Studies on microbial diversity: characterisation, classification and identification of clinically-relevant microorganisms

Current projects

2020-2022

CARe-Diagnostics Project, "Comprehensive Mass Spectrometry Proteomics-Based Diagnostics of Antibiotic-Multi-Resistance in Infectious Bacteria" (Project No. 5314-2020-205314021, PI: E. Moore); 

Tandem Mass Spectrometry (MS/MS)-based analyses have been developed for identifying bacterial peptide sequences that serve as biomarkers for specific proteins, enabling high-resolution bacterial characterisation. Proteomics-based analyses provides possibilities to detect and define up-and down-expression of genomic features, such as anti-microbial resistance (AMR), e.g., in response to antibiotic stress, etc. ‘Proteotyping’ is sensitive and can be employed for detecting and characterising infectious bacteria in clinical samples, directly, i.e., without prior cultivation. Proteotyping presents tremendous potential for detecting relevant AMR and markedly improving diagnostics of infectious disease, wherein single MS/MS analytical runs provide physicians with the information for effective treatment within hours, instead of days. We propose that such analytical power can be employed directly, as a diagnostic tool in the routine clinical lab or the results of proteotyping analyses can be used to develop other diagnostic strategies, such as DNA-based PCR assays or antibody assays for detecting the most relevant AMR biomarkers.

2018-2021

VGR ALF-LUA Project, “Proteomics and Genomics Diagnostics of Infection, Virulence and Antimicrobial Resistance: Rapid Diagnostics of Septicemia and Sepsis” (Project No. ALFGBG-720761, PI: E. Moore); 

This project is investigating biomarkers of pathogen bacteria, using Mass Spectrometry-based proteomics. ‘Proteotyping’, i.e., the use of tandem MS-proteomics for characterization and identification of microorganisms, is based on detection of unique peptide biomarkers from proteins (gene expression). The focus is on pathogens causing septicemia and sepsis, as well as finding markers for antibiotic resistance and virulence. The rationale for using MS/MS-proteomics stems from several benefits over other methodologies. The proteomics method has high potential in achieving strain resolution, and it can be applied to analyses of mixtures of bacteria (co-infections). 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 to assess proteomics for direct analyses of clinical samples, thus eliminating cultivation steps. We are using Escherichia, Staphylococcus and Streptococcus as model systems for a proof-of-concept of the proteomic methodology. We are detecting and characterising traits such as antibiotic resistance and virulence within these species. In order to speed up the analysis further, an in-house database and analysis pipeline for proteomic biomarkers has been generated. Mouse model for sepsis will be used to optimize the MS-proteomics protocols for direct analyses of clinical samples. Additionally, host protein biomarkers for inflammatory immune response to sepsis 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.

2018-2021

JPI-HDHL-INTIMIC Project, “Impact of Mediterranean Diet, Inflammation and Microbiome on Plaque Vulnerability and Microvascular Dysfunction after an Acute Coronary Syndrome: A Randomized, Controlled, Mechanistic Clinical Trial (MEDIMACS)” (Project No. FR-2017/0010, PI: E. Moore, F. Fernández-Aviles);

Coronary atherosclerosis is a leading cause of mortality and disability worldwide. Continuous efforts are needed to improve secondary prevention and understand the mechanisms underlying disease progression. Based on primary prevention trials, a potential benefit of the Mediterranean diet after an acute coronary syndrome is anticipated. The integrated microbiome-mediated/immunological and metabolic pathways by which the Mediterranean diet modifies cardiovascular risk remain mostly unknown. Intestinal, as well as oral dysbiosis is involved in the pathogenesis of atherosclerosis and intestinal microbiome dynamics may account for observed benefits of Mediterranean diet. Our first objective is to address the impact of a well-controlled Mediterranean diet intervention on atherosclerotic plaque vulnerability and coronary endothelial dysfunction when started soon after an episode of acute coronary syndrome. The second objective is to decipher the complex interplays between diet, microbiota, inflammation and metabolism that are responsible for observed effects. We have established a small-sized, randomized, mechanism-based clinical trial, using state-of-the-art efficacy read-outs. The multidisciplinary consortium includes highly experienced cardiologists, nutritionists and translational research experts in the fields of immunology, microbiomics, genomics, proteomics, metabolomics and metagenomics. The UGOT team is responsible for ‘meta-proteomics’, in conjunction with meta-genomics analyses of the microflora of cohort patients, in response to the Mediterranean diet. The MS-based proteomics analyses are carried out in parallel also with NMR- (GU-based Sweden NMR Centre) metabolomics analyses. This study will provide valuable insights into microbiome therapeutic targets for coronary artery disease.

2018-2020

CARe-Diagnostics Project, "Rapid and Reliable Proteomics-Based Diagnostics of Antibiotic-Multi-Resistance in Infectious Disease" (Project No. 5314-2018-205314021, PI: E. Moore); 

In this project, we have developed and applied characterisation of protein biomarkers (‘proteotyping’) associated with antibiotic multi-resistance (AMR) in bacteria, with focus on carbapenem-resistance in clinically-relevant bacteria. State-of-the-art tandem mass spectrometry (MS) has be used for rapid, cultivation-independent, improved comprehensive clinical diagnostics of AMR in infectious disease. We have 1) applied high-throughput proteomics for identification of protein biomarkers associated with AMR; 2) established databases of protein biomarkers and bioinformatics tools for data analysis required for characterising AMR in infectious bacteria in routine diagnostics and validation of analyses; 3) Applied targeted proteomics directly on clinical samples and evaluate the performance in relation to traditional diagnostic methods.

2016-2020

JPIAMR Project, “Predicting Cell-Cell Horizontal Transmission of Antibiotics Resistance from Genome to Phenome (TRANSPRED)” (Project No. VR-2016-06504, PI: E. Moore, J. Warringer); 

We are analysing candidate drug targets controlling the horizontal cell-cell transmission of anti-microbial resistance (AMR), to predict AMR and its transmission dynamics, to help personalized antibiotics treatment. We have integrated leading expertise from bacteriology, -omics and mathematical biology for the development of an integrated theoretical-empirical framework of plasmid borne transmission of antibiotic resistance cassettes. We are using massive-scale experimental evolution of Escherichia coli gene deletion and overexpression, where adaptation requires transfer of antibiotic resistance carrying conjugative plasmids. We will select for de novo mutations that promote horizontal transmission during long-term experimental evolution, to disclose cellular functions controlling horizontal AMR transmission. High-throughput genomic sequencing is applied to disclose variants likely to alter transmission properties. Sequence data will be complemented and refined by data on transcriptome, proteome and AMR, allowing reconstruction of the history of AMR. We will integrate the omics data into a mathematical framework capable of predicting AMR transmission in clinical isolates. The project seeks to unify complementary, cutting-edge competences from diverse fields to counter the spread of antibiotic resistance by original and previously unexplored means.

The Culture Collection University of Gothenburg, CCUG

Edward Moore is also Curator/Director of  the Culture Collection University of Gothenburg, CCUG. The CCUG is the largest and most diverse public repository in Europe for clinically-relevant microorganisms