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

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.