Antimicrobial resistance (AMR) is a critical challenge in both human and veterinary medicine. The microbiome of animals such as horses can act as a reservoir for genes conferring resistance. Primarily kept as companion animals in close contact to humans, horses are an essential part of the One Health approach to targeting antibiotic resistance. However, the microbiome and resistome of horses remain understudied.

The goal of this study was therefore to gain further insight into the microbiome and resistome of horses. Twelve fecal samples were obtained from healthy adult horses in six different locations in Western Pomerania. Shotgun metagenomic sequencing was performed to analyze antimicrobial resistance genes and to gain insight into the microbiome composition. Additionally, ESBL­E. coli isolates could be obtained from two fecal samples and were further analyzed by antimicrobial susceptibility testing and whole genome sequencing.

In the metagenomic datasets genes conferring resistance to the antimicrobial class of Macrolides, Lincosamides and Streptogramines (MLS) could be identified in all samples. Next to MLS the highest relative abundance occurred in the classes of Tetracyclines, and Sulfonamides. Overall, the normalized abundance of AMR gene counts was 0.0041 on average. The ESBL­E. coli isolates carried a blaCTX-M-15 gene and displayed phenotypical resistance against Gentamicin and Trimethoprim in addition to Cephalosporins. The predominant phyla in the microbiome of all samples were Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota.

These findings provide valuable insights into the burden of AMR genes in the microbiome of horses in the Western Pomeranian region, which was generally lower than in farm animals like cattle in the same area. It may be useful to conduct further studies on horses in the future, ideally involving different species on the premises of horse stables and their owners, to identify possible transmission routes in this environment. This study also offers a unique opportunity to compare and evaluate the respective advantages of metagenomic and cultural approaches in studying the resistome and microbiome of animals.