SOLIDNESS

Project members

Contact Information

Call: +31 50 361 3480

Email: j.w.a.rossen@rug.nl

Prof. dr. John W. A. Rossen

Professor for Medical Microbiology
Medical Molecular Microbiologist
Coordinator SOLIDNESS

Department of Medical Microbiology and Infection Prevention
University of Groningen, University Medical Center Groningen

John W. A. Rossen has a 30-year history in molecular virology and molecular microbiology, and more than 160 peer reviewed publications (H-index 35). He is tenure track Professor for Medical Microbiology, in particular Personalised Microbiology, at the University of Groningen and head of the molecular unit which has successfully implemented the use of next generation sequencing for routine clinical microbiology and infection prevention. The method is used to determine the genetic relationship between pathogens (used to guide infection prevention measures) and for the molecular detection and further characterisation of (emerging) pathogens. This includes analyses for revealing (new) antibiotic resistance mechanisms and for determining the virulence of pathogens resulting in improved risk assessment and infection prevention. In addition, based on comparing whole genomes of bacteria, tailor-made diagnostic tests are developed used for specific detection of outbreak and/or virulent bacterial strains. Nowadays, his research group “Personalised Microbiology”, closely linked to Prof. dr. Alex Friedrich's research group "Genomics of Infection Prevention", focuses on implementing metagenomics and metatranscriptomics into clinical microbiology. These methods are not only applied to patient samples but also to animal-, food- and water samples. Apart from characterising the micro-organisms (including viruses) the interaction between them as well as with their host is studied. Prof. dr. Rossen is secretary of the ESCMID study group for genomic and molecular diagnostics (ESGMD) and board member of the Dutch Society of Medical Microbiology.

Contact Information

Call: +31 50 361 2455

Email: n.monge.gomes.do.couto@umcg.nl

Dr. Natacha Couto

Senior Researcher
Co-Project leader SOLIDNESS

Department of Medical Microbiology and Infection Prevention
University of Groningen, University Medical Center Groningen

Natacha Couto is a Researcher at the University of Groningen in the Netherlands where she currently develops work in the groups of Prof. dr. John W. A. Rossen (Personalized Microbiology) and Prof. dr. Alex W. Friedrich (Genomics for Infection Prevention). Her PhD research focused on the pathogenesis of bacterial infections, by determining the mechanisms involved in infection, and on the dissemination of antimicrobial-resistant bacteria. Her PhD results were pioneering in the field of vaccine development against S. pseudintermedius infection in dogs and also on characterizing the molecular mechanisms involved in antimicrobial resistance in animals, humans and the environment (One Health). At the UMCG, she has been involved in the optimization (both wetlab and elab) of shotgun metagenomics, transcriptomics and long-read sequencing. Recently, she has been developing her own research line, which involves understanding the missense polymorphisms that occur during S. aureus colonization and their role for infection. Natacha is the secretary of the ESCMID Study Group for Epidemiological Markers (ESGEM) and is currently an Editorial Board Member for Nature Scientific Reports.

Contact Information

Call: +49 30 838 61627

Email: Stefan.Schwarz@fu-berlin.de

Prof. dr. Stefan Schwarz

Professor
Team leader Laboratory

Institut für Mikrobiologie und Tierseuchen

Stefan Schwarz has studied veterinary medicine in Giessen/Germany. After his post-doc time, he worked for the Federal Agricultural Centre (FAL) from 1992-2007 and for the Friedrich-Loeffler-Institut (= Federal Research Institute for Animal Health) from 2008-2016. Since October 2016, he is the head of the Institute of Microbiology and Epizootics at the Department of Veterinary Medicine of the Freie Universität Berlin in Berlin/Germany. His research group is involved in both, monitoring of antimicrobial resistance and analysis of the molecular genetics of antimicrobial resistance. He is particularly interested in mobile genetic elements that spread antimicrobial resistance genes among bacteria. Prof. Schwarz is a specialist veterinarian in (a) microbiology, (b) epidemiology, and (c) molecular genetics and gene technology. He has published >450 peer-reviewed papers, 2 books and >35 book chapters, and also acts as editor/editorial board member of six international journals.

Contact Information

Call: + 351 21 799 94 58 ext 47212

Email: jcarrico@medicina.ulisboa.pt

Dr. João André Carriço

Researcher
Team leader Bioinformatics

Molecular Microbiology and Infection Unit
Instituto de Medicina Molecular
Faculdade de Medicina de Lisboa

João André Carriço is currently working as a Researcher in the Molecular Microbiology and Infection Unit at the Instituto de Medicina Molecular in the Faculty of Medicine, University of Lisbon. He studied Applied Chemistry, Biotechnology and did his PhD on Microbial typing and data analysis methodologies. João’s research interests are in Bioinformatics and the development of novel analysis and visualization methodologies for  molecular and genomic epidemiology with special emphasis on High Throughput Sequencing data analysis. For more detailed information you can check his homepage : https://jacarrico.github.io/

Contact Information

Call: +45 386 22409

Email: Henrik.torkil.westh@regionh.dk

Prof. dr. Henrik Westh

Professor for Clinical Microbiology
Clinical microbiologist
Team leader Typing

MRSA Knowledge Center
Department of Clinical Microbiology 445
Hvidovre Hospital

Henrik Westh is an MD (1980) from the University of Copenhagen, specialist in Clinical Microbiology (1994) and a Doctor of Medical Science University of Copenhagen (1996). He has published more than 175 peer-reviewed scientific papers. He has worked as a consultant microbiologist at Hvidovre Hospital for more than 20 years building up molecular biology, a MRSA Knowledge Center and currently is head of a large Genome Sequencing facility used daily for clinical microbiology and infection control purposes. The Genome sequencing facility uses Illumina and Nanopore technology and has sequenced more than 13 000 bacterial genomes and is currently analyzing 15 samples per week with shotgun metagenomics.

Contact Information

Call: +32 2 642 51 11

Email: Pieter-Jan.Ceyssens@sciensano.be

Dr. Pieter-Jan Ceyssens

Partner SOLIDNESS

Division of human bacterial diseases
Sciensano

Pieter-Jan Ceyssens heads the unit on antimicrobial resistance in the division of human bacterial diseases at Sciensano, which is Belgian’s public health institution. With a background in bacteriophage genomics, he is an experienced molecular biologist with a keen interest in applying cutting-edge tools in the study of transmission of drug resistance genes and vectors. He published 50+ papers and book chapters in the field of phage, surveillance and AMR. In 2018, he was appointed as ‘One Health AMR focal point’ for Sciensano, and is participating in drafting the new national action plan on AMR.

Contact Information

Call: +312 30 274 91 11

Email: engeline.van.duijkeren@rivm.nl

Dr. Engeline van Duijkeren

Doctor of Veterinary Medicine
Partner SOLIDNESS

Centre for Zoonoses and Environmental Microbiology
National Institute for Public Health and the Environment

Engeline van Duijkeren is a specialist in veterinary microbiology and equine veterinary medicine. She is an internationally respected expert in the field of antimicrobial resistance with focus on the epidemiology and mechanisms of antimicrobial resistance in staphylococci and Enterobacteriaceae including transmission of zoonotic bacteria between animals and humans. Dr. van Duijkeren is coordinator on antimicrobial resistance at the Centre for Zoonoses and Environmental Microbiology at the National Institute for Public Health and the Environment. She is a member of the Antimicrobials Working Party (AWP) of The Committee for Medicinal Products for Veterinary Use (CVMP) and the Antimicrobial Advice Ad Hoc Expert Group (AMEG) of the European Medicines Agency (EMA). She has authored or co-authored over 130 research papers (google scholar h-index 42; scopus h-index 39) and is senior editor of the Journal of Antimicrobial Chemotherapy. After studying veterinary medicine at Utrecht University (1977-1984), she worked in several private practices for companion animals and farm animals. From 1986-1991, she was a staff member at the Department of Veterinary Obstetrics and the Department of Clinical Science of Companion Animals of the Faculty of Veterinary Medicine of Utrecht University. From 1991-1995 she worked as a staff member at the Department of Large Animal Medicine and Nutrition of Utrecht University, where she received her PhD degree on a thesis entitled “Trimethoprim/sulphonamide combinations in relation to equine salmonellosis”. From 1995-2011 she worked as assistant professor at the Department of Infectious Diseases and Immunology of Utrecht University. Her responsibilities were teaching students (bachelor and master) in all aspects of infectious diseases including zoonoses and deputy head of the Veterinary Microbiological Diagnostic Laboratory. In addition, she was a researcher with special interest in antimicrobial resistance. From 2011 until now she works as senior researcher at the National Institute of Public Health and the Environment at the Centre for Infectious Disease Control.

Contact Information

Call: +44 (0)151 7053247

Email: Adam.Roberts@lstmed.ac.uk

Dr. Adam Roberts

Senior Lecturer, Antimicrobial Chemotherapy and Resistance
Partner SOLIDNESS

Liverpool School of Tropical Medicine

Adam Roberts is a senior lecturer in antimicrobial chemotherapy and resistance and AMR lead at Liverpool School of Tropical Medicine. His current research is focussed on AMR, its association with mobile genetic elements and the evolutionary consequences of acquisition of these with the aim of translating laboratory observations to prescribing policy and practice in order to minimise the emergence of biologically fit, multidrug resistant, pathogens,. He has published more than 70 research articles and reviews on these topics, is an advisor to the Longitude Prize in the UK and the Drug Resistance policy advisor for the Royal Society for Tropical Medicine and Hygiene. In 2006 he set up the international transposon registry , now located at the LSTM, and oversees the designation of numbers for transposons using this nomenclature system globally. He also co-ordinates another JPIAMR network, from the 8th call, called the Network of European and African Researchers on AMR (NEAR-AMR) aimed at understanding expectations for AMR surveillance data sharing platforms and early career training requirements within Europe and Africa.

Contact Information

Call: +34 91 336 9280

Email: mariateresa.coque@salud.madrid.org

Dr. Teresa Coque

Researcher
Partner SOLIDNESS

Ramón y Cajal Health Research Institute (IRYCIS)
Ramón y Cajal University Hospital
Department of Microbiology

Teresa Coque, PhD graduated as a Pharmacist (1986) and Clinical Biochemist (1989) and received her PhD in Medical Microbiology (1991) from the Complutensis University of Madrid (Spain). After a postdoctoral training at the Internal Medicine Department in the School of Medicine at the University of Texas at Houston in the USA (1993-1995) and the Center for Emerging and Reemerging Pathogens also at the University of Texas at Houston (1996-97), she returned to Spain in 1998. Currently she is Senior Research Scientist at the Microbiology Department of the Ramón y Cajal University Hospital within the Division of Microbial Biology and Infections at the Ramón y Cajal Institute for BioHealth Research (IRYCIS) in Madrid (Spain), leading a research group focused on Population Biology of Human Bacterial Pathogens and their Mobile Genetic Elements. Her special interests and expertise include molecular epidemiology, evolutionary biology, and microbial ecology, with emphasis in the genetic bases for transmission of antibiotic resistance and the adaptation of commensal and pathogenic Gram-negative and Gram positive bacteria to different hosts. Advanced genomics and metagenomics to be applied on diagnosis of antibiotic resistant bacterial pathogens and as predictive markers of infection in the personalized medicine perspective is becoming a priority in the group. TMC has published more than 110 articles in refereed journals and 10 book chapters, and regularly participates in international events in the field of antibiotic resistance and plasmid biology. She is a leading investigator of research grants funded by national agencies since 1999 and has participated in different EU projects since 2001 (EVOTAR-F3-2011-282004; R-GNOSIS-282512; TROCAR-2009-223031; BIOHYPO-LSHM-CT-2007-037410; ACE-LSHM-CT-2005-0180705; DRESP-LSHM-CT-2005-518152, COBRA- QLK2-CT-2001-873). The group also participate in Spanish consolidated Networks at national (CIBER-ESP_ISCIII-MINECO, REDEEX_MINECO) and regional level (deResMicrobiana_CAM, PROMPT_CAM) working on different aspects of antibiotic resistance (epidemiology, public Health, biology of mobile genetic elements and system biology). TMC has directed seven doctoral thesis and coordinates research projects of students associated with the European programs Leonardo da Vinci (2000- 2008) and Erasmus (2007-) and several universities from Europe and South America. She is member of several international scientific committees and associations and regularly serves as a referee of different journals and evaluator of national and international research funded programs in the field of microbiology and infectious diseases.

Contact Information

Call: +46 19 303000

Email: martin.sundqvist@oru.se

Dr. Martin Sundqvist

Affiliated Researcher
Partner SOLIDNESS

School of Medical Sciences
Örebro University

Martin Sundqvist is a Medical Doctor and Affiliated Researcher at the School of Medical Sciences, Örebro University. He has a special focus on antibiotic resistance.

Contact Information

Call: +351 253 604 414

Email: jazeredo@deb.uminho.pt

Prof. dr. Joana Azeredo

Associate Professor with habilitation
Partner SOLIDNESS

Laboratório de Investigação em Biofilmes Rosário Oliveira
Department of Biological Engineering
University of Minho

Joana Azeredo is an Associate Professor with habilitation at the Department of Biological Engineering of the University of Minho and develops her research activity at the Centre of Biological Engineering, where she leads the Biofilm Science and Technology research Group and the Bacteriophage Biotechnology Group. Her current research focuses on interaction of bacteriophages with biofilms and development of bacteriophage based biotechnological applications for detection and control pathogens. Joana Azeredo was graduated in 1994 as Biological Engineer from the University of Minho and obtained a PhD in Microbial Technology from the University of Minho (1998). She regularly serves as international expert project reviewer for national and international funding agencies and as peer-reviewer for international scientific journals. She has extensive publishing and editorial experience, both as a prolific author (+150 international peer reviewed papers), member of editorial boards and editor of thematic issues and books. Her work has received +5000 citations and her current h-index is 43 (Scopus, January 2019).

The Bacteriophage Biotechnology Research Group (BBiG) aims at developing research activity on fundaments and biotechnological aspects of bacteriophages (phages) covering different areas of application, namely Agro-Food, Veterinary and Health. BBiG has a collection of well-characterized phages that infect the most important human pathogens. Fundamental research is mainly focused of phage-host interaction namely biofilm-phage interaction. Applied research covers several applications of phages (native and genetic manipulated) and phage-derived peptides (namely host receptor binding proteins, depolymerases and lysins) to detect and/or control bacterial pathogens. The group is specialized in phage isolation and characterization, in vitro and in vivo evaluation of phages efficacy against bacterial pathogens and biofilms, bacteria-phage interaction modelling, phage production in bioreactors, expression and characterization of phage-derived peptides and genetic manipulation of phages. BBiG has an inspiring research environment based on multidisciplinary cooperation and scientific excellence. BBiG group currently comprises 8 Postdoctoral researchers, 9 PhD students and other researchers including project researchers and master students.

Contact Information

Call: +49 (0) 40 7410 - 57035

Email: rohde@uke.de

Dr. Holger Rohde

Senior physician
Partner SOLIDNESS

Institute of Medical Microbiology, Virology and Hygiene
Universitätsklinikum Hamburg-Eppendorf

Holger Rohde is a Medical specialist in Microbiology, Virology and Infectious Disease Epidemiology. His group is interested in the pathogenesis of staphylococcal infections, mainly focussing on implant-associated infections. Infections occurring after implantation of medical devices (e.g. prosthetic joints, central venous catheters, artificial heart valves) are a major cause of the ever increasing number of nosocomial infections. In Germany alone up to 100.000 infections per year are observed, significantly contributing to in-hospital morbidity and mortality. Pathogens most frequently isolated during device-related infections are staphylococci, especially Staphylococcus epidermidis and Staphylococcus aureus. Both species organize multilayered bacterial consortia termed biofilms on artificial surfaces. Biofilm formation contributes to S. epidermidis and S. aureus pathogensis by protecting the bacteria from effector mechanisms of the host innate immune system and increasing resistance against antibiotics. By addressing molecular mechanisms involved in staphylococcal biofilm formation a future goal is to identify novel means to combat devastating staphylococcal infections.

Contact Information

Call: +39 06 4990 3081

Email: stefano.morabito@iss.it

Dr. Stefano Morabito

Senior Scientist & Deputy Director
Partner SOLIDNESS

European Union Reference Laboratory (EU RL) for E. coli
Veterinary Public Health and Food Safety Department
Istituto Superiore di Sanità

Stefano Morabito is the Director of the Unit of Food-borne diseases of the Department of Food Safety, Nutrition and Veterinary Public Health of the Istituto Superiore di Sanità in Rome, Italy. He is the Director of the European Union Reference Laboratory for E. coli and conducts researches on STEC and other pathogenic E. coli since 1996. His interests include the molecular bases and the evolution of the virulence of STEC O157 and other STEC, with particular emphasis on the genomic asset of the strains causing severe disease in humans. Other research areas include the emergence of the different STEC clones as well as the characterisation of E. coli toxins and their capability to disseminate among the different E. coli groups. He is author of more than 80 peer-reviewed publications and edited the book “Pathogenic Escherichia coli, molecular and cellular microbiology”, published by Caister Academic press. He acts as reviewer for a number of scientific journals and sits in the editorial board of the scientific journals Euroreference and Journal of Medical Microbiology and Diagnosis and was the chair of the local organizing committee for the international symposium on STEC, VTEC 2018.

Contact Information

Call: +49 7071 29-81527

Email: silke.peter@med.uni-tuebingen.de

Dr. Silke Peter

Head of Molecular Diagnostics
Partner SOLIDNESS

Universitätsklinikum Tübingen

Silke Peter holds the position of the Head of Molecular Diagnostics, at the Institute of Medical Microbiology and Hygiene at the University Hospital Tübingen, Germany. She established Next-generation sequencing including Nanopore Oxford promethION, for application of both clinical routine aspects including whole-genome for typing and antimicrobial resistance gene determination, metagenomics for pathogen detection and plasmid analysis, as well a research projects, with a focus on multi-drug resistant bacteria. For this effort she was awarded the Becton-Dickinson Research prize 2018 by the German Society of Hygiene and Microbiology. She is the principle investigator of several multi-centre metagenome trials funded by the German Centre for Infection Research (DZIF).

Contact Information

Call: +49 (0) 761 270 82050

Email: hajo.grundmann@uniklinik-freiburg.de

Prof. dr. Hajo Grundmann

Lecturer
Partner SOLIDNESS

Universitätsklinikum Freiburg
Institut für Infektionsprävention und Krankenhaushygiene

Hajo Grundmann studied Nursing and Human Medicine and at the University of Freiburg, Germany. He specialised in Clinical Tropical Medicine, Medical Microbiology and Hygiene & Environmental Medicine and received his PhD (habilitation) at the University of Freiburg, Germany and an MSc in Epidemiology of Communicable Diseases at the London School of Hygiene. He worked clinically as a medical doctor at university hospitals in Freiburg, Berlin, Nottingham and Groningen and carried out extensive field studies in Taiwan, Venezuela and Tanzania. For eight years, he was the Project Leader of the European Antimicrobial Resistance Surveillance System (EARSS) funded by the European Commission and the Dutch Ministry of Health at the Dutch National Institute for Public Health and the Environment (RIVM). He holds an honorary Chair for Infectious Diseases Epidemiology at the University of Groningen and is now responsible for Infection Prevention and Hospital Epidemiology at the University Hospital Freiburg, Germany. His major research interests are the epidemiology, population dynamics and health impact of health care associated infections and emerging antimicrobial resistance.

Contact Information

Call: +358294157106

Email: Annamari.Heikinheimo@helsinki.fi

Prof. dr. Annamari Heikinheimo

University Lecturer
Partner SOLIDNESS

University of Helsinki
Finnish Food Authority

Annamari Heikinheimo is a tenure track professor, holding a position both in University of Helsinki and Finnish Food Safety Authority. Her One Health approached research focuses on the epidemiology of Zoonotic Antimicrobial Resistance (i.e. bacteria transmitting between animals and humans), aiming to improve the knowledge on the occurrence and transmission routes of zoonotic antimicrobial resistant bacteria along the food chain, such as ESBL/pAmpC/carbapenemase-producing Enterobacteriaceae and livestock-associated methicillin-resistant Staphylococcus aureus. Her studies also aim towards implementing strategies to prevent further development and spread of antimicrobial resistant bacteria between animals and humans.

Contact Information

Call:

Email: spournaras@med.uoa.gr

Prof. dr. Spyros Pournaras

Professor of Clinical Microbiology
Partner SOLIDNESS

Department of Microbiology
National and Kapodistrian University of Athens

Spyros Pournaras is Professor of Clinical Microbiology at the National and Kapodistrian University of Athens, Greece. He is currently Head of the Laboratory of Clinical Microbiology in a large teaching Hospital (ATTIKON University Hospital) in Athens, where he is Chair of the Infection Control Committee and Chair of the Clinical Laboratories Division. His research interests are focused to the detection and characterization of pathogens and new antibiotic resistance mechanisms and phenotypes, infection prevention, antibiotic stewardship and other tasks of clinical microbiology. His Lab is using a variety of molecular  techniques. In his 25 years in clinical and molecular microbiology, Prof. Pournaras has published more than 185 peer reviewed studies with a Sum IF≈760, H-Index: 35.

Contact Information

Call: +386 1 543 74 35

Email: tjasa.cerar@mf.uni-lj.si

Dr. Tjaša Cerar Kišek

Teaching Assistant
Partner SOLIDNESS

Institute of Microbiology and Immunology
Faculty of Medicine
University of Ljubljana

Tjaša Cerar Kišek is a postdoctoral researcher in Laboratory for Diagnostics of Borreliosis and Leptospirosis and Laboratory for Molecular Bacteriology and Mycology, Faculty of Medicine, University of Ljubljana. Ljubljana, Slovenia. Her primary research interest is clinical microbiology with a special focus on Lyme borreliosis and antimicrobial susceptibility of bacteria, prevalence of multi-drug resistant bacteria as well as determination of epidemiological relationship of isolates in suspected outbreaks. At present she and her colleagues focus on implementation of next generation sequencing for pathogen characterization.

Contact Information

Call: +44 (0) 1225 383021

Email: E.Feil@bath.ac.uk

Prof. dr. Edward Feil

Professor
Partner SOLIDNESS

University of Bath

Edward Feil research interests' lie in using sequence data to study bacterial pathogens, both from a point of view of managing infections (molecular epidemiology) but also in terms of understanding fundamental evolutionary dynamics. The early part of his research career was spent generating and interpreting multilocus sequence typing (MLST) data for numerous species. He developed the BURST algorithm to help visualise these datasets (J Bacteriol. 186(5):1518-30). More recently, he has focussed on whole genome sequence (WGS) data, and was joint lead author on the first demonstration of WGS data for molecular epidemiology (Science 327: 5964 469-474). He is currently a PI on a large CRCUK project, headed by Prof Sharon Peacock, looking at implementing this technology into routine epidemiological surveillance, and was previously a work package leader on the FP7 Project TROCAR, headed by Prof Jordi Villa, which aimed to characterise and manage high risk antibiotic resistant clones in Europe.

Contact Information

Call: +41 31 632 95 40

Email: alban.ramette@ifik.unibe.ch

Dr. Alban Ramette

Group Leader Biostatistics / Bioinformatics
Partner SOLIDNESS

Universität Bern
Institut für Infektionskrankheiten

Alban Ramette is the head of the Bioinformatics/Biostatistics group at the Institute for Infectious Diseases (IFIK), University of Bern. His projects focus on the molecular characterization of human pathogens (viruses, bacteria) and on the development of Next Generation Sequencing tools for clinical diagnostics and research.