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