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- Backyard production systems in Portugal: exploring associated risk factors and antimicrobial resistancePublication . Baroni, Bruno Morbeck; Nunes, Alexandra Isabel Cardoso; Ferreira, Susana Margarida Paraíso; Sobral, Daniel Vieira Noro e SilvaThe One Health approach recognizes that human, animal and environmental health are interconnected and aims to create effective solutions to complex problems. Animal production is associated with the spread of zoonoses and antimicrobial resistance (AMR) throughout the food chain and the environment. However, there is limited knowledge about the impacts of backyard animals raised for self-consumption. Backyard production systems (BPS) usually have poor biosecurity implementation, with several studies identifying a diverse community of zoonotic pathogens and AMR genes in those systems. Thus, the aim of this work was to evaluate the safety and impacts of Portuguese BPS, with specific focus on zoonoses and AMR. To achieve this, the first specific objective was to apply a questionnaire to BPS owners to obtain data on husbandry and biosecurity practices implemented in BPS. The second specific objective was to evaluate, through an innovative metagenomic methodology, the presence of zoonotic pathogens and AMR genes in fecal and soil samples from BPS that raise poultry, small ruminants and pigs. In the questionnaire, a total of 283 responses were analyzed, obtaining valuable data about the characteristics of BPS in Portugal, such as that 92% of BPS owners have backyard animals for the consumption of animal products, but only 28% have training in animal production or welfare. Also, neglect of biosecurity protocols and animal health measures were reported in some BPS. For example, 43% of respondents did not use personal protection equipment when handling animals and 83% did not isolate sick animals. Some practices that could promote pathogen and AMR dissemination to the environment and other productions systems were also reported, such the use of manure as fertilizer in 95% of BPS, backyard animals being exposed to the wildlife in 39% of BPS and carcass disposal in the house waste in 6.5% of BPS. For the metagenomic analysis, fecal and soil samples were collected from 2 Portuguese BPS and submitted to DNA extraction, amplification, library preparation and sequencing. According to the bioinformatics analysis, 18 zoonotic pathogens, including Escherichia coli, Enterococcus faecium and Bacteroides fragilis, and more than 100 AMR genes were identified in all the fecal samples. This is alarming considering the presence of pathogens and AMR genes in BPS could lead to infections with limited treatment options. Although the metagenomic technology employed in this project still needs to be validated and presents some limitations, it showed potential as a powerful tool for the surveillance of zoonotic pathogens and AMR in animal production systems. In conclusion, in accordance with a One health approach, this study indicates that the risks that husbandry and consumption of backyard animals represent to the public health, animal welfare and environment cannot be overlooked. Therefore, it is critical that measures to prevent the dissemination of zoonoses and AMR, such as more rigorous biosecurity protocols, should be implemented in BPS.