Projects

PEACH Project

Pathogènes Entériques Associés à l’environnement Côtier et aux Huîtres Enteric Pathogens Associated with the Coastal Environment and Oysters

At the interface with the marine environment, oysters can filter more than 200 liters of water per day. This filtration process enables them to concentrate human-pathogenic bacteria present in coastal waters, revealing the surrounding contamination. However, detecting these bacteria is not an easy task, making it crucial to develop effective identification tools. This requires a better understanding of these pathogens, so we propose to characterize enteric bacteria isolated from shellfish. Human-pathogenic enteric bacteria primarily originate from the gastrointestinal tract of mammals. This animal reservoir poses a significant danger because fecal matter, present in livestock effluents and wastewater, can contaminate watersheds, coastal areas, and shellfish production zones. Understanding the fate of these pathogens is a key research question, as their presence in shellfish indicates environmental contamination stemming from human activities. Today, Salmonella and Campylobacter are the two main bacterial genera responsible for diarrheal diseases, and they can also contaminate shellfish. Given the sources of coastal contamination linked to human activities, we anticipate a significant diversity of bacteria beyond these species. Therefore, exploratory work is essential to better understand this diversity and detect potential emerging pathogens. The PEACH project directly addresses this issue by contributing to the development of knowledge regarding the diversity of these pathogens in shellfish and their pathogenicity. It aims to: 1. Optimize the isolation of human-pathogenic enteric bacteria from shellfish collected from sites vulnerable to contamination (monitored monthly). We will focus on the genera Salmonella, Campylobacter, Escherichia, Enterobacter, and Klebsiella (the latter three are part of the ESKAPEE group of priority pathogens). 2. Characterize these pathogens at the genomic level (through whole genome sequencing) to assess their diversity and predict their virulence factors. 3. Conduct a physiological characterization of the environmental bacterial strains, in addition to genomic analyses, to study their pathogenicity and antibiotic resistance. The combination of complementary approaches, including cultural methods and NGS for genomic characterization, will facilitate the development of tools needed for monitoring known or emerging pathogens and collecting bacterial isolates for studying their pathogenicity mechanisms. The data -omics analysis will be carried out in collaboration with the bioinformatics service of Ifremer (SeBiMER).

MetaCRISPy Project

Diversity and Dynamics of CRISPR-Cas Systems in Campylobacter from Different Sources

Campylobacter are pathogenic bacteria for humans and represent the fourth leading cause of gastroenteritis worldwide, especially in developed countries. Ninety percent of infection cases are caused by Campylobacter jejuni and are linked to the consumption of contaminated food, particularly poultry meat. The possible contamination of shellfish by Campylobacter lari and jejuni has also been demonstrated (Rincé et al., 2018). Campylobacter have been relatively understudied due to their difficulty in cultivation. The microaerobic culture and viable but non-cultivable state of these bacteria can pose challenges for their isolation from shellfish. Subtyping methods are available to study the population structure and origins of strains, primarily based on Multi-Locus Sequence Typing (MLST) after isolation. This method involves sequencing housekeeping genes of isolated bacteria (or identifying alleles from whole genomes). To bypass the need for strain isolation, genomic regions with sufficient polymorphism can be targeted. Among these, CRISPR loci offer this potential. CRISPR-Cas systems are found in 40% of bacterial species, where they serve as a defense mechanism against invasive nucleic acids, such as bacteriophages or plasmids. Elements of the Type II-A CRISPR-Cas system were used to develop CRISPR-Cas9, a widely used genome-editing tool. The variability of the bacterial CRISPR locus, composed of repeated regions and spacers with variable sequences, has also been exploited for strain typing, as seen in Streptococcus, Enterococcus, and Salmonella (Fabre et al., 2012; Dos Santos et al., 2020; Philippe et al., 2020; Yousfi et al., 2020; Shariat and Dudley, 2021; Huo et al., 2023). This approach has been particularly developed in Salmonella to trace strains found in poultry farms. The "CRISPR-SeroSeq" method, developed for this purpose, involves Illumina sequencing followed by the assembly of the CRISPR locus to assign a serovar (Yousfi et al., 2020). The organization and diversity of the CRISPR locus in Campylobacter also allow for the establishment of a typing scheme. Studies have shown the presence of a CRISPR system in up to 98% of Campylobacter jejuni and that its polymorphism can be used to study the population structure in a more discriminating manner than MLST (Yeh and Awad, 2020; Yeh, Awad, and Rothrock, 2021). Thus, our objective is to study the diversity of CRISPR systems in Campylobacter from different environments within a OneHealth context and to assess whether this genomic region is relevant for tracing the origin of the strains.