Proteomics and Genomics Diagnostics of Infection, Virulence and Anti-Microbial Resistance: Rapid Applications for Septicemia and Sepsis

Registration number: ALFGBG-720761

A research project funded by the Västra Götaland ALF-projektmedal with 2.25 MSEK for 2018-2020.

The principle researchers of the ALF-LUA consortium are: 1) Edward Moore, Sahlgrenska Academy UGOT (Principle Investigator); 2) Tao Jin Läkare, Avd-/sektionschef, bitr, inst Reumatologi, Sahlgrenska sjukhuset, Avd för reumatologi och inflammationsforskning vid Institutionen för medicin vid GU; 3) Roger Karlsson, Sahlgrenska Universitetssjukhuset; 4)Susann Skovbjerg, Läkare, Klinisk mikrobiologi, Bakteriologiska laboratoriet, SU, Avd för infektionssjukdomar vid Institutionen för biomedicin vid GU.

This project is investigating biomarkers of pathogen bacteria using mass spectrometry based proteomics.
Proteotyping, the use of MS-proteomics for characterization and identification of microorganisms, is based on detection of unique peptide biomarkers from proteins (gene expression). The focus of the research is pathogens causing septicemia and sepsis, as well as finding markers for antibiotic resistance and virulence.
The rationale of using tandem mass spectrometry-based proteomics stems from several benefits over traditional methodologies. The proteomic method has a higher potential in achieving strain resolution as compared to phenotyping or genotyping, and it can also be used for mixtures of bacteria (co-infections), whereas MALDI-TOF-MS need pure cultures. In septicemia the need for speed is critical, as the condition can rapidly become serious for a patient with an ongoing infection of the bloodstream.
A major part of the application is thus to explore the capability of using proteomics for direct analysis of clinical samples, thus eliminating culturing steps, which not only adds time to the overall analysis, but also adds bias towards bacterial species that cannot be cultured. We aim to use Escherichia, Staphylococcus and Streptococcus as model systems for a proof-of-concept of the proteomic methodology. We will explore traits such as antibiotic resistance and virulence within these species.
In order to speed up the analysis further, an in-house database containing the proteomic biomarkers will be generated. Mouse model for sepsis will be used to optimize the MS-proteomics protocols for direct analyses of clinical samples, without prior cultivations. Additionally, protein biomarkers for sepsis inflammatory immune response will be analysed to assess the stage of septicemia and sepsis of the patient.
The ultimate goal will be to generate a diagnostic protocol, employing expressed protein biomarker profiling for reliable, rapid, point-of-care diagnostics.