STRESS: Pathogenicicty and environment: riSk of paThogen and antibiotic RESiStance dispersal
HFRI #20714
The spread of pathogens and antimicrobial resistance (AMR) represents a significant public health concern. While modern agricultural practices (such as manuring and the use of reclaimed water) offer clear benefits, they also increase the risk of pathogen and AMR dispersal. From production to post-harvest handling, these risks may ultimately affect consumers.
We seek to understand the pathways and model the dynamics of pathogen and AMR dispersal across the farm-to-fork continuum, identifying sources and examining their interaction with environmental microbial communities under ecological constraints.
To this end, we employ microcosm and mesocosm experiments to analyze microbial load, diversity, resistance markers, horizontal gene transfer markers, and the associated genomic background in soils, recycled water, and, plants and harvested products. Advanced techniques (including amplicon and shotgun metagenome sequencing, qPCR, immunomagnetic assays, and FISH/FACS) are employed to characterize microbial diversity and assess virulence and overall pathogenicicty potential. Selective pressure compounds (i.e. antibiotic residues), are quantified via HPLC and LC-MS/MS. Finally, computational models and risk assessment strategies developed within this context, are expected to enable the identification of critical control points and the creation of regulatory tools for safer agricultural production and post-harvest management.
Marios Valmas (project role: Fellow) is a PhD candidate at DBB (UTh), specializing in Molecular Microbial Ecology & Environmental Epidemiology, and associated Bioinformatics Biostatistics
Sotirios Vasileiadis (project role: Primary Ivestigator) is Assistant Professor at the department of Biochemistry and Biotechnology (DBB), of the University of Thessaly (UTh), with expertise in Microbial Ecology, Meta-omics and associated Bioinformatics
Myrto Veligrati (project role: research group member) is an undergraduate student of (UTh) occupied with sequencing data analysis, molecular microbial ecology and microbiological methods
Psomiadou Marina (project role: research group member) is an undergraduate student of (UTh) occupied with molecular microbial ecology and microbiological methods
Stefanopoulou Stefania (project role: research group member) is an undergraduate student of (UTh) occupied with molecular microbial ecology and microbiological methods
- 2/06/2025 Our review publication with colleagues from the University of Thessaly (Volos, Greece), the Georgia Institute of Technology (Atlanta, USA), the University of Helsinki (Helsinki, Finland), the Ruđer Bošković Institute (Zagreb, Croatia), and the Freie Universität Berlin (Berlin, Germany), on the topic of targeted metagenome mining and analysis, is published! Check it out:
Marios I. Valmas, Konstantinos Kormas, Dimitrios G. Karpouzas, Konstantinos T. Konstantinidis, Svjetlana Dekić Rozman, Nikolina Udiković-Kolić, Mitja N.P. Remus-Emsermann, Sotirios Vasileiadis* (2025). Targeted analysis of metagenomes: divide and conquer. Biotechnology Advances, DOI https://doi.org/10.1016/j.biotechadv.2025.108619
*corresponding author
- 2/07/2025 Initial results of the project were presented at the BAGECO 2025 symposium by Marios through a flash talk (book of abstracts)!
M. I. Valmas, M. Polasek, D. Nikolaidou, C. C. Papagiannitsis, D. Ntinouli, A. Georgios, J. Rhodosthenous, C. Hadjimichael, M. Omirou, N. A. Alygizakis, D. G. Karpouzas, S. Vasileiadis (corresponding author). Modelling and fate analysis of manure and recycled water introduced microbiome, resistome and mobilome to soil, reveals persisting and dissipating taxa and genes. 17th Symposium on Bacterial Genetics and Ecology, 1-4 July 2025, Graz, Austria.
- 24/09/2025 Results of the first WP were presented at the joint mikrobiokosmos & CEESME conference by Marios through an oral presentation (book of abstracts)!
Marios I Valmas, Massa Polasek, Domna Nikolaidou, Costas C Papagiannitsis, Dimitra Ntinouli, Georgios Argyris, Johanna Rhodosthenous, Christiana Hadjimichael, Michalis Omirou, Nikiforos A Alygizakis, Dimitrios G Karpouzas, Sotirios Vasileiadis (corresponding author). The fate of manure and recycled water introduced microbiome, resistome and mobilome to soil: the persisting and dissipating ones. Joint international conference of mikrobiokosmos and CEESME, 22-24 September 2025, Thessaloniki, Greece.
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