Candida albicans is responsible for the majority of life-threatening fungal infections occurring in hospitalized patients and is also the most frequently isolated fungal commensal of humans. Microevolution of C. albicans isolates has been observed in a number of instances, being in particular characterized by loss-of-heterozygosity events. Yet, most studies that have investigated such microevolutions have not used whole-genome sequencing. In this project, we aim to characterize C. albicans microevolution at the genome-wide level. To this aim, we will take advantage of multiple isolates collected at the same time in healthy individuals and that share the same molecular type, thus providing information on the extent of genetic diversity of commensal isolates. We will also take advantage of series of isolates collected in patients with different forms of candidiasis and/or that have received antifungal therapy, thus providing information of the impact of pathogenic interaction and antifungal treatment on genome dynamics.

Legionella pneumophila is from a genomic point of view a very diverse species, however, only few clones are responsible for over 50% of all human disease cases. Thus we aim to understand the evolution and emergence of these 5 major disease related clones. We have sequenced a large number L. pneumophila strains belonging to these clones and are undertaking comparative and phylogenetic genome analyses.

A major program of evolutionary and comparative genomics of yeasts has been in progress in my laboratory for many years (see publications). In the next few months (before summer 2015) I need to finish a few comparisons about a new clade to publish as soon as possible.

Comparative genomics approaches in microbiology now use thousands of genomes to analyze a given species in different environmental or medical contexts. By collecting and comparing these genomic sequences, many  studies are focusing on  the overall gene content of a species (i.e. the pan-genome) to understand their evolution in terms of core and accessory parts. Variable regions are of primary importance to understand the adaptive potential of bacteria and contain genomic regions that are exchanged between strains by horizontal gene transfer (i.e. the mobilome). As recently suggested (Chan et al., Genome Biology 2015), a consensus representation of multiple genomes would provide a better analysis framework than using individual reference genomes. Here, we propose to extend this concept by giving it a formal mathematical representation using a graph model and by applying statistical methods to cluster gene families.

The genome of C. tetani contains a chromosome of approximately 2,8Mb and a large size plasmid (74 kbp) harboring the tetanus-toxin gene. The genome of the strain E88 was sequenced and annotated (PNAS 2003, 100:1316-1321). We have sequenced and performed a first comparison of the genomes of three additional strains (Res Microbiol 2015, 166:326-331). Fourteen additional C. tetani strains were sequenced including historical strains (1952-1968) and recent French clinical isolates. We have the raw data obtained by Illumina sequencing. Sequence comparaison of chromosome and plasmid will be done. For this, in a first time the assembly of sequence read of each strain will be done, in a second time a comparaison of chromosome and the plasmid of these 14 strains by BLAST approach will be made. Finally, a phylogenetic tree will be generated allowing us to see the evolution of this bacteria.

Whooping cough is a vaccine-preventable disease due to Bordetella pertussis. Even if vaccination has allowed the control of the disease, isolates are still circulating and cyclic increases of incidence are observed every 3 to 5 years even in vaccinated countries. Most developed countries now use acellular vaccines containing 3 to 5 vaccine antigens (pertussis toxin (PT), filamentous hemagglutinin (FHA), pertactin (PRN) fimbrial proteins (FIM2/FIM3)) that have replaced whole cell vaccines. In regions vaccinating with acellular vaccines with a high coverage, isolates no more producing some vaccine antigens (mainly PRN) have been reported in the last years.   Bordetella pertussis reference genome has been fully annotated in 2003 by the Sanger Institute. Analysis and comparison of different B.pertussis genomic sequences showed that circulating B.pertussis isolates differ from vaccine and reference strains. Genome evolution is characterized by gene deletions, antigenic divergences, SNP accumulations…Recent genomic analysis gathering isolates from different countries showed that the worldwide B. pertussis population has evolved in the last 60 years,. Gene categories under selection were identified underlying that Bvg-activated genes and genes coding for surface-exposed proteins were important for adaptation. However these analyses concerned only overall vaccine antigen producing isolates.   The PTMMH Unit includes the National Center of reference for Bordetellosis. In the last years some particular B.pertussis French isolates no more producing PRN but also FHA or PT have been collected, analyzed and sequenced. We would like to further analyze these genomic data with a focus on the vaccine antigen deficient isolates through a SNP-based comparison of these isolates vs co-circulating isolates producing all vaccine antigens and vs a reference strain.

One project of our laboratory is to characterize the function of small proteins specifically expressed in nongrowing Salmonella cells under the tight control of SigmaS.  Our current works focus on small proteins secreted or targeted to the membrane since their characterization might reveal novel aspects of membrane functions and secretion in persistent bacteria, including pathogens. The proposed project is an extension of a former project on the phylogenetic distribution of the small orfs, and aims at analyzing the genomic context of orthologs.

Recherche de SNP chez une souche de leptospira biflexa devenue résistante à un bactériophage.

We submitted an article about the diversity of Clostridium botulinum strains based on MLST analysis. One reviewer of the article asked further study of our NGS data.

We are interested to look at evolution of bacteria in presence of bacteriophages within the gastrointestinal tract of animals.    

Bacillus cereus is ubiquitous in nature, and while most isolates appear to be harmless, some are associated with food-borne illnesses, periodontal diseases, and more serious infections. Moreover, emerging B. cereus strains that cause anthrax-like disease have been isolated in Cameroon and Côte d’Ivoire. These strains are particular, because although they belong to the B. cereus species genetically speaking, they harbor two plasmids, pBCXO1 and pBCOX2, that are very similar to the pOX1 and pOX2 plasmids of Bacillus anthracis that encode the toxins and the polyglutamate capsule, respectively. Around one hundred strains of Bacillus cereus from different origins (environment, clinical and food) deposited at the Collection de l’Institut Pasteur (CIP)  are studied and whole genome sequencing has been performed in order to characterize the pathogenicity of the strains by looking for virulence genes and by comparing the strains (genes of interest), depending on their origin.

Identification de SNP entre 2 souches bactériennes la souche sauvage et le révertant (Pseudomonas aeruginosa)

The microbiota of the gastrointestinal tract is a diverse mixture different species and strains of bacteria. We aim to identify regions of dissimilarity between two different bacterial strains to be able to quantitate their relative abundance and thus obtain information about their ability to cohabitate a common environment. In addition, we are interested in assessing the surface localised protein repertoir of specific species through a combination bioinformatic analysis and proteomics.

Escherichia coli is one of the major bacterial pathogens that are responsible for numerous nosocomial infections. While most of the E. coli infections are rather related to colonisation of the urinary

Trichosporon asahii is a yeast responsible of human invasive infection worldwide. Actually, no genotyping method is available to determine relationship between clinical isolates. At the NRCMA we have more than 40 clinical isolates and 2 collection strains associated with clinical data. Thanks to P2M facility, whole genome for 33 isolates was sequenced. The aim of this project is to study the genetic diversity of Trichosporon asahii and the potential relationship with clinical and/or phenotypic data and finally propose a new genotyping method that could be usefull for clinician in case of local or national outbreak.

Alterations of the cellular proteome over time due to spontaneous or enzymatic deamidation of glutamine (Gln) and asparagine (Asn) residues is a probable source of aging-related diseases. In particular, deamidation of a conserved glutamine in all GTPases of the Ras superfamily that are essential for cellular GTP turnover, confers to these molecular switches gain-of-function properties that can stimulate oncogenic signaling pathways. The CNF1 toxin produced by pathogenic Escherichia coli, a prevalent resident in human gut microbiota, is an example of a bacterial factor with the potential to cause somatic “oncogenic mutation” of Rho GTPases through deamidation. Development of holistic approaches for personalized medicine to monitor healthy microbiota could led to improved public health and increased lifespans.

- The Institut Pasteur genomic taxonomy database of microbial strains (“Pasteur MLST”) is a free, publicly-accessible resource that hosts nucleotide sequence-based definitions of microbial strains, al

Helicobacter pylori is a Gram-negative pathogen whose infection results in various gastric diseases including gastric cancer in Humans. Current drug therapy against the bacteria involves a combination

Members of the genus Yersinia include environmental as well as pathogenic bacteria. Pathogenic species (Y. pestis, Y. pseudotuberculosis and Y. enterocolitica) have historically been targets for resea