We wish to investigate the extent of conservation and prevalence of small orfs of unknown function expressed in stationary phase of growth in Salmonella

Whole genome sequencing is revolutionizing the surveillance of foodborne and waterborne bacterial pathogens. The speed with which public health laboratories obtain information after the onset of symptoms and the regular sharing of this information between public health laboratories and epidemiologists are critical for the successful use of information to detect outbreaks early and to identify their source. For this purpose, this project aims at providing the most relevant bacterial genomic information in a timely-manner by integrating different validated in silico tools (core genome MLST, CRISPR, O and H molecular serotype, ....) into a single automated analysis pipeline.

The CRBIP, Centre de Ressources Biologiques de l’Institut Pasteur, is a structure created in 2001 that encompasses the Pasteurian culture collections: the CIP (bacteria collection), the PCC (cyanobacteria collection), the ICAReB (human samples collection) and the Eukaryotic virus collection. Since January 2016, the CIP, has sequenced more than a thousand bacterial genomes and assembled them using the P2M pipeline. An initiative has been proposed by the CRBIP, in line with its new strategy of valorization, to annotate all genomes and make publicly available those from type strains with a private section for non-type strains that will be available to users on demand. To attain this objective, a long-term collaboration will be established between the CIP, the C3BI (Natalia Pietrosemoli's team) and the CRBIP that will start with a small project to do the draft annotation of the available bacterial genomes using the open source software, Prokka.

A number of mammalian cell types are susceptible to Salmonella Typhimurium infection, including epithelial cells, fibroblasts and macrophages. It has recently been demonstrated that Salmonella display specific lifestyles in a host cell type-specific manner, where these lifestyles are remarkable for the subcellular localization and replication rate of Salmonella. During epithelial cells infection, Salmonella are first uptaken by the host cell and being encapsulated in a unique endocytic compartment termed Salmonella-containing vacuole (SCV). Within the SCV, Salmonella could remodel the SCV into a viable replicative niche or rupture the SCV and hyper-replicate in the host cytosol. Salmonella replicate at distinct rates in the two localizations, the Salmonella replication in SCV commences from 5 hours post-infection (pi) and infected host cell harbors less then 10 bacteria at 8h pi. While the cytosolic Salmonella begins replication within the first hour of infection at a rate of 30 minutes per division and accumulates up to over 50 bacteria in the host at 8h pi. To understand how Salmonella achieves the two distinct intracellular lifestyles as well as the pathophysiological impacts of the two lifestyles, the primitive goal of my project is to develop a bacterial-borne fluorescent reporter that clearly depicts the subcellular localization and replication rate of Salmonella. With this multiplex fluorescent reporter, we will set to explore the fundamental biological questions: to determine the immune response of epithelial cells against the two Salmonella lifestyles.

Salmonella enterica serovar Typhimurium (S. Tm) and Shigella flexineri actively invade non-phagocytic human epithelial cells in a similar fashion. Both pathogens use bacterial effectors injected through a Type III Secretion System to interfere with host pathways for invasion, survival and proliferation within host cells. Our team has performed different screening approaches to identify subverted host pathways during infection. The wide range of obtained data includes functional data from loss-of-function screens, proteomics datasets of the involved cellular compartments, and transcriptomics data on pathogen-localization dependent gene expression responses. In this project, we aim to implement an analytical bioinformatics approach that integrates the data from our different screen datasets for the identification of the most relevant host pathways implicated in Shigella and S. Tm lifestyles in human epithelial cells.

Identification of a secondary mutation which likely appeared during the construction of a mutant strain of Salmonella serotype Typhimurium