Research Areas
Our research areas include a wide variety of aspects important for infectious diseases and pandemic preparedness. One important aspect is epidemiology, as well as vaccine effectiveness studies and pathogen surveillance – both locally as well as internationally. Another important aspect that goes hand in hand with epidemiology and pathogen surveillance is the development of diagnostics. Here we focus on the establishment and implementation of laboratory developed tests but not on routine diagnostics. Another focus of the Semmelweis Institute will be on pathogenicity research. Understanding which strains of a given pathogen will cause disease or will efficiently spread, allows to assess risk even before larger outbreaks happen. This type of research also allows to understand changes in virulence that may occur even with pathogens that are already well established in the human population. Understanding the biological mechanisms behind infection – both on the pathogen as well as the host side – is another very important focus of the Semmelweis Institute, which will be assessed in advanced cell culture models as well as in vivo. Both innate and adaptive immune responses provide protection against infection. Our research also focuses on the detailed mechanisms, on how these immune responses work on the individual and population level. Finally, the Semmelweis Institute has a strong focus on the development of vaccines and therapeutics that can be used to protect the population from infectious diseases. We will leverage on collaborations with academic and industry partners to bring these interventions from the bench to the market.
Research Groups
Krammer Laboratory
Research Focus
The focus of the Krammer laboratory within the Semmelweis Institute is on RNA viruses, especially influenza viruses, coronaviruses and hantaviruses but also other emerging viruses. We are interested in understanding pathogenicity of these viruses, their potential for human-to-human transmission (a pre-requisite for a pandemic), as well as immune responses that protect us from these infections and how prevalent protective immunity in the human population is. We are especially interested in humoral immune responses to the surface glycoproteins of these viruses, their antiviral potential and their antiviral mechanisms. Furthermore, we are studying mucosal immunity and how it can block transmission of respiratory viruses. Based on these findings, we are developing vaccines candidates and therapeutics which can help to prevent or treat these infections.
Biography
Florian Krammer
Florian Krammer, PhD, graduated from the University of Natural Resources and Life Sciences, Vienna.
He received his postdoctoral training in the laboratory of Dr. Peter Palese at the Icahn School of Medicine
at Mount Sinai, New York, working on hemagglutinin stalk-based immunity and universal influenza virus vaccines. In 2014, he became an independent principal investigator and is currently the endowed Mount Sinai Professor of Vaccinology at the Icahn School of Medicine at Mount Sinai. He is also the co-director of the Center for Vaccine Research and Pandemic Preparedness (C-VaRPP). Furthermore, since 2024, Dr. Krammer is Professor for Infection Medicine at the Ignaz Semmelweis Institute at the Medical University of Vienna. Dr. Krammer’s work focuses on understanding the mechanisms of interactions between antibodies and viral surface glycoproteins and on translating this work into novel, broadly protective vaccines and therapeutics. The main target is influenza virus but he is also working on coronaviruses, flaviviruses, hantaviruses, filoviruses and arenaviruses. He has published more than 400 papers on these topics.
Dr. Krammer is an elected fellow of the American Academy of Microbiology and the Henry Kunkel Society,
he is on the Board of Directors of the European Scientific Working Group on Influenza (ESWI) and he serves as one of the chairs of the SAVE group which tracks SARS-CoV-2 variants for the US NIH. He is also the recipient of the 2024 Geoffrey Schild Award.
Wilflingseder Laboratory
Research Focus
Zoonotic viruses are among the most tantalizing threats to global health, with their ability to mutate, adapt, and leap between species, sparking the pandemics that define our century. To stay one step ahead, we need vigilant surveillance, innovative research into host-virus dynamics, and proactive measures to prevent the next global outbreak.
Our research dives into the fascinating science of innate immunity—especially the unique defenses at mucosal surfaces that spring into action when viruses strike. We are unraveling how animals can coexist with viruses that are often deadly for humans. These discoveries hold the potential to unlock new therapeutic targets and reveal preventive strategies to keep both animals and people safe from future outbreaks.
One of our core goals is to decode how certain species, like bats, tolerate highly pathogenic viruses, hoping to translate this knowledge into strategies to treat severe infections in humans and reduce spillover risks. By creating and studying organoid lung models from bats, pigs, cattle, and birds, we can observe these species’ intrinsic defense mechanisms, comparing them to our own. Our laboratory is developing and refining these respiratory tissues in organoid form, using both submerged and air-liquid culture methods to mimic physiological conditions.
Where possible, we are also integrating immune cells from the same individual donor to build immune-competent, species-specific barrier models in vitro. Infecting these tissues with influenza or coronaviruses, we are mapping the earliest immune responses at epithelial barriers using cutting-edge tools and technologies. By incorporating microfluidic systems and advanced screening methods, we create standardized models for comparative infectiology studies. With these microfluidic platforms, we will build a barrier/lymph node two-organ model to observe adaptive immune responses in a whole new light.
In parallel, we are pioneering animal-origin immune cell-based drug and vaccine testing strategies, backed by powerful in silico analyses. This dual approach aims to create an efficient drug and vaccine pipeline for veterinary applications, allowing us to streamline testing and significantly reduce the need for animal experimentation.
Biography
Doris Wilflingseder
Doris Wilflingseder studied Zoology at the University of Innsbruck. Cell biology sparked her fascination, leading her to pursue early research in signaling mechanisms and protein purification. In her Post Doc, Dr. Wilflingseder specialized in immunology, with a particular focus on dendritic cell – HIV-1 interactions and the impact of virus opsonization on antigen presentation and T cell responses. A research stay at the University College London (UCL) enabled her to perform transcriptomics analyses of dendritic cells following exposure to differentially opsonized HIV-1. More recently, Dr. Wilflingseder advanced the development of immune-competent 3D barrier models to allow targeted studies of pathogen entry, processing, and therapeutic interventions. In 2012, Dr. Wilflingseder served as Assoc. Professor and deputy chair of the Department of Hygiene and Medical Microbiology at the Medical University of Innsbruck. In 2020 she received a Professorship for Infection Biology, and in 2024 she became Professor of Infectious Diseases at the Ignaz Semmelweis Institute and the Veterinary University of Vienna. Dr. Wilflingseder received several awards like the Austrian State Award 2021 for promoting Alternatives to Animal Testing or the Austrian Microbiology Prize. She is deputy chair of the Austrian Society for alternative Biomodels (RepRefRed Society) and the governmentally funded Austrian 3Rs Center (A3RCs) and member of the Austrian Society of Allergology and Immunology (ÖGAI). As such, she organized the Austrian 3R Days 2023 and the Annual Meeting of the ÖGAI 2016 as congress president.
Biswas Laboratory
Research Focus
Monocytes and macrophages are key immune cell types that perform diverse functions ranging from homeostatic processes (e.g. organogenesis, thermoregulation, innervation) to host defense against pathogens and cancer. However, a dysregulation in their functions is often associated with various pathologies like sepsis, cancer, metabolic diseases and allergy. Hence, studying the dysregulated phenotype of monocytes/macrophages in a disease provides a direct insight into the disease mechanism. The overall aim of our laboratory is to i) characterize the dysregulated phenotype of monocytes/macrophages in selected human diseases (with an aim to identify immune signature-based biomarkers); ii) identify the mechanisms which drive this dysregulation, and iii) target mechanisms to re-program these cells to fight disease progression. In the current laboratory, we will focus on dissecting the role of these cells (as well as other innate immune cells) in fungal diseases, which constitute a substantial impact on human health, especially under immunocompromised conditions. We intend to investigate the host (immune)-fungal pathogen interactions using deep immunoprofiling techniques in various cohorts of human fungal disease with an aim to characterize their dysregulated immune signatures (hence potential biomarkers) as well as identify and evaluate immune targets to regulate fungal disease. In the later stages, our work will expand to other infectious diseases and vaccine responses.
Biography
Subhra K. Biswas
Subhra K. Biswas completed his Ph.D. in Biotechnology (Cellular Immunology) at Banaras Hindu University, India, followed by postdoctoral studies at the Istituto di Ricerche Farmacologiche “Mario Negri”, Milan, Italy, working on the first molecular characterization of tumor associated macrophages. In 2005, he joined the Bioinformatics Institute of Agency for Science Technology & Research (A*STAR) in Singapore as Research Scientist in charge of the Cell Interaction group. From 2007-2024, he was a Principal Investigator and then a Senior Principal Investigator at the Singapore Immunology Network (SIgN, A*STAR), heading the Human Innate Immunity Lab. In 2024, he moved to Austria as a tenure track Professor in Host-Fungal Pathogen Interaction at the Division of Infectious Diseases, Medical University of Graz, Austria. Prof. Biswas has held various adjunct positions as an associate Professor at LKC School of Medicine, Nanyang Technological University, Singapore, National University of Singapore, and a visiting Professor at Humanitas University, Milan, Italy. He is a Clarivate Highly-Cited Scientist 2019, 2020, 2021, 2022.
Willeit Group
Research Focus
The research of Peter Willeit and his group is focused around population-based studies, clinical trials, and public health interventions. First, during the COVID-19 pandemic, Peter Willeit was responsible for the analysis of the Austrian SARS-CoV-2 School Study conducted in 250 school nationwide (“Gurgelstudie”), howing a close link of SARS-CoV-2 infections in schools to the general community and to social deprivation. Second, in 2021, we evaluated the real-world effectiveness of ultra-rapid rollout vaccination delivered to inhabitants of the Schwaz district in Tyrol and assessed the suitability of binding and neutralizing antibodies as correlates of protection in an open-label phase-4 trial. Third, the research group collaborates closely with the blood donation services to quantify the seroprevalence for SARS-CoV-2, hepatitis B and other pathogens at the population level. As part of a wider PhD-program focused on antifungal resistance, his group aims to determine azole burden among blood donors with respect to environmental and dietary exposures and thereby provide insights into the consequence of the dual use of this class of antifungals in human medicine and agriculture, following a One Health approach. Fourth, we perform research in the Bruneck Study, which is a prospective cohort study involving 2000 inhabitants of the municipality of Bruneck, South-Tyrol. Since 1990, the study population has been re-examined up to seven times and clinical outcomes have been recorded over up to 33 years of follow-up, with potential scope of research into inflammatory parameters, chronic infections, microbiota, and occurrence of specific infectious diseases. More broadly, in the context of the Semmelweis, we aim to build up precisely characterized patient cohorts and contribute expertise in study design and medical statistics.
Biography
Peter Willeit
Peter Willeit is Professor of Epidemiology and Public Health and the Director of the EpiCenter Innsbruck located at the Medical University of Innsbruck. This institute brings together experts in the fields of epidemiology, public health, health economics, medical statistics and informatics. Through this interdisciplinary approach, the institute aims to unlock the potential of medical data and create strategies to improve public health and patient outcomes. Professor Willeit trained in epidemiology at the University of Cambridge in the UK (MPhil in Epidemiology 2010, PhD in Public Health and Primary Care 2013) and holds a medical degree from the Medical University of Innsbruck. Before returning to Austria in 2016, he worked as a University Lecturer in Medical Epidemiology at the University of Cambridge. Peter Willeit is a recipient of a FWF Erwin Schrödinger Fellowship and has been leading scientifically the population-based Bruneck Study and international consortia, such as the Emerging Risk Factors Collaboration and the Proof-ATHERO consortium involving a total of 200 cohort studies with 2.6M participants. Peter Willeit acts as a Senior Collaborator of the Global Burden of Disease consortium and as an Honorary Research Fellow of the School of Medicine, University of Cambridge.
Clinical Research Group
Prof. Salzer
Research Focus
The aim of our research group is to promote clinically oriented research in infectious diseases with a strong scientific focus on acute and chronic respiratory infections. We see our research group as a link between basic science and clinical research to support translational research, especially within The Semmelweis Institute. Our research activities include local and multinational clinical data collection and -analyses to enable a better understanding of the disease burden- and clinical characteristics of certain infections. There is a strong interest on chronic pulmonary infections such as drug-susceptible- and drug-resistant tuberculosis including post-tuberculosis lung diseases, non-tuberculous mycobacterial infections, endemic mycoses, and chronic pulmonary aspergillosis. We are also interested in studies directly comparing and evaluating the performance of different diagnostic tests in well-defined patient cohorts to improve diagnosis of certain infectious diseases (e.g. fungal infections). Furthermore, we support with our ID-study team large international treatment studies to enable the development of new drugs or to test new therapeutic drug regimes.
Biography
Helmut Salzer
Dr. Salzer studied medicine at the Medical University of Graz in Austria, where he also started his professional career in 2008 as a research physician in the clinical infectious diseases research group of
Prof. Krause. During this time, he also completed a Master program in Public Health (MPH) with study periods in Norway, Denmark, and Germany. In 2011, he moved to the University Medical Center Hamburg-Eppendorf in Germany, where he began his training as a specialist in Internal Medicine. During this time, he was associated with the renowned Bernhard Nocht Institute for Tropical Medicine. From 2015 to 2019, he worked in the research group of Prof. Lange at the Research Center Borstel in Germany, one of the leading research institutes for mycobacterial infections. During this time, he also founded the international research network CPAnet and completed his training as an internist and infectious disease specialist. Since 2019, he works at the Department of Prof. Lamprecht at the Kepler University Hospital in Linz in Austria, where he also completed his training as a specialist in pulmonary medicine. Since September 2023, Prof. Salzer is the head of the division of infectious diseases and tropical medicine at the Kepler University Hospital in Linz. He became Professor for Clinical Infectious Diseases at the Medical Faculty of the Johannes Kepler University and at The Semmelweis Institute in Vienna. In addition to his clinical- and research work, Prof. Salzer is engaged in teaching of medical students and resident doctors.