Probe-based spatial host-pathogen genes expression to study bacterial pathogenesis and the regulation of bacterial virulence factors in tissue.

Co-localization of host and pathogen spatial transcriptome information can improve our understanding on how inflammatory environments modulate pathogen virulence in tissues and vice versa. Here, we demonstrate for the first time that bacterial probes can be used to simultaneously identify host-pathogen mutual interactions in formalin-fixed, paraffin-embedded (FFPE) tissues using spatial transcriptomics technology. With properly designed probes targeting pathogens of interest, our approach could provide an improved definition of infection processes by detecting pathogen and host genes expression simultaneously, spatially distributed, and unbiased. Overall design: We collected lung tissue section of mice displaying chronic infection by Mycobacterium abscessus (ATCC 19977 strain). Spatial Gene Expression assay was performed on lung tissue section of mouse chronically infected with M. abscessus (14 days post bacterial challenge) and of sham infected mice as negative control