These 7 teams bring together a range of complementary expertise in the fields of environmental chemistry (integrative sampling and analysis of so-called 'emergent' chemical pollutants in various environmental matrices such as water, periphyton, sediment; UR RiverLy LAMA), microbial ecology (study of microbial diversity, genetic potential, and expression; UMR CARRTEL, UMR LEM, UMR Agroecology), microbial ecotoxicology (PICT approaches; UR RiverLy EMA), and environmental (UMR Agroecology, UMR LEM), clinical (Bacteriology Laboratory of the University Hospital of Dijon ; UMR LEM), and veterinary (UMR LEM) bacteriology (detection, isolation, and characterization of environmental pathogens).

RU RiverLy (EMA - Aquatic Microbial Ecotoxicology and LAMA - Laboratory of Aquatic Environmental Chemistry), INRAE, Villeurbanne

INRAE RiverLy Research Unit (research unit for multidisciplinary development on hydrosystems' functioning) brings together two laboratories involved in the project.

• EMA laboratory investigates responses of benthic microbial communities (periphyton and sediments) to varying levels of toxic pressure in contexts of multiple stressors. To tackle this goal, natural environment approaches are coupled with the use of experimental systems, such as microcosms or artificial channels, to: i) study toxic effects on the structure and functioning of studied communities, ii) assess their adaptive capacity to chronic exposures and their resilience, and iii) contribute to the development of bioindication tools based on functional microbial measurements (e.g., PICT approaches and monitoring of biodegradation potential).
• LAMA laboratory aims to assess the fate of contaminants in hydrosystems to reduce inputs and risks. To achieve this, it conducts research to: i) characterize the sources and pathways of contaminant transfer, ii) understand the behavior and fate of contaminants in aquatic environments, iii) develop innovative methods and technologies to improve monitoring of contamination in aquatic environments, and iv) characterize organism exposure and assess contaminant bioavailability.

In PharmOneHealth project, RiverLy UR will be responsible for setting up and monitoring experiments conducted in laboratory artificial channels, organizing and conducting sampling campaigns in the two studied rivers, performing physico-chemical analyses (including pharmaceutical substance quantification in various matrices), and implementing PICT approaches.
Staff involved: S Pesce (Project coordinator - Research Director - microbial ecotoxicology), C Miège (Research Director - environmental chemistry, pharmaceuticals), M Masson (Research Engineer - environmental chemistry, nutrients and organic matter), B Volat (Engineer - PICT approaches), B Motte (Assistant Engineer - in situ sampling), A Daval (Assistant Engineer - pharmaceutical substance analysis), C Rosy (Technician - artificial channel management), C Brosse (Engineer - organic matter analysis), H. Rogue (PhD student - Dec 2022 - Dec 2025), A. Thiery (master intern - Feb 2024 - Jun 2024), T. Chapuis (Assistant Engineer - Nov 2023 - Apr 2024).

MRU LEM (BPOE - Opportunistic pathogenic bacteria and environment)
Lyon I Iniversity, CNRS, VetAgro sup, INRAE

LEM is a mixed research unit composed of 7 teams bringing together researchers from the Lyon 1 Claude Bernard University, VetAgro Sup (veterinary school), CNRS, and INRAE. Research of LEM-BPOE team encopases One Health/global health domains where holistic approaches are developed to better understand interconnections between human organizational levels, practices impacting the quality of natural or urban environments, and bacterial infections of environmental origin. Microbiomes' complexity are taken into accountand to specify their resistance/resilience to opportunistic pathogenic bacteria invasions. Research is also conducted to identify genetic elements, metabolic properties, and secondary metabolites explainig the synergies or antagonisms observed between opportunistic pathogenic bacteria and other components of microbiota. This team is coordinated by B. Cournoyer (> 108 publications, h-index=32 - Google Scholar).
In PharmOneHealth project, LEM-BPOE team will be responsible for the development of the qPCR/ddPCR array chip to track the evolution of virulence gene contents and pathogenic bacterial species within microbial communities. This work will require a validation phase of the developed PCR array (6 months) (n=50 PCR targets) followed by its application on DNA extracts. Biases in distribution based on environmental variables will be studied using statistical tools applied in other works of the team. Correlations between occurrence of pharmaceutical substances, virulence genes, pathogenic bacteria, and sources of contamination will be investigated.
Staff involved: B. Cournoyer (Research Director - microbial ecology); W. Galia (Associate Professor - microbial ecology), V. Roddriguez-Nava (Professor - microbial ecology), D. Mouniée (Technician - molecular approaches), L. Marjolet (Engineer - molecular approaches), B. Luton (Engineer - Mar 2023 - Jan. 2024).

MRU CARRTEL
Savoie Mont Blanc University – INRAE,

Le Bourget-du-Lac

CARRTEL - Alpine Research Center on Trophic Networks and Limnic Ecosystems is a mixed research unit comprising researchers from Savoie Mont Blanc University and INRAE. This unit conducts research in functional ecology applied to aquatic ecosystems, particularly lakes. One of its main areas of expertise concerns the characterization of the diversity of benthic communities (especially microbial) and the functional role of this diversity within lacustrine ecosystems. CARRTEL has been developing molecular approaches focused on periphytic and sedimentary environmental matrices for many years.
In PharmOneHealth project, CARRTEL MRU will be responsible for characterizing bacterial diversity of periphytic and sedimentary biofilm communities through molecular approaches such as 16S rRNA massive gene sequencing followed by bioinformatic analysis of the obtained sequence sets.
Staff involved: E. Lyautey (Associate Professor - Microbial Ecology), N. Tissot (Assistant Engineer - Molecular Biology), L. Susset (Master intern, Mar. 2024 - Jul. 2024).

MUR Agroecology
INRAE, Bourgogne University / Agro Dijon Institut/ UBFC Dijon

Agroecology MRU gathers two laboratories involed in the project.

• The Environmental Microbiology Team (MERS) has extensive experience in deciphering the fate of human and animal pathogenic bacteria in soil and plant environments. Dissemination of antibiotic resistance in environmental matrices is a team's major topic of investigation. Various models have been explored, including ESBL-producing E. coli and Klebsiella pneumoniae. Significant results have been obtained on determining the persistence parameters of Listeria monocytogenes in soils and on plant root surfaces. Since 2012, MERS team demonstrated the environmental persistence of ESBL-producing E. coli in soil, surface water, and groundwater. Thr team has participated in two ANR projects (Environmental Contaminants Health) and coordinated an ANSES PNREST program on the role of Waste Water Treatment Plants in the dissemination of ESBL-producing E. coli in soils and water bodies. MERS team has also participated in two EJP METVEBKLEB and LISADAPT programs focusing on the comparative genomics of Klebsiella and Listeria from various environments (clinical to soil) following a One Health approach. MERS team has been collaborating since 2009 with the Bacteriology Laboratory of the University Hospital of Dijon (former UMR ChronoEnvironnement) on the "One Health" theme. This longstanding collaboration has resulted in several joint publications and communications.
  In PharmOneHealth project, MERS team will be responsible for isolating certain strains of the ESKAPE group, particularly Klebsiella and Enterobacter, from in situ samples, as well as characterizing the E. coli and ESBL-producing strains load of environmental matrices. Environmental dissemination of these genes will also be studied. Several GRA and characteristic integron genes (including sul1, intI1, qnr, qepA, etc.) will be detected by qPCR. The use of electrochemical tools for biosurveillance of E. coli as well as genes encoding ESBLs will be tested.
  Staff involved: A. Hartmann (Research Director - microbial ecology), L. Gal (Associate Professor - microbial ecology biochemistry), M. Rochelet (Associate Professor - electrochemistry), G. Depret (Engineer - molecular ecology).
• Members of the Bacteriology Laboratory at the University Hospital of Dijon involved in the project study the epidemiology and mechanisms of resistance in Gram-negative bacilli (cultivation and molecular approaches): i) study of the genetic environment of antibiotic resistance genes (particularly beta-lactams) in Enterobacteriaceae responsible for nosocomial infections, ii) study of bacteria belonging to the genus Achromobacter. The laboratory investigates epidemiology in patients by detecting contamination sources and comparing strains through genotyping. Specific methods have been developed for strain isolation from the environment and for species identification using mass spectrometry. The laboratory also studies mechanisms of innate or acquired antibiotic resistance in strains, particularly efflux pumps and beta-lactamases' role . Upon exposure of strains to fluoroquinolones, it has been demonstrated through transcriptomic analysis and gene inactivation that certain efflux pumps were overexpressed, which could lead to resistance to other antibiotics.
  In PharmOneHealth project, the Bacteriology Laboratory at the University Hospital of Dijon will be responsible for the detection of Achromobacter strains in in situ samples using cultivation approaches, describing the resistance phenotypes of Achromobacter strains according to pollution levels, comparing detected strains with clinical isolates, and studying the acquired resistance mechanisms of isolated strains at different sites and after exposure to 3 model molecules in artificial channels (particularly studying efflux by cultivation and transcriptomic approaches). In collaboration with MERS team, phenotypes and resistance mechanisms of ESKAPE group strains will also be studied.
  Staff involved: L. Amoureux (Associate Professor-Hospital Practitioner-Medical Bacteriology), C. Neuwirth (Professor-Hospital Practitioner-Medical Bacteriology), J. Bador (Hospital Practitioner-Medical Bacteriology), A. Magallon (University Hospital Assistant-Hospital Practitioner-Medical Bacteriology), C. Demeule (Intern-Medical Bacteriology).