In vivo single cell transcriptomics reveals Klebsiella pneumoniae rewiring of lung macrophages to promote infection

The strategies deployed by antibiotic resistant bacteria to counteract host defences are poorly understood. Here, we elucidate a novel host-pathogen interaction that results in the control of lung macrophage polarisation by the human pathogen Klebsiella pneumoniae. We identify interstitial macrophages (IMs) as the main population of lung macrophages associated with Klebsiella. Single cell transcriptomics and trajectory analysis of cells uncover that type I IFN and IL10 signalling, and macrophage polarization are characteristic of infected IMs, whereas Toll-like receptor (TLR) and Nod-like receptor signalling are features of infected alveolar macrophages. Klebsiella-induced macrophage polarization is a singular M2-type we termed M(Kp). To rewire macrophages towards M(Kp), K. pneumoniae hijacks a hitherto unknown TLR-type I IFN-IL10-STAT6 innate axis. Absence of STAT6 limits the intracellular survival of Klebsiella whereas the inhibition of STAT6 facilitates the clearance of the pathogen in vivo. Glycolysis characterises M(Kp) metabolism, and inhibition of glycolysis results in clearance of intracellular Klebsiella. We demonstrate the capsule polysaccharide is the Klebsiella factor governing M(Kp). Klebsiella also skews human macrophage polarization towards M(Kp) in a type I IFN-IL10-STAT6-dependent manner. Altogether, our work demonstrates that Klebsiella induction of M(Kp) represents a hitherto unknown strategy to overcome host restriction during pneumonia.