Detection of fungal and bacterial organisms from clinical uterine samples of horses using next-generation sequencing in comparison with culture.
Authors: Cheong Soon Hon, Franklin-Guild Rebecca, Goodman Laura B, Lago-Alvarez Yamilka, Lee Yoke Lee, de Aguiar Luis Henrique, Diel de Amorim Mariana, Altier Craig
Journal: Journal of equine veterinary science
Summary
# Editorial Summary Conventional culture techniques remain the diagnostic standard for identifying bacterial and fungal pathogens in equine uterine samples, yet their reliance on organism viability and growth requirements may result in false negatives. Researchers compared culture results against next-generation sequencing (NGS) across 63 fungal and 57 bacterial samples collected from horses with suspected endometritis, analysing concordance rates and correlation coefficients between the two methods. NGS identified the causative organism in 62.5% of culture-positive fungal samples and 78.1% of culture-positive bacterial samples; however, moderate agreement (80% for fungi, 74% for bacteria) and moderate correlation (Kappa coefficients of 0.508 and 0.46 respectively) indicate these methods detect different microbial populations. Notably, NGS identified potential pathogens in 9.5% of culture-negative fungal samples and bacteria in 35.7% of culture-negative bacterial samples, suggesting culture may be missing clinically relevant organisms due to suboptimal growth conditions or polymicrobial infections. For equine practitioners, these findings indicate NGS could enhance diagnostic sensitivity in cases of suspected endometritis unresponsive to empirical treatment or where culture results don't match clinical presentation, though the methods may be complementary rather than interchangeable at present.
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Practical Takeaways
- •NGS can enhance detection of fungal and bacterial pathogens in equine endometritis cases where culture results are negative or inconclusive, potentially improving treatment outcomes
- •While NGS shows good correlation with culture (74-80% agreement), it should be considered complementary to rather than a direct replacement for culture in diagnostic protocols
- •NGS may identify polymicrobial infections and organisms that culture methods miss, providing more comprehensive pathogen profiles for treatment planning in subfertile mares
Key Findings
- •Next-generation sequencing and fungal culture showed 80% agreement with moderate correlation (Kappa = 0.508) in detecting fungal pathogens from equine uterine samples
- •Next-generation sequencing identified the same bacterial organism in 78.1% (25/32) of culture-positive samples with 74% overall agreement (Kappa = 0.46)
- •Next-generation sequencing detected fungal agents in 11.9% (5/42) of culture-negative samples, suggesting potential for identifying organisms missed by culture
- •Next-generation sequencing identified bacterial DNA in 5 of 14 culture-negative samples, indicating enhanced detection capability beyond traditional culture methods