Hospices Civils de Lyon - EUPHEM

Contact person

Bruno Lina

Tel: +33 472 07 10 20/+33 472 07 10 57

Description of the institute

The Hospices Civils de Lyon is the public hospital in Lyon. This multi-site hospital with around 6 000 beds is a referral hospital for a very large number of infectious diseases, including those caused by BSL-3 and BSL-4 agents. The core of laboratories involved in the training have public health mandates for the surveillance of several specific pathogens in link with Santé Publique France - Institut de Veille Sanitaire and the WHO.

The hospital has very strong links with research teams headed by the co-supervisors of this proposal. The hospital-based structure of the laboratory network allows for the rapid identification of public health infectious diseases and the possibility for real-time intervention if needed.

The human and technical resources available in the laboratories will provide full access to state-of-the-art technology to undertake molecular and genetic studies, such as next generation sequencing, with a specialist bioinformatics and mathematical modelling department for the interpretation of specialised molecular sequence to perform epidemiological surveillance, studies on pathogenesis and pathogen evolution or on antimicrobial resistance. In addition, new epidemiological tools are available for the measurement of contact between healthcare workers.

Four national reference microbiology laboratories and a large Next Generation Sequencing Capacity for epidemiological and diagnostic purposes (GENEPII) are within the frame of the offered package for this training site, including state-of-the-art technology for strain characterisation and microbial epidemiology in support of outbreak investigations and surveillance programmes.

The main public health programs are:

• Respiratory infections ;
• Vector-borne infections ;
• Gastrointestinal and foodborne infections;
• Healthcare-associated infections;
• Nosocomial infections;
• Parasitic and fungal diseases;
• Vaccine-preventable diseases;
• Antimicrobial resistance (bacteria, parasites, fungi, and viruses);
• Sequencing of emerging and reemerging pathogens;
• Epidemiology of infectious diseases;
• Epidemiology and impact of vaccination;
• Phage therapy.

The main public health core-functions are:

• Microbiological surveillance of vaccine-preventable diseases;
• Microbiological surveillance of emerging pathogens (including One-Health pathogens);
• Investigation and control of communicable diseases;
• Investigation of nosocomial infections;
• Research activities linked with public health microbiology;
• Surveillance for specific diseases (linked with the National Reference Centres).

Training opportunities

Virology

Prof Bruno LINA, Prof Florence MORFIN and Dr Jean Sebastien CASALEGNO
Institut des agents Infectieux, Laboratoire de Virologie Nord (Clinical lab)
Nat ref centre for Influenza, WHO National Influenza Centre, Nat ref centre for Enterovirus and Parechovirus, WHO National Polio Lab.
The training will include work in a BSL-3 lab

Bacteriology

Prof Francois VANDENESCH, Prof Gérard LINA, Prof Frederic LAURENT
Institut de Microbiologie, laboratoire de Bactériologie (Clinical lab)
Nat ref centre for Staphylococcal diseases, Nat ref centre for Legionella, Ref lab for Mycobacteria and Nocardia

The training will include work in a BSL-3 lab.

Parasitology

Prof Stephane PICOT, Prof Martine WALLON
Laboratoire de Parasitologie

Hygiene

Prof Philippe VANHEMS
Unité Hygiène, Epidémiologie et Prévention,
Corevac Vaccine research program

Training supervision

Supervisor: Dr Jean Sebastien CASALEGNO / Pr Bruno LINA
Laboratoire de Virologie Nord, Institut des agents Infectieux, CBPN, GHN, 103 grande rue de la Croix-Rousse, 69371 Lyon cedex 04
Tel +33 472 07 10 23

Co-supervisor: Prof Philippe VANHEMS
Unité Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, 5, place d’Arsonval, 69437 LYON cedex 03
Tel +33 472 11 07 21

Language requirements

• English (required)
• French

Training history

• Number of EUPHEM fellows trained at institute: 3
• EUPHEM fellow trained in 2011-2013 (Cohort 2) in 2017-2019 (Cohort 8) and in 2021-2023 (Cohort 12)