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    Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms

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    Author
    Mencía-Ares, Oscar
    Cabrera-Rubio, Raúl
    Cobo-Díaz, José F
    Álvarez-Ordóñez, Avelino
    Gómez-García, Manuel
    Puente, Héctor
    Cotter, Paul D
    Crispie, Fiona
    Carvajal, Ana
    Rubio, Pedro
    Argüello, Héctor
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    Keyword
    Feces
    Farm environment
    Mobilome
    One health
    Sustainable farming
    Swine
    Antimicrobial resistance
    Date
    2020-11-19
    
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    URI
    http://hdl.handle.net/11019/2722
    Citation
    Mencía-Ares, O., Cabrera-Rubio, R., Cobo-Díaz, J.F. et al. Antimicrobial use and production system shape the fecal, environmental, and slurry resistomes of pig farms. Microbiome 8, 164 (2020). https://doi.org/10.1186/s40168-020-00941-7
    Abstract
    Background The global threat of antimicrobial resistance (AMR) is a One Health problem impacted by antimicrobial use (AMU) for human and livestock applications. Extensive Iberian swine production is based on a more sustainable and eco-friendly management system, providing an excellent opportunity to evaluate how sustained differences in AMU impact the resistome, not only in the animals but also on the farm environment. Here, we evaluate the resistome footprint of an extensive pig farming system, maintained for decades, as compared to that of industrialized intensive pig farming by analyzing 105 fecal, environmental and slurry metagenomes from 38 farms. Results Our results evidence a significantly higher abundance of antimicrobial resistance genes (ARGs) on intensive farms and a link between AMU and AMR to certain antimicrobial classes. We observed differences in the resistome across sample types, with a higher richness and dispersion of ARGs within environmental samples than on those from feces or slurry. Indeed, a deeper analysis revealed that differences among the three sample types were defined by taxa-ARGs associations. Interestingly, mobilome analyses revealed that the observed AMR differences between intensive and extensive farms could be linked to differences in the abundance of mobile genetic elements (MGEs). Thus, while there were no differences in the abundance of chromosomal-associated ARGs between intensive and extensive herds, a significantly higher abundance of integrons in the environment and plasmids, regardless of the sample type, was detected on intensive farms. Conclusions Overall, this study shows how AMU, production system, and sample type influence, mainly through MGEs, the profile and dispersion of ARGs in pig production. Video Abstract
    Funder
    Ministerio de Educación y Formación Profesional; Junta de Castilla y León; European Social Fund; European Union; Ministry of Science and Innovation of the Spanish Government
    Grant Number
    FPU 16/03485; FPU 17/00466; LE131-18; BEAGAL-18-106; 818368; AGL2016-78085-P
    ae974a485f413a2113503eed53cd6c53
    https://doi.org/10.1186/s40168-020-00941-7
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    Teagasc publications in Biomed Central

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