In 2024, Brazil produced 4.5 million tons of pork and exported around 33 % of this amount, highlighting the country's relevance in the world ranking of meat production (United States Department of Agriculture - USDA, ). Pig farming is an important economic activity practiced in Brazil due to the climatic conditions favorable to the adaptation of animals and different breeding systems. It is also mainly boosted due to the country's grain production capacity.

Despite the numerous benefits to the economy, several negative environmental impacts are inherent to pig farming. This activity is related to high water consumption and waste production (Ferreira et al., 2003; Zheng et al., 2021) due to the confinement of animals in stalls, which are washed frequently throughout the day. Pig manure can also be a source of contamination due to its various constituents, such as organic matter, solids, and organisms with pathogenic potential (Ndegwa et al., 2001; Hill, 2003; Li et al., 2025). Furthermore, the presence of antibiotics used in the treatment of diseases that affect pigs stands out, which can be excreted practically unchanged in feces and urine (Sarmah et al., 2006; Pereira et al., 2025).

Regions with high swine production activity have impacted surrounding communities, especially in terms of health. For example, high- and medium-density swine farms have been associated with an increased incidence of urinary tract infections linked to extraintestinal pathogenic Escherichia coli strains (Holcomb et al., 2022). Communities in North Carolina/USA located near concentrated animal feeding operations (CAFO) have shown higher all-cause and infant mortality, mortality due to anemia, kidney disease, tuberculosis, sepsis, and increased hospital admissions/emergency room visits among infants (Kravchenko et al., 2018). Exposure to air pollution from swine confinement operations has also been associated with wheezing symptoms in adolescents (Mirabelli et al., 2006). Livestock-related odors around schools may indicate the presence of hazardous air contaminants from nearby animal protein production centers (Barrett, 2006).

Regarding potentially pathogenic organisms that can cause enteric infections in humans, the bacterial species Salmonella ssp., Yersinia enterocolitica, Leptospira ssp., Erysipelothrix rhusiopathiae, and pathogenic Escherichia coli are frequently detected in pig manure (Hill, 2003). Considering the removal of these organisms in units frequently used for pig wastewater treatment, it is observed that, due to the penetration of light in the facultative ponds (0.8–3.0 log), the inactivation of these organisms tends to be more effective, as contrary to anaerobic digestion (0.1–3.0 log), which offers good conditions for the growth of microorganisms in general, with pH and temperature in the optimal growth range (Hill, 2003).

The problem of antimicrobial resistance has gained increasing notoriety in the agricultural sector. According to O'Neill (2016), if this problem is neglected, by 2050, around 10 million people could die as a result of the ineffectiveness of antibiotics. Furthermore, several sectors could be affected, with economic losses of up to 100 trillion dollars between 2016 and 2050 (O'Neill, 2016).

The Brazilian Ministry of Agriculture, Livestock and Food Supply (MAPA) has been restricting the use of antibiotics as feed additives since the 1980s, banning the use of several substances (MAPA. Ministério da Agricultura, 2025). Currently, Normative Instruction No. 110/2020, which establishes the list of permitted additives, does not include antibiotics, making this practice restricted in the country. For therapeutic use, which is permitted in the country, the most commonly used antibiotics in pig farming belong to the classes of aminoglycosides, beta-lactams, lincosamides, phenicols, macrolides, polypeptides, quinolones, sulfonamides, chloroquinolines and ionophores (Pereira et al., 2021).

In swine farming, the presence of antibiotics, even in low concentrations, can exert selective pressure on the microbial community, both in the animal's intestinal tract and in its excreta, inducing the selection of antibiotic-resistant bacteria (ARBs) and the transfer of antibiotic resistance genes (ARG) (Joy et al., 2013; Zhu et al., 2013; Luo et al., 2017; Zalewska et al., 2023; Chen et al., 2024). The problem of spreading ARG in the environment is directly linked to the occurrence of multi-resistant strains that can affect humans, which is especially important from a clinical point of view, as it makes the treatment of infections more costly and slow, which can be fatal in the hospital environment (Chander et al., 2007).

Van Boeckel et al. (2019) identified different levels of resistance in the potentially pathogenic bacterial Escherichia coli, Campylobacter spp., Salmonella spp., and Staphylococcus aureus, associated with animal husbandry in underdeveloped countries. Additionally, Dias et al. (2024) identified multiresistant (MDR) bacterial isolates in a Brazilian swine wastewater treatment plant (SWWTP) belonging to the Enterobacteriaceae family, Staphylococcus, and Enterococcus ssp., revealing an increase in the proportion of MDR Enterococci species in the final effluent. In 2024, the World Health Organization (WHO) updated the list of priority antibiotic-resistant pathogens that pose the greatest threat to human health to guide and promote research to create new antibiotics (WHO. World Health Organization, 2024). This list includes groups of bacteria of medium, high, and critical priority, such as Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacterales order, and Streptococci.

It is important to highlight that during wastewater treatment, there is a variation in the composition of the microbial community, and this may be strongly related to the dynamics of ARG carrying these elements (Tao et al., 2014). Knowing that SWWTP can also be favorable environments for the exchange of genetic material between bacteria (Rizzo et al., 2013; Manaia et al., 2020), driven by the presence of antibiotics, monitoring these units becomes relevant to defining strategies to mitigate the spread of antibiotic resistance in the environment.

In previous research, norfloxacin and genes – related to beta-lactams, macrolides, sulfonamides, quinolones, and tetracyclines – were detected in a typical Brazilian swine wastewater treatment plant consisting of a biodigester followed by three facultative ponds. Additionally, we found a correlation between usual monitoring parameters (solids, NH4+, chemical oxygen demand - COD), the antibiotic norfloxacin, and the abundance of ARG (Pereira et al., 2023). Now, this study aims to investigate in detail the composition of the microbial community (bacteria and archaea) in the same SWWTP, signaling the possible hosts of ARG, with an emphasis on potentially pathogenic organisms (WHO. World Health Organization, 2024) and correlating them with usual monitoring parameters.