Detection of fungal and bacterial organisms from clinical uterine samples of horses using next-generation sequencing in comparison with culture

Fungal and bacterial culture is currently the primary method for pathogen detection and identification. Next-generation sequencing is a powerful method for detecting and identifying the presence of microbial DNA in samples. We evaluated the correlation between fungal and bacterial culture with next-generation sequencing in equine uterine samples. Fungal cultures (n=63) were evaluated based on their culture results. In culture positive (n=16) samples, next-generation sequencing identified the same organism in 10 samples (62.5%), 5 samples did not identify fungal agents, and 1 sample identified other species of fungal agents. In no growth samples (n=42), next-generation sequencing did not identify fungal agents in 37 samples (88.1%), 4 samples had a potential fungal pathogen identified, and one sample identified only non-pathogenic fungal organisms. Fungal culture and next-generation sequencing had an 80% agreement and moderate correlation by Kappa coefficient (0.508). Bacterial culture (n=57) was also evaluated based on bacterial culture results. In bacterial culture Positive samples (n=32), next-generation sequencing identified the same organism in 25 (78.1%) samples, and identified different organisms from the remaining 7 samples. In bacterial no growth samples (n=14), next-generation sequencing detected bacterial presence in 5 samples, and 9 samples had no bacterial DNA identified. The agreement between bacterial culture and next-generation sequencing was 74% with a moderate correlation by Kappa coefficient (0.46). In conclusion, culture and next-generation sequencing have moderate correlation, and next-generation sequencing has the potential as a diagnostic option for enhancing pathogen detection for equine endometritis.