The Prevalence of Antimicrobial Resistance Genes in the Environments of Small Ruminant Farms from Central Portugal

Abstract

Background: Antimicrobial resistance is a pressing global concern affecting both human and animal health, with environment playing a key role in the dissemination of resistance determinants. This study aimed to investigate the presence of antimicrobial resistance genes (ARGs) associated with tetracyclines, β-lactams, macrolides, and sulfonamides in environmental matrices collected from 65 sheep and goat farms in central Portugal.

Methods: Environmental samples, including water, soil, pasture, and bedding, were analyzed through qPCR for the detection of clinically relevant ARGs.

Results: ARGs were detected in 83% of the samples, with over half exhibiting genes from three or more antibiotic classes, suggesting potential multidrug resistance. β-lactamase genes were the most prevalent, followed by those conferring resistance to tetracycline and sulfonamide resistance, while macrolide resistance genes were least frequent. The distribution of ARGs varied by farm type, host species, and municipality.

Conclusions: These findings suggest that small ruminant farms serve as important reservoirs for ARGs. The results underscore the need for systematic surveillance and further research into the ecological and genetic factors driving ARG persistence and dissemination in extensive livestock systems, including proper waste management strategies to limit the spread and persistence of antibiotic resistance and mitigate broader public health risks.

Keywords: Portugal; antimicrobial resistance; goat; sheep.

Figure 1

Geographical distribution of samples collected in Portugal. Dark orange represents the municipality from where the samples were retrieved, and the brown yellow the remaining territories of mainland Portugal.

Figure 2

The number of ARG classes detected per individual farm, with sheep farms (n = 45) on the upper panel (A) and goat farms (n = 20) on the lower panel (B). Each bar represents a farm, and colors indicate the ARG class: tetracyclines (light orange), β-lactamases (orange), macrolides (red-orange), and sulfonamides (dark red); asterisks represent the absence of ARG. Profiles reflect heterogeneity in ARG class presence across farms and between host species.

Figure 3

The relative abundance of ARGs by class and gene level. The upper panel (A) shows the overall distribution of ARG classes in sheep and goat samples (n = 45 and n = 20, respectively), as well as the combined total across both hosts, highlighting differences in class dominance between species. The lower panel (B) presents the relative contributions of individual ARGs within each class and host species, revealing shifts in gene prevalence across ARG types and host animals.

Figure 4

Relative abundances of ARG classes across central Portugal municipalities for sheep (n = 13) (A) and goat farms (n = 9) (B). Consistent color coding is used to represent ARG classes, emphasizing variation in resistome profiles by both municipalities and animal hosts.