In Vivo Dual RNA-Seq Analysis Reveals the Basis for Differential Tissue Tropism of Clinical Isolates of Streptococcus pneumoniae

Abstract

Streptococcus pneumoniae is a genetically diverse human-adapted pathogen commonly carried asymptomatically in the nasopharynx. We have recently shown that a single nucleotide polymorphism (SNP) in the raffinose pathway regulatory gene rafR accounts for a significant difference in the capacity of clonally-related strains to cause localised versus systemic infection. Here we have used dual RNA-seq to show that this SNP extensively impacts both bacterial and host transcriptomes in infected lungs. It affects expression of bacterial genes encoding multiple sugar transporters, and fine-tunes carbohydrate metabolism, along with extensive rewiring of host transcriptional responses to infection, particularly expression of genes encoding cytokine and chemokine ligands and receptors. The dual RNA-seq data predicted a crucial role for differential neutrophil recruitment in the distinct virulence profiles of the infecting strains and single cell analysis revealed that while reduced expression of the RafR regulon driven by a single rafR SNP provides a clear advantage for pneumococci to colonize the ear, in the lung it leads to massive recruitment of neutrophils and bacterial clearance. Importantly, the observed disease outcomes were confirmed by in vivo neutrophil depletion showing that early detection of bacteria by the host in the lung environment is crucial for effective clearance. Thus, dual RNA-seq provides a powerful tool for understanding complex host-pathogen interactions and revealed how a single bacterial SNP can drive differential disease outcomes.

Isolation and characterization of human monoclonal antibodies to pneumococcal capsular polysaccharide 3

“…However, we do not know if the reduced efficacy of C27 in this model reflects an inability to prevent dissemination, and/or distinct features of the ST3 clinical strain, B2. Tissue specific differences in virulence have been identified for other STs (36,37), but further work is needed to dissect the roles that humAbs and ST3 strain specific differences may play in the reduced efficacy of C27 observed in the lethal IN infection model.…”

Look Who’s Talking: Host and Pathogen Drivers of Staphylococcus epidermidis Virulence in Neonatal Sepsis

“…Using novel approaches, such as dual RNA-seq [ 214 ], host–pathogen interactions between the murine host and the opportunistic pathogens S. aureus and Streptococcus pneumoniae have recently been characterized [ 215 , 216 , 217 , 218 ] and provided new insights into the infection environment. Consequently, it has become evident, that in vitro gene expression studies are not representative of the complex in vivo host–pathogen interplay [ 217 , 218 ].…”