Comparison of Next-Generation DNA Sequencing and Bacterial Culture in Bile from Dogs and Cats

Abstract: Background – Bacterial infection is a common cause of hepatobiliary disease in small animals. The utility of next-generation sequencing (NGS) on bile hasn't yet been fully defined. Hypothesis/Objectives – To compare the biliary transcriptome to results of bacterial culture in dogs and cats with hepatobiliary disease. We hypothesized that NGS would have a higher sensitivity for detecting the presence of bacteria. Animals – Twenty-six client-owned animals (17 dogs and 9 cats) that had bile culture submitted where additional bile was available for NGS. Methods – Bile was collected by ultrasound-guided cholecystocentesis or surgical laparotomy/laparoscopy. Aerobic culture was performed on all samples, and most (22/26 samples) had anaerobic culture. NGS samples were stored frozen in a DNA stabilization solution immediately after collection and were processed upon conclusion of all sample collection. Descriptive statistics were utilized. Results – Fifteen percent (4/26) of samples had positive cultures, and 75% (3/4) of these yielded multiple bacterial species. All but one cultured bacterial species (scant Micrococcus) were also detected using NGS. In one cat with positive aerobic (E. Coli, Streptococcus) and anaerobic (Bacteroides) cultures, NGS detected these species and multiple additional species (Fusobacterium, Fretibacterium, Desulfomicrobium, Schaalia, Lactobacillales, Tannerella, and Campylobacter) in high abundance. NGS did not reveal a high bacterial abundance (>100,000 cells/sample) in any culture-negative sample. Conclusions and clinical importance – NGS may be a clinically useful tool in detecting bacteria present in bile samples obtained from dogs and cats, particularly in cases where multiple species of bacteria and/or anaerobic infection is present.