Extended Data Fig. 6: Single-cell analysis of M. tuberculosis.

a, Representative snapshots of M. tuberculosis replisome reporter strain (MTB::gfp-dnaN, green channel) expressing cytoplasmic TdTomato (magenta channel), before (67 h), during (127 h) and after (284 h) exposure to 2.5 µg mL⁻¹ ciprofloxacin. Bacteria undergoing DNA replication are identified by the green foci which represents the active replisome complex. The bacteria cultured in microfluidic device were exposed to the compound between 73–163 h. Scale bar represents 3 µm. b, Plot depicting the number of bacteria with a GFP-DnaN foci before, during exposure to 2.5 µg mL⁻¹ ciprofloxacin (CIP; gray area) and after washout. Cumulative number of foci observed across 13 independent xy fields. n = 242 cells. c, Mouse bone marrow-derived macrophages were infected with M. tuberculosis expressing TdTomato and imaged by timelapse microscopy at 2 h intervals for 190 h. Representative time series snapshots showing macrophages infected with fluorescent bacteria (green) over time, untreated (upper panels); treated with 3 µM JNJ-6640. Numbers on top right indicate hours elapsed. Scale bar represents 25 µm. d, Plot depicting the bacterial load in infected macrophages over time under the different treatment conditions: no treatment; 3 µM JNJ-6640; 3 µM JNJ-6640 plus 100 ng mL⁻¹ IFNγ; 3 µM JNJ-6640 plus 100 ng mL⁻¹ IFNγ plus 1x nucleobases mix (NB mix). Bacterial load was determined from the fluorescence area in each time frame. Data shown are median ± interquartile range. n = 11 independent xy fields for each condition. Representative dataset from two independent experiments.