Antimicrobial resistance gene carriage in Escherichia coli isolated from healthy sheep and goats

Introduction

Escherichia coli is a common commensal inhabitant of the gastrointestinal tract of small ruminants; however, fecal shedding from apparently healthy sheep and goats represents an important reservoir of pathogenic and antimicrobial-resistant strains with potential zoonotic significance (Moriarty et al., 2011; Orden et al., 2003) [5,7] . Several studies have demonstrated that fecal E. coli populations in small ruminants frequently harbor virulence determinants, including Shiga toxin-producing genes, even in the absence of clinical disease, highlighting their role in silent transmission within animal populations and the environment (Ramatla et al., 2024) [8] . In addition to pathogenicity, the emergence and dissemination of antimicrobial resistance (AMR) among fecal E. coli isolates have become a major concern, with reports indicating high levels of resistance to commonly used antibiotics and the presence of mobile genetic elements facilitating horizontal gene transfer. The persistence and environmental survival of E. coli in fecal matter further enhance the risk of transmission across the animal-human-environment interface, emphasizing its importance within the One Health framework (Moriarty et al., 2011) [5] . Therefore, systematic detection and characterization of E. coli from fecal samples of small ruminants, along with assessment of their antimicrobial resistance profiles, are essential for understanding their epidemiological role and mitigating potential public health risks.

Materials and Methods

Sample Collection

A total of 50 faecal samples were collected aseptically from apparently healthy small ruminants, comprising 25 sheep and 25 goats. [2] .

Molecular Confirmation of Escherichia coli

Genomic DNA was extracted from presumptive isolates using a standard boiling method. Molecular confirmation of E. coli was performed by polymerase chain reaction (PCR) using species-specific primers: [9] .

Antimicrobial Susceptibility Testing (AST)

Antimicrobial susceptibility testing of confirmed E. coli isolates was performed using the Kirby-Bauer disk diffusion method on Mueller-Hinton agar.

Results

A total of 50 small ruminant faecal samples, including 25 goats and 25 sheep, were analyzed. Out of the 25 goat samples, 18 were positive for Escherichia coli, while in sheep, 13 out of 25 samples were confirmed positive. The isolates were further screened for selected antimicrobial resistance genes. Among goat isolates, the blaCMY and sul1 genes were each detected in 13 out of 25 samples (52%), while the intI1 gene was identified in 9 out of 25 samples (36%). In sheep isolates, blaCMY and sul1 were each detected in 11 out of 25 samples (44%), whereas intI1 was observed in 7 out of 25 samples (28%). Overall, across all samples analyzed, blaCMY and sul1 were the most prevalent resistance genes, each identified in 24 out of 50 samples (48%), followed by intI1 in 16 out of 50 samples (32%).

Discussion

The present study demonstrates a high prevalence of Escherichia coli in small ruminants, with higher occurrence in goats (72%) than sheep (52%), suggesting species-related differences in exposure or colonization. These findings support earlier reports identifying small ruminants as important reservoirs under grazing conditions (Moriarty et al., 2011) [5] . Significant interspecies differences in antimicrobial resistance were observed, with sheep isolates showing higher resistance to key antibiotics, including ceftiofur, amoxicillin/clavulanic acid, fluoroquinolones, and cotrimoxazole (p < 0.001). This indicates differential selective pressure, possibly due to variations in antimicrobial usage or management practices, consistent with previous studies (Ndegwa et al., 2019; Basnet & Kilonzo-Nthenge, 2024) [6,1] . In contrast, no significant differences were found for several critically important antibiotics, suggesting retained efficacy in the study population. The high prevalence of blaCMY and sul1 (48%) and the detection of intI1 (32%) indicate widespread distribution of resistance genes associated with mobile genetic elements, facilitating horizontal gene transfer (Shabana & Al-Enazi, 2020) [10] . Although virulence factors were not assessed, prior evidence of pathogenic E. coli in small ruminants raises potential zoonotic concerns (Orden et al., 2003; Ramatla et al., 2024) [7,8] . However, the limited sample size and absence of virulence gene characterization constrain comprehensive risk assessment. Overall, the findings highlight small ruminants as reservoirs of antimicrobial-resistant E. coli, emphasizing the need for targeted surveillance and antimicrobial stewardship.

Conclusion

In conclusion, the study highlights a notable prevalence of Escherichia coli in small ruminants, with goats showing higher occurrence than sheep. The detection of blaCMY, sul1, and intI1 genes indicates the presence of important antimicrobial resistance determinants and the potential for their dissemination. These findings suggest that small ruminants may serve as reservoirs of antimicrobial resistance, emphasizing the need for continuous monitoring and prudent antimicrobial use in livestock systems.

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