 lesions) (p < 0.001). All groups are significantly different by pairwise comparison (p < 0.001). Circles represent individual lesions. The median for latent animals is zero. (b) Individual monkeys necropsied at 4 weeks and 11 weeks are shown; circles represent individual lesions. By 11 weeks, there are significant differences between animals (p < 0.05). (c) The percentage of sterile lesions in monkeys with latent infection (n = 11) is significantly higher than in monkeys with active disease (n = 13, p < 0.05); however in both conditions the majority of animals contain sterile lesions. Squares represent individual animals. (d) CEQ per lesion is similar across all categories (n = 26 for 4 week, n = 23 for 11 week, n = 36 for active, n = 37 for latent). CEQ from lesions of active monkeys was significantly higher compared to 4 weeks p.i. reflecting additional replication. CEQ is also similar in sterile lesions (n = 22), supporting the observation that CEQ are stable in the absence of replication. Triangles represent individual lesions. (e) The ratio of CFU to CEQ in individual non-sterile lesions drops significantly after 4 weeks (n = 26), indicating bacterial killing over time (n = 22 for 11 week animals, n = 29 for active, n = 28 for latent), coincident with the onset of the adaptive immune response¹⁶ (p < 0.001). Open circles represent individual lesions. For all panels, *p < 0.05, **p < 0.01,***p < 0.001, statistical tests as indicated in Methods, bars represent medians.