Epidemiological and molecular surveillance of infectious diseases

Team 6 of UMR D 257 Vectors – Tropical and Mediterranean Infections (VITROME)
Aix-Marseille University (AMU), Institut de Recherche pour le Développement (IRD) – French Military Health Service (SSA)

Team leders
  • FOURNIER Pierre-Edouard CV
Team Members
  • EL KARKOURI Khalid
  • ROBERT Catherine
  • TOMEI Enora
  • CHAUDET Hervé
  • GAUTRET  Philippe
  • JAVELLE Emilie
  • JIMENO Marie-Thérèse
  • PELLEGRIN Lilliane
  • SAVINI Helene
  • TEXIER Gaëtan


Specific monitoring at the population level

  • Surveillance of infectious diseases at local (AP-HM) and regional (Provence-Alpes-Côte d’azur) levels.
  • Investigations of infectious diseases of travellers (Eurotravnet, GeoSentinel).
  • Investigation of infectious diseases in the homeless population in Marseille.

National Surveillance of Infectious diseases by reference centers

  • Monitoring by the reference center of rickettsioses, bartonelloses and Q fever.

Innovations in surveillance methods for infectious diseases

  • Characterization of the genomic and genotypic specificities of emerging pathogens and development of specific molecular detection tools for emerging pathogens
  • Development of MALDI-TOF mass spectrometry-based surveillance of epidemiological events
  • Development of methods for evaluating and optimizing outbreak detection algorithms.
  • Development of a simulation platform for the study of behaviors and supervisory skills (Project SOAP/DGA)

Research topics

Infectious diseases remain a major public health problem in the world and their surveillance is critical. As a result, the development of surveillance systems to control infectious diseases is a thriving area that is mobilizing more and more countries and resources. We plan to continue and extend several current monitoring actions.

a) Surveillance of infectious diseases at local (AP-HM) and regional (Provence-Alpes-Côte d’azur) levels.

To date, we have developed several specific disease and syndrome surveillance softwares for monitoring data from the AP-HM microbiology laboratory, including EPIMIC, an automated database to monitor 270 items on a weekly rate; BALYSES, which currently monitors 780 bacterial species; MARSS, which monitors 65 phenotypes of resistance. These surveillances have recently been extended at the regional level through the PACASURV network, which now covers 11 laboratory consortia for a total population of 5 million people and allows the monitoring of 673 bacterial species.

b) Surveillance of infectious diseases in travelers

i. Surveillance of travel-related diseases through international networks

Through collaborations with the international networks EuroTravNet and GeoSentinel:

  • Emergence of infections among European travelers.
  • Profile of travel-related illnesses among travellers seen in the AP-HM hospitals in Marseille.
  • Clinical pattern of Chikungunya virus infections in travelers worldwide.
  • Post-exposure prophylaxis to rabies offered to travelers during their stay abroad.
  • Long-term consequences of Chikungunya, dengue, Zika, and Plasmodium falciparum virus infections.
  • Infectious diseases associated with international mass gatherings.

ii. Hajj pilgrims and drug-resistant bacteria

We will conduct prospective cohort surveys of the rectal and respiratory carriage of multi-drug resistant bacteria before and after Hajj in the Pilgrims received at our travelers clinic

iii. Perception of the risk of infectious diseases by travelers from Marseille

We will conduct risk-perception studies for travelers who consult for pre-travel advice.

iiii. Surveillance of infectious diseases in the population of the homeless in Marseille

We wish to conduct one-day cross-sectional surveys in two homeless shelters annually to assess the profile of infectious diseases and their transmission in this population that is particularly vulnerable to disease and to assess risk factors and trends, with the aim of detecting the emergence of infectious diseases and alerting health authorities.

Our laboratory has been the French reference center for the diagnosis and study of rickettsioses, Q fever and bartonelloses for 30 years. We have described more than 20 new diseases and/or clinical forms caused by these microorganisms, and developed diagnostic reference tools and therapeutic protocols and recommendations that are currently used worldwide. We wish to continue monitoring these zoonotic infections, with the aim of detecting any abnormal events, alerting the health authorities and describing these new diseases.

a) Identification of genomic and genotypic specificities of emerging pathogens and development of molecular detection and analysis tools

  • Rapid detection of virulence and resistance factors of clinical isolates
  • Development of softwares dedicated to the detection of genes associated with antibiotic resistance or automated comparison of the genome of bacterial isolates.
  • Development of automated genome assembly and annotation pipelines.
  • Development of specific and ultra-sensitive genotyping and PCR tools.

b) Rapid Identification of clonal complexes by MALDI-TOF mass spectrometry

c) Development of methods for evaluating and optimizing epidemic detection algorithms

d) Development of a simulation platform for the study of behaviors and monitoring capabilities


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