Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm


  • The treatment of swine manure increased the bacterial diversity.

  • Macrolide and rifamycin resistance genes were found in swine manure after treatment.

  • Waste stabilization ponds failed to eliminate antimicrobial resistance genes.


The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil’s swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.


Antimicrobial resistance (AMR) is recognized by the World Organization for Animal Health (WOAH) and the World Health Organization (WHO) as one of the main threats to human, animal, and environmental health (World Health Organization, 2015; World Organization for Animal Health, 2020). The concern is related to the selection of resistant bacteria due to the inappropriate use of antibiotics (Ben et al., 2019) and the possibility that bacteria can exchange antimicrobial resistance genes (ARG) with each other through horizontal transfer (Juhas et al., 2009). In this way, genes present in animal production can be transmitted to the environment and infiltrate human and animal bacteria, making it difficult to treat diseases (Woolhouse et al., 2015).

Brazil is the fourth largest swine producer in the world, creating 4,983 million tons of swine meat in 2022 (Brazilian Animal Protein Association, 2023). During the nursery stage, lincomycin, spectinomycin, tilmicosin, and amoxicillin can be used in the diet, while florfenicol, lincomycin, spectinomycin, amoxicillin, tylvalosin, and oxytetracycline can be used in the growing/finishing stage (Güths et al., 2022). During swine production, a large amount of manure is produced daily, contributing to the spread of many antibiotics (Alcock et al., 1999). According to Brazilian legislation, swine manure must be treated before release into the environment (Brasil, 2011). The standard treatment methods are based on solid-liquid separation processes, anaerobic digestion, or precipitation, which are applied mainly for converting manure into fertilizer and biogas (Kunz et al., 2009; Araujo and Oliveira, 2023).

The microbiota and ARG dynamics in the animal production chain can be studied with metagenomic design (Vikram et al., 2017; Shui et al., 2022; Tams et al., 2023; Wang et al., 2023), allowing the understanding of the bacterial composition present in the environment and enabling comparisons among different sites during the route taken by the swine manure until it enters the treatment system (He et al., 2019). In addition, this approach explores the ARG modifications that occur in the farm environment (Chen et al., 2021).

Studies have demonstrated that the elimination of ARGs through the treatment of swine manure is inefficient, suggesting that effluents have the potential to spread antimicrobial resistance to the environment (He et al., 2019; Laconi et al., 2021; Rueanghiran et al., 2022; Watanabe et al., 2023). In addition, ARG composition varies according to farm and region, according to Shui et al. (2022) and Wang et al. (2023). However, the treatment system used in their studies differed from that used in Brazil, where waste stabilization ponds (WSP) are frequently employed due to their simplicity and low cost (Kunz et al., 2009).

Even though there is a debate about AMR in Brazilian swine production (Brisola et al., 2019; Güths et al., 2022), the bacterial communities and the ARGs present in swine farms and waste treatment system effluents remain unknown. Thus, this study aimed to follow the change in the microbiota profile from indoor facilities to the manure treatment system in an independent swine farm in south Brazil and the resistome associated with the wastewater treatment process.

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Farm and sampling

The study was conducted on a swine farm in the state of Rio Grande do Sul in southern Brazil. The farm used family labor and was not part of a large agroindustry production pyramid (contractor system). It occupied six hectares and encompassed 11 barns distributed among sows, boars, gilts, maternity, nursery, and growth/finishing. There were 22 nursery pens (0.33 m2/animal) and 28 pens with slatted floors for growing/finishing (0.8 m2/animal), 20 pens with solid floors, and eight pens with deep

Bacterial community of swine farm environments

Sequencing the V4 region of the 16S-rDNA revealed the microbiota diversity in the swine farm environment. The 13 16S-rDNA libraries generated 2,132,579 reads after quality filtering (Table S1). The rarefaction curves depicted that the amplicon sequence variants (ASVs) obtained were representative of the samples (Fig. S1).

Individually, the diversity of the pre-treatment group was lower than that of the treatment group – liquid and sediment samples (Fig. 2A). On the other hand, the Chao1 index


Analysis of the swine manure route in the studied farm, from the indoor facilities to the waste stabilization ponds, showed a significant variability in bacterial composition. Waste stabilization ponds are frequently used as a treatment system for swine manure in Brazil (Kunz et al., 2009). The pre-treatment samples had lower bacterial diversity than the treated samples, which could be due to the presence of feces, urine, bristles, feed remains, antimicrobials, and disinfectant residues in the


The present study identified variations in the bacterial community along the path taken by swine manure. In addition, the resistome profile in samples from the waste treatment process was also examined. The results indicate that the swine manure treatment system in the studied farm was unable to eliminate ARGs and MGEs. Finally, as the number of studies on the environmental microbiota of swine farms is scarce worldwide, especially in Brazil, our results contribute to an initial exploration of

Uncited reference

Brazil, 2011; World Organisation for Animal Health, 2020.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.


The authors are grateful to the National Council for Scientific and Technological Development (CNPq) – Controle da disseminação de resistência antimicrobiana – process n. 408693/2022-3; Desenvolvimento e Aplicação de Novas Tecnologias e Ferramentas de Bioinformática em Biotecnologia – process n. 440279/2022-4, and Coordination for the Improvement of Higher Education Personnel (CAPES) Finance code 001.

Parts of the Graphical abstract were drawn using pictures from bioicons (//bioicons.com/?query=

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