Microbial contaminants in resource recovery systems

Dynamics of microbial contaminants during resource recovery: exploring biotic and abiotic processes within the value chain 

The recovery of valuable resources from organic waste and wastewater holds strong potential to advance sustainable development. However, these streams often harbor biological contaminants that may not be fully removed by conventional treatment processes. As a consequence, resource recovery practices, such as the spreading of compost or digestate, or the irrigation with reclaimed wastewater, could unintentionally contribute to the dissemination of these microorganisms, along with their associated virulence and antibiotic resistance genes.
At LBE, we study the dynamics of microbial contaminants throughout treatment and recovery chains. Our research characterizes the biotic and abiotic processes that drive either their inactivation or their persistence within ecosystems. Our work focuses on:

• Monitoring the fate of microbial contaminants during treatment processes.
• Assessing the impact of resource recovery practices on their accumulation, persistence, and dissemination. 
• Identifying biotic and abiotic processes involved in their mitigation and/or dissemination.
• Analyzing the role of native microbial communities in shaping these dynamics.

The microbial contaminants studied include both fecal-origin pathogens (e.g., Salmonella spp.) and ubiquitous environmental species such as Listeria monocytogenes, Legionella spp., Pseudomonas spp., and Aeromonas spp., as well as classic microbial indicators such as Escherichia coli, Enterococcus spp. and Clostridium perfringens. Genes associated with antibiotic resistance and virulence are investigated using both targeted (gene-specific) and untargeted (shotgun metagenomics) approaches to better understand their diversity, abundance, and fate across matrices and ecosystems.
LBE’s research on microbial contaminants supports improved hazard assessment in resource recovery systems and helps to identify technological strategies to mitigate microbiological risks.

Projects

• ATBR-SOL (2024-2027): Determinants of the selection or attenuation of antibiotic resistance after the application of organic waste products on soil. ANSES.
• VIRULENCE (2023-2025): Assessing the (co)dissemination of virulence and antibiotic resistance genes during resource recovery applications. Marie Curie Postdoctoral Fellowship - European Union’s Horizon Europe Research and Innovation Programme.
• SULCLARES (2023-2024): Study of sulfamethoxazole and clarithromycin degradation and resistance in soils irrigated with reclaimed wastewater. Fundation Agropolis, Montpellier.
• ALLEA (2020-2023): Fate of organic micropollutants and microbial contaminants (including antibiotic markers and pathogens) on the treated wastewater - irrigation system - soil continuum. Funded by Montpellier Université d’excellence.
• METHASeq (2020–2023): Study of the hygienizing potential of different steps in the anaerobic digestion process using ddPCR and deep-shotgun sequencing (INRAE–GRDF).
• MADSLUDGE (2017-2020): Mitigating AMR dissemination by sludge treatment processes. ADEME/ANSES.

Publications

• Álvarez-Fraga L, Capson-Tojo G, Sanglier M, Hamelin J, Escudié R, Wéry N, García-Bernet D, Battimelli A, Guilayn F. A meta-analysis to optimize pathogen reduction during anaerobic digestion. Renew. Sustain. Energy Rev. 2025. 207, 114982. https://doi.org/10.1016/j.rser.2024.114982. 
• Della-Negra, O., Camotti Bastos, M., Bru-Adan, V., Santa-Catalina, G., Ait-Mouheb, N., Chiron, S., Heran M., Wéry, N., Patureau, D. 2025. Effect of sulfamethoxazole environmental concentrations on soil microbial communities and their antibiotic resistance strategies. Environmental Pollution 364, 125306. doi.org/10.1016/j.envpol.2024.125306.
• Della-Negra, O., Camotti Bastos, M., Bru-Adan, V., Santa-Catalina, G., Ait-Mouheb, N., Chiron, S., Patureau, D. 2025. Temporal dynamics of the soil resistome and microbiome irrigated with treated wastewater containing clarithromycin. Environmental research.
• Moulia, V., Heran, M., Lesage, G., Hamelin, J., Pinta, J., Gazon, A., Penlae, M., Bru-Adan, V. Wéry, N., Ait-Mouheb, N. 2024. Biofilm growth dynamics in a micro-irrigation with reclaimed wastewater in the field scale. Journal of Environmental Management, 370, 122976. https://doi.org/10.1016/j.jenvman.2024.122976
• Della-Negra, O., Camotti Bastos, M., Bru-Adan, V., Santa-Catalina, G., Ait-Mouheb, N., Chiron, S., Heran M., Wéry, N., Patureau, D. 2024. Role of endogenous soil microorganisms in controlling antimicrobial resistance after the exposure to treated wastewater. Sci Tot Env, 931, 172-977. doi.org/10.1016/j.scitotenv.2024.172977.
• Brienza, M., Sauvetre, A., Ait-Mouheb, N., Bru-Adan, V., Coviello, K., Lequette, K., Patureau, D., Chiron, S., Wéry, N. 2022. Reclaimed wastewater reuse in irrigation: Role of biofilms in the fate of antibiotics and spread of antimicrobial resistance. Water Research, 221:118830. doi: 10.1016/j.watres.2022.118830.
• Goulas, A., Belhadi, D., Descamps, A., Andremont, A., Benoit, P., Courtois, S., Dagot, C., Grall, N., Makowski, D., Nazaret, S., Nelieu, S., Patureau, D., Petit, F., Roose-Amsaleg, C., Vittecoq, M., Livoreil, B., Laouenan, C. (2020) How effective are strategies to control the dissemination of antibiotic resistance in the environment? A systematic review. Environmental Evidence, 9, 4, https://doi.org/10.1186/s13750-020-0187-x.