Molecular epidemiology
The characterisation of microbial population diversity with sequencing is an active field of research in Microb’UP

Phylogenetic tree of Escherichia coli from Denamur et al Nature Review Microbiology 2021
With the democratization of sequencing technologies, genomics has become a key element of the characterization of microbes and infectious diseases. Molecular epidemiology, with the study of a rising number of samples is offering snapshots of the diversity found within species. The benefit of full genome sequences is multiple. First, it allows fine scale analysis of the species phylogenies that are sometime not resolved for some microbes. Second, it allows to track the evolutionary dynamics occurring within species. At large scale, these dynamics are well illustrated with the propagation of a succession of SarsCov2 variant or with the spread of antibiotic resistance among bacterial species. But, full genome sequencing can also offer a high enough resolution to tackle viral or bacterial dynamics within a hospital or through a chain of contamination. Third, access to the full genome gives access to the functional elements of these microbes and can help identify genes or alleles associated with some clone successes, from antibiotic resistance or virulence genes, to patho-adaptative mutations.
With a vast number of teams with members directly involved in hospital virology, bacteriology and parasitology laboratory, Microb’UP network has access to a vast number of strains that are sequenced and studied in depth with the molecular epidemiology approach. On organisms ranging from HIV to Escherichia coli or sordariales. Modelers are also present in the Microb’UP to integrate these data and make inferences about the evolutionary processes at play.
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Webinar, 15th December 2023
15th December : Respiratory Viruses/Host Cell Interactions Host Laboratory : Ali Amara ( Biology of Emerging Viruses, Institut de recherche Saint Louis, Paris) Goujon Caroline, IRIM, Montpellier : Intrinsic and innate immune defenses against respiratory viruses...

Webinar, 22nd November 2023
Unveiling the Hidden Life of Parasites Watch the webinar at : https://u-paris.zoom.us/rec/share/link Luisa Miranda Figueiredo, Institute of Molecular Medicine (IMM), University of Lisbon, PortugalPauline Formaglio, Institut Pasteur, ParisTatyana Tavella, Institut...

Microb’UP meeting: October 20th, 2023
Microb’UP meeting: October 20th, 2023 During the symposium, we awarded two prizes for young researchers (500 euros to attend an international meeting) Best talk prize, Ana Raquel Cruz from INEM (Host-Microbiota Interaction - Schnupf Lab) Best poster prize, Jean Marc...

Webinar, 11th October 2023
11th October : Molecular Mechanisms and Genetic Diversity of Stress Tolerance and Persistance Host Laboratory : Olivier Tenaillon (Robustness and evolvability life, Institut Cochin, Paris) Jan Michiels, KU Leuven, Belgique. www.michielslab.org Defining the genotypic...