3 July 2023
NCCR AntiResist: From bed to benchsite
For the battle against antibiotic-resistant germs, a multidisciplinary network has emerged that closely links clinical and basic research.
In the first phase of the National Center of Competence in Research (NCCR) AntiResist, a project planned for a period of 12 years and funded by the Swiss National Science Foundation, clinical material and data from hospitalised patients with certain bacterial infections (see box) are being collected and made available for research. They present an important part of the foundation on which the search for new ways of fighting infections will be built.
Clinical data require special handling
Data collected in hospitals, whether contact data, treatment data, data on samples taken or isolated bacterial strains, are considered by law to require special protection because they are always linked to a person. Handling of clinical data, also referred to as sensitive data, require special technical and contractual measures. To establish these measures and ensure that they are fully complied with, a Medical Data Office run by experts from the Department of Clinical Research from the areas of regulatory affairs, data management, data science and IT has been formed.
Before sensitive data can leave the hospitals, a number of safeguards must be in place. For example, the necessary authorisations for data use for research purposes must be in place. Data collection and sampling must be carried out in a harmonised and standardised manner in all hospitals and quality controls must be in place. Data transfer must be secured by appropriate technical systems and contracts. Finally, all materials and patient data must be de-identified (encoded) before they can be made available to researchers. All of this is the responsibility of the Medical Data Office.
Broad data base
By combining clinical information from patients with information from basic research, a unique foundation is created for research enabling the development of new in vitro models and antimicrobial agents. The Medical Data Office is in close exchange with the Research Data Officer located at the Biozentrum, who is responsible for managing data from basic research such as cell imaging and data from genomics, proteomics or metobolomics research. Secure linkage of clinical and laboratory data is the joint responsibility of the Medical and Research Data Offices. The appropriate technical environment for this endeavour is provided by sciCOREmed at the University of Basel.
National Center of Competence in Research (NCCR) AntiResist
Better understanding of physiological properties of bacterial pathogens in vivo and development of new antibiotic agents
Prof. Christoph Dehio
Prof. Dirk Bumann, Prof. Urs Jenal, Biozentrum University of Basel, Prof. Dr. med. Nina Khanna, University Hospital Basel
Biozentrum University of Basel, ETH Zurich, University of Zurich, EPFL Lausanne, University of Lausanne, Ben-Gurion University of the Negev
University Hospital Basel, University Hospital Zurich, Soroka University Medical Center in Israel
Approximately 7500 samples from patients with urinary tract infection, pneumonia or invasive tissue infection with E. coli, Klebsiella species, S. aureus and P. aeruginosa from Switzerland. In addition, samples from approximately 500 patients from Israel with B.melitensis infections.
Currently, more than 2000 clinical samples have already been collected and processed so that the corresponding information can be fed into the research database. By 2025, the clinical researchers hope to deliver the remaining samples and data, paving the way for discoveries that will mitigate, if not solve, the looming problem of increasing antibiotic resistance.
«The clinical part of the NCCR Antiresist has been extremely successful. By collecting and analysing more than 1600 patient samples so far, important reference values for in vitro models could be established already.»
Prof. Dr. med. Nina Khanna, Leading Senior Physician Infectiology & Hospital Hygiene, Head of Transplant Infectiology, University Hospital Basel
«The Medical Data Office maintains a close exchange with the Research Data Officer at the Biozentrum so that clinical data can be linked to other research data and thus be accessible for the project.»
David Büchel, PhD, Data Manager at the Department of Clinical Research and Coordinator of the NCCR AntiResist Medical Data Office