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.
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