Genomic insights into the epidemiology of Contagious Equine Metritis in Germany

In Germany, Contagious Equine Metritis (CEM) is a persistent problem in equine populations. The often subclinical nature of the disease, which is caused by the bacterium Taylorella equigenitalis, poses a problem for the breeding industry. However, there is a lack of knowledge about the genomic diversity of the pathogen in Germany, as studies on the genome level are lacking. Thus, in this study we sequenced 63 T. equigenitalis isolates from a strain collection and contemporary clinical isolates from before 2007-2024. Most of these isolates came from Icelandic horses in southern Germany. Based on the sequencing data, we compared them by multilocus sequence typing (MLST) and determined nucleotide differences in the core genome region. The isolates exhibited a considerable genomic diversity, particularly within the MLST sequence type 46, to which most isolates belonged. Epidemiological connections were confirmed for an infection event, in which a stallion was suspected to be the source of infection of several mares. However, the results also indicated that there must be a large number of CEM cases that remained undetected. Further, the isolates were tested for their streptomycin resistance and it was found that the majority of resistant isolates shared a specific mutation of the rpsL gene. This study emphasized the need of molecular-based investigation of the prevalence of T. equigenitalis in Germany, also in presumably healthy animals, that might act as carriers for the infection, to assess the situation of CEM in the country and to identify risk factors for CEM outbreaks.