Next generation sequencing evaluation of the microbiome of equine paranasal sinusitis

Understanding of the microbe population and their sensitivity patterns is an important aspect of successful treatment of equine paranasal sinus infection. Studies utilizing traditional culture methods have suggested anaerobic bacteria are more likely to be identified in cases of sinusitis. Assumptions based on culture may not be accurate as it is well recognized in human medicine that not all organisms present in sinus infections are cultivable and molecular methods that detect DNA such as next generation sequencing (NGS) better capture the microbiome in health and disease. NGS determination of the equine sinus microbiota in health has recently been reported and similar to human studies, greater number and more diverse population of organisms were identified when compared with parallel cultures. Currently, there are no reports using NGS to determine the microbiome of clinical cases of equine sinusitis. Retrospective analysis of samples of 84 cases of equine sinusitis presented to a single referral hospital between 2016 -2021 were reviewed. The underlying cause of sinusitis was determined to be primary, dental-related, or other pathologies. The number, type, and diversity of organisms identified were determined as well as the presence of antimicrobial resistance genes, and any associations between microbiome detected and underlying cause of sinusitis. We hypothesize that a greater number and diverse population of predominantly anaerobic bacteria will be present in dental-related sinusitis when compared to primary and other causes of sinusitis.