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Bacteria and antimicrobial resistance profile during the composting process of wastes from animal production

  • Veterinary Microbiology - Research Paper
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Abstract

Livestock waste is widely used in agriculture. Although they provide benefits to the soil, and consequently to plants, they have the potential to contaminate the environment, as they contain pathogenic microorganisms and determinants of antimicrobial resistance, if not properly managed. Therefore, this study aims to evaluate the effect of composting horse bedding and poultry litter in organic and conventional production systems on the occurrence of bacteria in the Enterobacteriales order and to identify their antimicrobial resistance profiles. Bacterial strains were isolated from Salmonella-Shigella and eosin methylene blue solid media from animal waste during the composting process that was conducted for 125 days. After isolation, the strains were identified by the MALDI-TOF technique; the disk diffusion test was then performed for phenotypic detection of antimicrobial resistance. A total of 158 bacterial strains were isolated during composting of three wastes. The Enterobacteriaceae family was the most abundant, whereas Proteus mirabilis and Escherichia coli were the species with the highest percentage in the wastes, which also exhibited a multi-resistance profile. Poultry litter showed a greater abundance of resistant bacteria than horse bedding did. Similarly, a greater number of resistant bacteria was detected in conventional poultry litter than in organic poultry litter. The results obtained reinforce that animal wastes are reservoirs of pathogenic bacteria that are resistant to antimicrobials and highlight the importance of developing management strategies that aim to reduce and/or eliminate these contaminants to guarantee their safe use in agriculture.

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Acknowledgements

We thank Researchers Marco Antônio de Almeida Leal and Ednaldo da Silva Araújo from EMBRAPA Agrobiology for providing the infrastructure and support in the composting experiment.

Funding

The following research funding agencies provided financial support: CNPq (National Council for Scientific and Technological Development), CAPES (Coordination for the Improvement of Higher Education Personnel), and FAPERJ (Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro).

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  1. Department of Veterinary Microbiology and Immunology, Veterinary Institute, Federal Rural University of Rio de Janeiro, Seropédica, Rio de Janeiro, 23897-970, Brazil

    Paula Fernanda Alves Ferreira, Júlia Ferreira Xavier, Juliana Ferreira Nunes, Isabela Pinto Fonseca, Shana de Mattos de Oliveira Coelho, Miliane Moreira Soares de Souza & Irene da Silva Coelho

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  1. Paula Fernanda Alves Ferreira
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Contributions

All the authors contributed to the conception and design of the study. Material preparation, data collection, and analyses were performed by Júlia Ferreira Xavier, Juliana Ferreira Nunes, and Isabela Pinto Fonseca. The first draft of the manuscript was written by Paula Fernanda Alves Ferreira and Irene da Silva Coelho, and all the authors commented on the previous versions of the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Irene da Silva Coelho.

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Ferreira, P.F.A., Xavier, J.F., Nunes, J.F. et al. Bacteria and antimicrobial resistance profile during the composting process of wastes from animal production. Braz J Microbiol 54, 1157–1167 (2023). https://doi.org/10.1007/s42770-023-00912-8

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