Universität Bern, Institut für Infektionskrankheiten.

The Institute for Infectious Diseases, University of Berne, Switzerland provides training in clinical microbiology and the study of infectious diseases for university students from the disciplines of medicine, dentistry, pharmacy and cell biology. Research at the Institute is focused on pathogenesis of certain infectious diseases (respiratory and CNS infections), microbial population dynamics (at the Pneumococcal Centre) and the epidemiology and molecular mechanisms of antibiotic resistance of bacterial pathogens. The Institute works closely with the University Clinic for Infectious Diseases at the University Hospital, Bern. The Clinic cares for out-patients with infectious diseases including providing consultations for HIV patients. It serves as a center for travel and tropical medicine, infectious diseases in general, and acts as a consult service for infectious diseases, hospital hygiene and padiatric infectious disease. The Institute for Infectious Diseases (IFIK) is engaged in diagnostic microbiology in the fields of virology, bacteriology, mycology, parasitology and immunology and is thus the only university institute in Switzerland which encompasses all diagnostic microbiological disciplines under one roof.

The partner of the University of Berne in HONOURs is Spiez Laboratory which is the Swiss center of expertise for protection against nuclear, biological and chemical threats and hazards in the Federal Office for Civil Protection within the Swiss Federal Department of Defence, Civil Protection and Sports. The Spiez Laboratory carries out basic and applied research in this area and provides international organizations, the authorities and the Swiss population with a range of services in relation to disaster and emergency management, prevention, and the preparation of protective measures. The Objectives of the Spiez Laboratory include the assessment of threats by biological agents, either naturally occurring or man-made, analysis and diagnosis of highly pathogenic biological agents and toxins, research on epidemiology and pathogenesis, diagnosis of biological agents and toxins, maintaining expertise and technical readiness for biological incident-response, Scientific support for arms control and peace keeping activities, and biosafety education, training and research. As a member of the Swiss regional laboratory network, primary and secondary diagnostics of BSL-3 & 4 viruses are performed on behalf of the Cantonal laboratory of Berne. The Spiez Laboratory incorporates several BSL-2, two BSL-3 and two BSL-4 laboratories with integrated animal holding units for rodents and Cell culture facilities. In its function as the Swiss center of expertise for protection against biological threats it is fully equipped with the conventional and the latest technology in analysis and diagnosis for microbial pathogens including next generation sequencing and MALDI-TOF.

Web page: www.ifik.unibe.ch/index_eng.html

Web page: www.labor-spiez.ch

Key publications IFIK:

  • Development of real-time sequencing in infectious diseases: application to clinically relevant RNA viruses. Ramette A, Barbani MT, Terrazos Miani MA, Steinlin-Schopfer J, Bittel P, Suter FM, Leib SL. [BC]2 Basel Computational Biology Conference, 12-15 September  2017 
  • Heterogeneous Genetic Location of mcr-1 in Colistin-Resistant Escherichia coli Isolates from Humans and Retail Chicken Meat in Switzerland: Emergence of mcr-1-Carrying IncK2 Plasmids. Donà V, Bernasconi OJ, Pires J, Collaud A, Overesch G, Ramette A, Perreten V, Endimiani A. Antimicrob Agents Chemother. 2017 Oct 24;61(11)
  • Prevalence of cough throughout childhood: A cohort study. Jurca M, Ramette A, Dogaru CM, Goutaki M, Spycher BD, Latzin P, Gaillard EA, Kuehni CE. PLoS One. 2017
  • The R package otu2ot for implementing the entropy decomposition of nucleotide variation in sequence data. Ramette A, Buttigieg PL. Front Microbiol. 2014
  • A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses. Buttigieg PL, Ramette A. FEMS Microbiol Ecol. 2014

 Key publications Spiez Lab:

  • Seroprevalence of hantavirus infections in Switzerland in 2009: difficulties in determining prevalence in a country with low endemicity. Engler et al. Euro Surveill. 2013 Dec 2;18(50).
  • European surveillance for West Nile virus in mosquito populations. Engler O et al. bInt J Environ Res Public Health. 2013 Oct 11;10(10):4869-95.
  • A five-year perspective on the situation of haemorrhagic fever with renal syndrome and status of the hantavirus reservoirs in Europe, 2005-2010. Heyman P et al. Euro Surveill. 2011 Sep 8;16(36).
  • Phylogenetic and virulence analysis of tick-borne encephalitis virus field isolates from Switzerland. Gäumann R. J Med Virol.2011 May;83(5):853.
  • High-throughput procedure for tick surveys of tick borne encephalitis virus and its application in a national surveillance study in Switzerland. Gäumann R et al. Appl Environ Microbiol 2010 Jul;76(13):4241-9.
  • Close geographic association of human neoehrlichiosis and tick populations carrying "Candidatus Neoehrlichia mikurensis" in eastern Switzerland. Maurer F. P. et. J Clin Microbiol. 2013 Jan;51(1):169-76.
  • Genome-wide identification of pathogenicity factors of the free-living amoeba Naegleria fowleri. Zysset D.C. et al. BMC Genomics. 2014 Jun 19;15:496.
  • Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study. Schneeberger P.H. et al. Infect Genet Evol. 2016 Jun;40:389-97
  • Development and Evaluation of a Bioinformatics Approach for Designing Molecular Assays for Viral Detection. Schneeberger P.H. et al. Plos One 2017, submitted

Staff involved in HONOURs

Prof Dr. Stephen Leib MD


Prof Dr. Stephen Leib MD is the Director of the Institute for Infectious Diseases, Full Professor and Chair for Clinical Microbiology at the University of Bern. He is Swiss board certified physician in Infectious Diseases and internal Medicine. He will be involved in HONOURs as the academic supervisor of ESR 13, co-organizer of workshops and the CUSO Doctoral program in Microbial Sciences.

Dr. Alban Ramette

        Alban Ramette

Dr. Alban Ramette is Group Leader Biostatistics / Bioinformatics at the Institute for Infectious Diseases (IFIK). His team develops NGS solutions for clinical applications with strong emphasis on long read nanopore sequencing. Alban Ramette will be the scientific co-supervisor of ESR 13 at IFIK.

M Sc med Roger Koller

       Roger KollerRoger Koller works in the microbiological diagnostics unit at the Institute for Infectious Diseases. He is the responsible Biosafety officer and will be involved in administrative guidance, co-organizer of workshops and assist on teaching at the HONOURS training activities.

Dr. Olivier Engler

       Oliver Engler

Dr. Olivier Engler is the head of Virology at the Spiez Laboratory, he is responsible for the work in the BSL-3/4 Lab, training of new scientists in BSL-3/4 activities, and neutralisation assays in the frame of the VSV-EBOVAC (Ebola vaccine candidate) in the BSL-4 lab. Leading surveillance program for mosquito borne viruses and for rodent-borne hantaviruses in Switzerland. Olivier Engler is also co-organizer of the work-shops in the frame of CUSO (Doctoral Program in Microbial Sciences).

Dr Christian Beuret

        Beuret Christian

Dr. Christian Beuret is the deputy head of Virology at the Spiez Laboratory, he is responsible for the implementation of molecular detection methods and has BLS-4 lab-expertise in the frame of VSV-EBOVAC project. He has managed surveillance programs for tick born diseases in Switzerland and has the scientific lead for doctoral programs related to NGS developments. Christian Beuret will be the scientific co-supervisor of ESR 13 at the Spiez Laboratory.

Dr. Franziska Suter-Riniker PhD


Dr. Franziska Suter-Riniker PhD is head of the Department of Clinical Microbiology and deputy Director of the Institute for Infectious Diseases at the University of Bern. She is a specialist for medical-microbiological diagnostics (FAMH) and holds a Master of Medical Education. In 2016 she was awarded “teacher of the year “ by the medical students at the University of Bern. Franziska Suter-Riniker will be involved in the organisation of workshops and training.


Host switching pathogens, infectious outbreaks and zoonosis; a Marie Sklodowska-Curie Innovative Training Network.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 721367.