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Resistome in the pig farms: Comparison of the breeding and fattening units with a One Health approach.

English title Resistome in the pig farms: Comparison of the breeding and fattening units with a One Health approach.
Applicant Hilty Markus
Number 177452
Funding scheme NRP 72 Antimicrobial Resistance
Research institution Institut für Infektionskrankheiten Universität Bern
Institution of higher education University of Berne - BE
Main discipline Medical Microbiology
Start/End 01.03.2018 - 28.02.2021
Approved amount 350'000.00
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Keywords (6)

One health ; Breeding and fattening units; Resistome; Occupational risk ; Pig farms; ESBL

Lay Summary (German)

Dieses Projekt hat das Ziel, die Antibiotikaresistenz in den Schweineställen der Schweiz zu untersuchen und deren Verbreitung besser zu verstehen. Wir werden dabei Informationen mittels Fragebögen erheben und Proben von Mensch, Tier und Umwelt sammeln um die Antibiotikaresistenz zu untersuchen.
Lay summary

Inhalt und Ziele des Forschungsprojekts

Um die Antibiotikaresistenz zu untersuchen gibt es sogenannte standardisierte Kulturprotokolle, aber auch neue, molekulare Methoden. Letztere können die Gesamtheit der Resistenzgene, das ‚Resistome‘, viel genauer beschreiben. In unserer Studie haben wir somit folgende Ziele; 1) Die Untersuchung von Antibiotikaresistenz bei Schweinen mittels Rektalabstrichen 2) Die Quantifizierung der Übertragung von Resistenzgenen von Tier auf Mensch  
3) Die Untersuchung der wichtigen Colistinresistenz (Colistin wird oft als Reserveantibiotikum in Spitälern gebraucht).
4) Informationen über die Häufung von Resistenzgenen in der unmittelbaren Umwelt der Schweineställe. 
5) Eine komplette Charakterisierung des ‚Resistomes‘ in Schweineställen durch das Benutzen von molekularen Methoden.


Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts

Um die Auswirkungen von Antibiotika in Schweineställen auf Mensch und Tier besser zu verstehen  ist es wichtig, möglichst viele Samples von Tier, Mensch aber auch Umwelt mit verschieden, modernen Methoden zu untersuchen. Diese Informationen sind wiederum wichtig um effiziente Strategien vorzuschlagen, wie eine Verbreitung von Resistenzgenen ausgehend von Schweineställen möglicherweise minimiert werden könnte.

Direct link to Lay Summary Last update: 15.01.2018

Responsible applicant and co-applicants


Name Institute

Project partner


Group / person Country
Types of collaboration
Dr. Patricia Scheer, SUISAG, Sempach Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
Dr. Weihong Qi, Functional Genomics Center, University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Dr. Rémy Bruggmann, Interfaculty Bioinformatics Unit, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Annual Swiss Society for Microbiology Meeting 2019 Poster Decreasing prevalence of extended-spectrum beta-lactamase producing Escherichia coli in pig faeces coincides with age-dependent decline in the abundance of Enterobacteriaceae 03.09.2019 Zurich, Switzerland Oppliger Anne; Overesch Gudrun; Hilty Markus; Moor Julia;
Annual Swiss Society for Microbiology Meeting 2018 Talk given at a conference Setting up of a functional metagenomics methodology to reveal the resistome in pig farms 28.08.2018 Lausanne, Switzerland Hilty Markus; Moor Julia; Oppliger Anne;

Associated projects

Number Title Start Funding scheme
152880 Structure des communautés bactériennes nasales des fermiers: Impact d'un travail en contact étroit avec les animaux 01.09.2014 Project funding (Div. I-III)


Pig farming requires the use of antibiotics either to prevent or to cure infectious diseases. Nowadays, due to ethical and economic reasons, it is not possible to give up totally the antibiotic treatments in animal production. Therefore, in order to minimize the environmental spread and zoonotic transmission of antibiotic resistant (ABR) bacteria originated from animal farms it is urgent to have a precise picture of the fate and persistence of resistant genes in the farm environment. Culture and non-culture based (metagenomics) sequencing are the two main approaches used to characterize the resistome in sample with complex microbial communities. By studying the non- culturable resistome, additional resistant genes might potentially be discovered, In Switzerland, Colistin is the most used antibiotic in the breeding units of pig farms to cure or prevent neonatal diarrhoea whereas, amoxicillin and/or trimethoprim/sulfonamide are the first choices in the fattening units to cure respiratory or arthritis/joint infections.Within this proposal, we aim at studying the transmission dynamics of ABR bacteria (the resistome) in the breeding as compared to the fattening units within Swiss pig farms. We will a) investigate the risk factors for a high prevalence of extended-spectrum cephalosporin-resistant (ESC-R-Ent) and carbapenem-resistant Enterobacteriaceae within pigs of breeding and fattening units. Similarly, the prevalence will also be b) investigated for pig farmers and risk factors for potential zoonotic transmission evaluated. We will also inspect the quantity of and the risk factors for c) colistin-resistant Enterobacteriaceae within pigs and pig farmers. Furthermore, we will d) evaluate the degree of spread of ESC-R-Ent, carbapenem and colistin resistant Enterobacteriaceae to the environment. Finally, we will investigate e) the relevance of the non-culturable resistome within samples from humans and animals.Results of this study are indispensable for implementing efficient preventive measures to reduce antibiotic resistance within pigs, to minimize zoonotic transmission of antibiotic resistance and to reduce the spread of these bacteria into the environment.