Genome-based analysis of the pathogen spectrum and virulence profile of periprosthetic joint infections

Together with the Institute of Clinical Immunology and the Orthopedics, Trauma and Plastic Surgery, Spine Center at the University of Leipzig, the CardiOmics group is developing a method to improve clinical decision making on antibiosis therapies or re-intervention strategies in case of prosthesis infections and infections of surrounding tissue. The decision depends largely on the pathogen spectrum and its detection. Microbiology reaches its detection limits in daily clinical routine. The aim of the research work is to uncover the possible mono- or polymicrobial pathogen load and its virulence potential by combining metagenome sequencing (NGS) and specific PCR analyses in comparison to microbiological findings and to determine its virulence potential. On the basis of the findings obtained in this way, new therapy options or treatment schemes will then be developed.

Verification of the virulence profil of organ-specific infection

In the past decade, infectious diseases in the cardiovascular sector have been increasingly emerging as a clinical challenge. This is not only to be attributed to an increasing pathogen-specific resistance to chemotherapy but also to an improved therapy landscape, such as implanting cardiac pacemakers, heart valve systems and artificial heart systems. Current research results show that a polymicrobial pathogen infiltration defines the disease status and course. Previous research efforts focused on identifying pathogen spectra by means of total genome investigations. Further, the goal of the research effort is to identify disease-causing pathomechanisms. To this end, it is necessary to ensure the identification agents up to the root level to allow conclusions on disease mechanisms. Initially, the microbial community of a patient sample was analyzed via a specifically defined PCR panel. The PCR allows a quick analysis of known pathogenic germs. As unknown bacteria, which may also be pathogenic, remained undetected, the T-RLFP analysis was also used to characterise the diversity of the samples. This non-targeted method is based on the amplification and restriction of 16S RDNA and then uncovers unknown germs via cloning and sequencing. However, the sensitivity of the method is limited by the number of clones analyzed, and in some cases it does not read a differentiation of the species of a genus. A more sensitive process is genome sequencing based on the 16S RDNA or the overall genome. It was possible analyse the microbial composition of a patient sample and also detect bacteria in low concentrations up to the species level. The main challenge in applying the new analysis methods lies at the level of bioinformatics diagnostic strategies. This ranges from the assignment of pathogen-specific DNA molecules to the identification of the pathogen stem to the classification of virulence factors. These virulence factors must be correlated with the patient outcome in prospective clinical trials and thus their clinical relevance will be developed. The aim of the working group is to develop this clinical molecular biological diagnostic path, to establish necessary bioinformatic tools and to incorporate the findings into the daily routine in clinics.

Infectious diseases relevant to cardiac surgery

The "Infectious diseases relevant to cardiac surgery" project aims to depict the pathogen spectrum of infectious diseases affecting the cardiovascular system. Special attention is given to infective endocarditis (IE), which is becoming more and more clinically relevant due to increasing heart valve interventions. In spite of the medical advancement seen over the past century, patients suffering from IE are faced with just as poor an outlook as in the past. The unit is developing a comprehensive approach which shall serve as a model and aim to improve clinical diagnosis based on next-generation sequencing (NGS), electron microscopy (EM) and a point-of-care (PoC) platform, thus facilitating more targeted treatment and prevention strategies. The knowledge gained from OMICS technnologies will be used to establish immunology-based assays, which will be developed to clinical market-maturity.

Diagnosis of primary and secondary haemostasis

The "Diagnosis of primary and secondary haemostasis" project focuses on establishing thrombin generation as a clinical monitoring tool for the sensitive determination of the entire plasma coagulation cascade. Determining the final stage of plasma coagulation is also suitable to sufficiently map the factor X inhibitors and their effect on the coagulation system. Based on experimental molecular biology experiments, a point-of-care assay will be developed and later validated during the course of routine clinical practice.