Detailed information about the course

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Novel microbes and pathogens


November 9

Responsable de l'activité

Stefan Kunz


Prof. Gilbert Greub, IMUL/CHUV

Prof. Stefan Kunz, IMUL/CHUV


Prof. Pierre-Edouard Fournier, Aix-Marseille Université, Marseille, France

Prof. Matthias Fischer, Max-Planck-Institut für medizinische Forschung Heidelberg, Germany

Prof. Lloyd Vaughan, PathoVet, Effretikon, Switzerland

Dr. Maja Ruetten, PathoVet, Effretikon, Switzerland



The advent of sequencing technologies of unprecedented power has lead to the discovery of entire new classes of microbes in the past years, including giant viruses of enormous size and genetic complexity. Climatic changes and increasing urbanization and migration of human populations further promoted the emergence or re-emergence of novel human pathogens.This workshop will give an overview of important novel microbes, including emerging viral and bacterial pathogens. Presentations by experts will cover the principles of pathogen discovery and characterization from a basic science and medical point of view. Pathogen discovery in the clinic will further illuminate the use of cutting-edge technologies for the identification and characterization of emerging pathogens with relevance for human health. The first part of the workshop (morning session) will consist of four talks on novel microbes and pathogens, presented by invited and resident experts, followed by discussion. This first session will be followed by a joint lunch that will allow discussion and exchange in a relaxed atmosphere. The second part (afternoon) will consist of an interactive session developing some key aspects on emerging pathogens covered in the morning session. For this purpose, groups of 2-3 participants will present key papers in the field that will then be discussed in an open round table format.


Institut de Microbiologie, Lausanne University Hospital, Rue du Bugnon 48


Morning session:

Auditoire Yersin, CHUV

9:00 Welcome and presentation of the program (Gilbert Greub and Stefan Kunz)

9:15 – 10:00 Pierre-Edouard Fournier

"Genomics sheds light on rickettsial evolution"

10:00 – 10:45 Matthias Fischer

"Beneficial viruses and the puzzling evolution of virophages"


Coffee break 10:45 – 11:00


11:00 – 11:45 Lloyd Vaughan

11:45 – 12:30 Gilbert Greub

12:30 – 13:00 Maya Ruetten


Lunch: 13:15 – 14:30 Restaurant Falaises


Afternoon session:

Salle séminaire DG BH08 – 629

Presentation of key papers by groups of 2-3 participants. We recommend 20-25 minutes for the presentation (short introduction, key results). The presentation will be followed by a 10-15 minutes discussion.

14:30 – 15:10 Presentation paper

14:10 – 15:50 Presentation paper


Coffee break 15:50 – 16:00


16:00 – 16:40 Presentation paper

16:40 – 17:20 Presentation paper

17:20 – 17:30 Conclusion of the workshop


ARTICLES related to the workshop:


Fischer, M.G., Hackl, T., 2016. Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature 540, 288-291.


Krupovic, M., Koonin, E.V., 2015. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat Rev Microbiol 13, 105-115.


Lagier, J.C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., Trape, J.F., Koonin, E.V., La Scola, B., Raoult, D., 2012. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18, 1185-1193.


Mourembou, G., Lekana-Douki, J.B., Mediannikov, O., Nzondo, S.M., Kouna, L.C., Essone, J.C., Fenollar, F., Raoult, D., 2015. Possible Role of Rickettsia felis in Acute Febrile Illness among Children in Gabon. Emerg Infect Dis 21, 1808-1815.




CUSO Microbiology students: Train ticket, 2°class, half-fare from your institution to the place of the activity; meal expenses (1meal/day) up to 25CHF/meal.


Reimbursement form attached with original tickets has to be sent to: CUSO Microbiologie, Aline Kopf, Institut de Biologie, Rue Emile-Argand 11, CH-2000 Neuchâtel


contact: microbiologie[@]




Deadline for registration 01.11.2017
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