Fig. 2: Spatial and quantitative analysis of rpoB and lsr2 probes in Ctrl and Chronic infection slices.

A Spatial plot showing the UMI counts of rpoB and lsr2 probes in “Ctrl" and “Chronic infection” representative slices. The color scale indicates the number of UMIs per spot (Scale bar, 1 mm). B Spatial plot showing the summed UMI counts of rpoB and lsr2 probes in “Chronic infection” slices (n = 2). The color scale indicates the total number of UMIs per spot (Scale bar, 1 mm). (I–IV) Representative images of immunofluorescence staining in infected mouse for M. abscessus (with specific antibody against M. abscessus, stained in green, and with Hoechst 33342, Trihydrochloride, stained in blue) in airways and submucosal airways (B I), in granuloma-like structure areas (B II, III), and area of not inflamed parenchyma (B IV) all captured in the successive slice of the infected sample used for spatial transcriptomics (Scale bar, 20 μm). C Barplot showing the gathered UMI counts of rpoB and lsr2 probes in “Chronic infection” slices. The y-axis shows the number of UMIs. The bars are color-coded by the respective probe. D Bubble plot showing the differentially expressed genes in MABS+ (positive) and MABS− (negative) spots in “Chronic infection” slices (n = 2). The color scale shows the log fold change of the genes. The size of the bubbles indicates the percentage of spots expressing a gene. E The bubble plot illustrates the significantly different cellular populations between MABS+ (positive) and MABS− (negative) spots, categorized by clusters. Red dots indicate enrichment in MABS-positive spots, while blue dots indicate enrichment in MABS-negative spots. The size of each dot corresponds to the median cellular proportion observed for the specific cluster. F Violin plot for the levels of iNOS pathway grouped according to MABS+lsr2- or MABS+lsr2+ infection (generated with “Chronic infection” slices, n = 2) (Mann–Whitney test, **p-value  < 0.01).