Proteome-wide analysis of severe bacterial infections. The battle between host and pathogen

Sammanfattning: The pathogenesis of severe infectious diseases is a complex interplay between the host and the pathogen. The development and progression of a disease encompasses a multitude of processes, which balance between host-damage and host-protection. Proteomic analysis provides the necessary tools to interpret the extensive protein networks of host-pathogen interactions underlying the pathogenesis of a particular disease. This thesis focuses on proteome analysis of two blocks; the host-response during disease, as well as the pathogen during colonization and disease. Data-independent acquisition (DIA) mass spectrometry (MS) was utilized to acquire near-to-complete proteome maps of processes involved in the pathogenesis of one severe infectious disease; meningitis, as well as the host-pathogen interaction counterparts of its leading bacterial cause; Streptococcus pneumoniae.High quantitative ability of DIA-MS was used to construct compendiums of digital cerebrospinal fluid (CSF) proteome maps to define the pathogen-specific host response patterns in meningitis. We generated a predictive multiprotein panel of eighteen human proteins with a high sensitivity and specificity, for discrimination of the meningitis-causing pathogens in the CSF during meningitis. The results also showed a large number of neutrophil-associated proteins in the CSF during bacterial meningitis, and these were found to be due to the presence of neutrophil extracellular traps (NETs). The presence of NETs was further confirmed in the CSF in a rat model of pneumococcal meningitis. Treating the animals with DNase resulted in the abolishment of NETs, and led to increased bacterial killing. We further continued to explore the transcriptional landscape and adaptation of S. pneumoniae in human blood plasma by generating a large number of perturbations. A comprehensive pneumococcal proteome repository was constructed to unravel complex protein-protein networks of the bacteria. The results revealed specific regulatory patterns in response to human blood plasma, and pneumococcal transcriptional reorganization regulated by important virulence factors. Furthermore, to describe processes involved in bacterial dissemination in the human nasopharynx, we investigated differences between pneumococcal populations associated with colonization (biofilm bacteria), disease (biofilm-dispersed bacteria) and the conventional broth-grown, planktonic bacteria. The investigated populations showed distinct proteome patterns, especially in regards to metabolic pathways. The virulence of these models was investigated in a murine pneumococcal infection model, where it was showed that virulence of the populations is largely mediated on the investigated pneumococcal serotype. In conclusion, large-scale proteome analyses produced in this thesis generate fundamental knowledge in understanding host-pathogen interactions as a whole. Furthermore, the constructed repositories can be repetitively queried by the scientific community to deepen the understanding in host-pathogen interactions in bacterial infections.