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Research activities

Antibiotic free raising

Antibiotic-free poultry production has become more popular, contributing to expanding the participation of this type of production in the poultry industry. Although there are no universal standards for antibiotic-free production. To identify the main drivers that enable flocks to be raised antibiotic-free comparative studies will be performed. For this purpose, field studies exploring the prevalence of antibiotic resistant bacterial strains in antibiotic-treated and antibiotic-free farms will be conducted. Data concerning levels of drug-resistant strains will be correlated with particular approaches implemented on individual farm, what allow accurate identification of key factors for success in the development of antibiotic-free production.

Outcomes of field studies will be prerequisites in education on important drivers for the policy regarding animal health and the use of antibiotics of poultry producers and veterinarians. Together with avian pathologists, the outcomes of these discussions will be implemented in training courses and other educational materials. The most promising interventions will be suggested to applied to conventional antibiotic-treating farms according to their individual situation. It will be analysed if a reduction of AMR patterns could be achieved after implementation of proposed solutions.

Therapeutic Alternative to the Use of Antibiotics in Chicken Farming





Bacteriophages (phages) are considered as an important alternative to antibiotic treatment of human and animal infections caused by pathogenic bacteria. Phages are self-replicating and self-limiting bacterial viruses since they multiply only at the site where the host is located and are eliminated gradually when host bacteria are cleared. Low inherent toxicity, lack of cross-resistance with antibiotics, and application versatility are the advantages of phage application. Phages are very specific to their host and generally limited to one species and do not affect microflora of treated organism.

Since little is known how phages impact antibiotic-resistant bacteria in the environment, this study aims to evaluate the ability of the UPWr_E phages to reduce the number of antibiotic-resistant E. coli strains in controlled poultry environment. State of affairs of experimental broiler flock obtained from local farm with high level of antibiotic-resistant strains will reflect the herd density corresponding to standard farm conditions, ensuring AMR transfer between birds similar to commercial flocks.

Treatment of Manure

Antimicrobial resistant (AMR) bacteria that are excreted with broiler feces and the manure are used as organic fertilizer on agricultural land. After manure application on the field, AMR bacteria can contaminate the environment by dispersal in soil, surface water, plants and air. The effectiveness of different chicken manure treatments to reduce antimicrobial resistant bacteria will be tested experimentally (in the laboratory) and standardized conditions and in the field (on the broiler farms) under practical conditions. From the obtained results, feasible interventions for reducing AMR transmission from chicken manure into the environment will be deduced.

The experimental testing of chicken manure treatments will cover composting, storing, fermentation and the addition of an additional carbon source (molasses). Thereby, parameters as temperature, pH, moisture, and duration will be varied and their influence on AMR bacterial survival will be tested. Different bacterial species and their resistance against different antibiotics will be studied. AMR bacteria and resistance genes will be investigated by classical microbiological methods on selection media, genotyping and whole genome sequencing of single bacteria. A minimum of 100 isolates will be analyzed before and after each treatment.


Decontamination of Farm Effluents


Existing Knowledge Synthesis

A comprehensive synthesis of existing knowledge (peer reviewed and grey literature) in the field of environmental antimicrobial resistance in poultry production and environment, especially focusing on hazards relevant to this project (i.e. ESBL-, colistin-, and quinolone-resistant Enterobacteriaceae or resistance-genes), will be carried out. This will directly inform the risk assessment model, by providing data on those model parameters that are not covered by the intervention studies in the ENVIRE consortium.

Risk Assessment Modeling

A stochastic quantitative risk assessment model will be developed accounting for the selection of antimicrobial resistance in animals (chicken), its release by the animals, its spread through food and the environment and the subsequent exposure of humans. Two quantitative risk assessment modules will be developed to evaluate the effect of selected interventions on the reduction of human exposure to antimicrobial resistance from chicken origin, via two routes of major interest: i) foodborne (i.e. via consumption of chicken products) and ii) occupational (e.g. via direct contact with positive flocks) routes. The third module –the environmental module – of the QRA model will map the pathways of environmental exposure to risks from chicken farms, including recreational exposure to contaminated surface water (via recreational swimming), consumption of contaminated drinking water and fresh produce contaminated via chicken manure spread. The three modules will be joined to represent the full process of antimicrobial resistance selection, release, spread through food and the environment and human exposure to antimicrobial resistance from various routes of chicken origin (Figure 1).