FED-AMR: The role of free extracellular DNA in dissemination of antimicrobial resistance over ecosystem boundaries along the food/feed chain

Start: 1 January 2020
Duration: 2.5 Years
Domain: Antimicrobial Resistance
Key Words: Bacterial transformation, free extracellular DNA, antimicrobial resistance, horizontal gene transfer, ecosystem boundaries.
Contact: Werner Ruppitsch (AGES)

The Project #FEDAMR

Over the course of this project, the relevance of horizontal antimicrobial resistance gene (ARG) transfer on free extracellular DNA (exDNA) over ecosystem boundaries relative to bacterial conjugation will be evaluated. ExDNA is widely present in natural environments and sufficiently stable to constitute an important reservoir for ARGs. The dissemination of AMR on exDNA over ecosystem boundaries will be monitored under controlled but naturally occurring environmental conditions in an open-air agricultural research area: The Hydrology Open Air Laboratory (HOAL) in Petzenkirchen, Austria. ARG concentrations, diversity, dynamic variability, mobility and bacterial biodiversity will be determined in an annual longitudinal study covering a crop growing period, different fertilisation and land management techniques and various different – but interlinked – environmental compartments along the route: pig farm –> manure –> soil –> crop/food/feed –> ground/surface water –> pig farm (and other associated human compartments). The results obtained from HOAL will be compared with data retrieved from equivalent compartments in Northern, Eastern and Southern Europe. Movement of ARGs over ecosystem barriers will be inferred by sequence comparisons and construction of phylogenetic trees of ARGs and ARBs. The linkage between human and non-human reservoirs of AMR will be investigated exemplarily with C. difficile as ARG transfer platform over ecosystem boundaries and conjugation as means for HGT.

The prevailing selection pressure in each tested habitat during the longitudinal study will be determined by quantifying antimicrobials, herbicides and trace elements in the tested compartments. Environmental conditions which may induce or inhibit the expression of competence genes that are necessary to enable the uptake of free extracellular DNA by bacteria will be identified in soil microcosms and in a pig gut model. The impact of transformation relative to conjugation will be evaluated using Acinetobacter sp. (transformation) and C. difficile (conjugation) as model organisms in these experiments.

Experimental data obtained during the project will be used to feed and tune probabilistic modelling of the emergence of AMR in target bacteria and to delineate the relative contribution of transformation and conjugation to ARG acquisition in soil environments. Mechanistic models will address key questions regarding the spatio-temporal changes observed in microbial communities and shall support the identification of critical control points for intervention to reduce the spread of AMR from environmental sources


Alves, F., Nunes, A., Castro, R., Sequeira, A., Moreira, O., Matias, R., Rodrigues, J. C., Silveira, L., Gomes, J. P., & Oleastro, M. (2022). Assessment of the Transmission Dynamics of Clostridioides difficile in a Farm Environment Reveals the Presence of a New Toxigenic Strain Connected to Swine Production. Frontiers in Microbiology. 13, 858310. DOI: https://doi.org/10.3389/fmicb.2022.858310

Gardner, B., Hassan, M. M., Chambers, M., La Ragione, R. M., & Lo Iancono, G. (2022). Modelling the dynamics and long-term stability of perturbed gut microbiota. Poster presentation at ONE Conference 2022, Brussels, Belgium. 21-24 June 2022. DOI: https://doi.org/10.5281/zenodo.6860460

Cabal Rosel, A., Peischl, N., Daza, B., Stöger, A., Rab, G., Rathammer, K., Allerberger, F., Wögerbauer, M., & Ruppitsch, W. (2022). Antimicrobial resistance and genetic relatedness among Escherichia coli isolates across the animal-human-wildlife interface in Austria. Poster presentation at 32nd European Congress of Clinical Microbiology and Infectious Diseases, Lisbon, Portugal. 23-26 April 2022. DOI: https://doi.org/10.5281/zenodo.6641985

Kořínková M, Štěpánková M, Drahošová Z, Matoušková N, Matějů L, Hochmalová K, Zimová M. (2021). International project to map the potential for horizontal transfer of antibiotic resistance genes across different ecosystems. Project presentation by SZU during an Ekomonitor seminar on Waste Analytics. DOI: https://doi.org/10.5281/zenodo.5770032

Cabal A, Peischl N, Rab G, Stöger A, Springer B, Sucher J, Allerberger F, Ruppitsch W. (2021). Draft genome sequence of a multidrug-resistant Escherichia coli sequence type 1193 pandemic clone isolated from wastewater in Austria. Microbiol Resour Announc 10:e00762-21. DOI: https://doi.org/10.1128/MRA.00762-21.

OpenAIRE Publications

Project Events

FED-AMR Kick-off meeting- 27th January 2020

One Health EJP Project Kick-off meeting- 13th November 2019, Berlin, Germany

Project Updates

FED-AMR also have a project specific webpage on the AGES website:


Project Deliverables

D1.1- Scientific Supervisory Board and local Administrative representatives nomination

D1.2- Unified sampling and experimental protocols, which are core part of the project

D1.3- Data and Protocol Management Plan

D1.4- Webinars

D1.4 – Annex 1

D1.5- 12 Month Report Y3

D2.1- 9 Month Report Y3

D2.1 List of sampling compartments, points and European test areas and harmonised protocols in alignment with other project protocols available in data repository

D2.1- Annex 1

D2.1- Annex 2

D2.1- Annex 3

D2.1- Annex 4

D2.1- Annex 5

D2.1- Annex 6

D2.1- Annex 7

D2.1- Annex 8

D2.1- Annex 9

D2.1- Annex 10

D2.1- Annex 11

D2.1- Annex 12

D2.1- Annex 13

D2.1- Annex 14

D2.1- Annex 15

D2.1- Annex 16

D2.1- Annex 17

 D2.2- Preliminary data collection on ARG prevalence and ARG background load in the compartments analysed so far

D2.3- Annual report Y3 of Work Package 2

D2.5- Shotgun Sequencing: ARG Diversity in Tested Environmental Compartments 

D2.5 Annex 1,2

D3.1-Database of zoonotic C. difficile isolates across participants countries

D3.1- Annex 1

D3.1- Annex 2

D4.1- Standardised Protocol for sampling and testing of environmental samples

D4.1- Annex 1

D4.1- Annex 2

D4.1- Annex 3

D4.2- Quantitative results of antibiotics in water

D4.3- Quantitative results of antibiotics in manure

D4.4- Quantitative results of antibiotics in faeces

D4.5- Quantitative results of antibiotics in soil

D4.6- Quantitative results of herbicides in environmental sample

D5.1- E. coli strains demonstrated to be suitable for transformation

D6.1- Protocol for a systematic review on environmental factors influencing the prevalence of antibiotic resistance in the environment