The project

Improving monitoring and environmental risk assessment of pharmaceuticals, antimicrobial resistance and pathogens from terrestrial to aquatic environments

Pharm-ERA context

Pharmaceutical micro-pollutants are chemicals used for human and animal health care that are found everywhere including in soil, water and sediment. This chemical contamination is usually associated with microbiological contamination (by microorganisms and/or their genetic material) from humans, animals and the environment. Both PhACs and microbiological contaminants contribute to the development and dispersal of antimicrobial resistances and pathogens in terrestrial and aquatic environments, generating adverse effects and risks on biodiversity and ecosystem health. It can lead to huge repercussions on human and animal health as stated in the World Health Organisation’s ‘One Health’ approach, which recognizes that human health is closely connected to animal health and our shared environment.
While invisible to the naked eye, terrestrial and aquatic microbial communities harbour high abundance and enormous taxonomic and functional diversity, which provide a wide range of ecological functions and services. These functions and services include primary production, organic matter degradation, nutrient recycling, soil fertilisation, pollutant dissipation, etc., which are essential for the proper functioning of ecosystems and, as a consequence, for human and animal well-being and health. Moreover, high microbial diversity can act as a barrier against the invasion of antimicrobial-resistant microorganisms and pathogens in the environment. Preserving ecosystem health from pharmaceuticals, their transformation products, antimicrobial resistance and pathogens thus requires efficient monitoring strategies and appropriate environmental risk assessment to protect microbial diversity and functions in terrestrial and aquatic environments. This is required, for instance, by the EU Water Framework Directive, needed for the prioritisation of emerging chemical and microbiological contaminants, and imperative to contribute reaching several United Nation Sustainable Development Goals.

Pharm-ERA objectives

Pharm-ERA pursues three principal inter-linked research objectives structured in four research work packages (Wps):

- Research objective 1: Assess and predict the fate of pharmaceuticals and their transformation products along the soil-water-sediment continuum using in silico tools and innovative approaches in environmental and analytical chemistry [WP3]

- Research objective 2: Investigate the ecotoxicological effects [WP4] and environmental risks [WP5] of pharmaceuticals and their transformation products on soil and aquatic ecosystems taking into account effects at different levels of biological organisation from molecular early responses to microbial community effects

- Research objective 3: Determine the main drivers of antimicrobial resistance and pathogens establishment and dissemination along the soil-water-sediment continuum with a specific focus on the role of microbial diversity, environmental continuum (between connected compartments), pharmaceutical contamination and various environmental factors (e.g. kind of substrate colonised by aquatic microorganisms, organic matter content in soil and sediment, etc.) [WP6]

Pharm-ERA at a glance (Fx = Fellow number; in black/blue = major/minor contribution to the associated WP) © Pharm-Era

The operational objective is to boost the rational development and implementation of operational tools and methods from Pharm-ERA at EU level for improving the monitoring and the a priori & a posteriori environmental risk assessment of pharmaceuticals , antimicrobial resistance and pathogens, as well as for preserving microbial diversity and functions from terrestrial to aquatic environments.

Pharm-ERA provides the gear-shift necessary to tackle these urgent needs, sitting at the frontier of recent advances in the complementary fields of environmental chemistry, microbial ecology, molecular biology, ecotoxicology, and environmental fate & effect modelling. Pharm-ERA proposes a novel position as we integrate ecosystem compartments across soil, water and sediment to better consider the wide environmental distribution of pharmaceuticals and their transformation products, as well as the specificities and interconnection of the terrestrial and aquatic microbial communities.

Pharm-ERA doctoral network

Pharm-ERA will tackle this challenge by overcoming the lack of appropriate PhD training programmes, which are mostly mono-disciplinary, mono-sectoral and/or only focused on one environmental compartment. We will thus implement a high-level training programme involving world-leading scientists and institutions highly experienced in previous European projects, internationally recognized experts from different public and private non-academic structures, as well as environmental managers and policy makers.
Different methods will be tailored to the 10 PhD Projects to reach the research objectives: (1) Cutting-edge analytical methods in environmental chemistry with the development of TP analyses by High Resolution Mass Spectrometry; (2) Multi-Omics, innovative approaches combining meta-genomics, transcriptomics and metabolomics; (3) Mesocosm experiments to establish cause-effect relationships in controlled conditions and identify specific microbial responses to pharmaceutical exposure; (4) Field surveys to apply, test and validate the methods in situ, and (5) Up-to-date modelling methods to simulate the fate and effects of unknown transformation products. These methods will be applied in interlinked research WPs .

PhD offers
Overall scientific philosophy of the Pharm-ERA project. (F.x = Fellow number)


Modification date : 20 March 2024 | Publication date : 17 June 2022 | Redactor : Stéphane PESCE