Detection of bacterial pathogens directly from synovial fluids using digital PCR: A proof of concept study

Diagnosis of joint infections is often challenging due to low specimen volumes, low sensitivity of Gram stains and long incubation times of cultures. Digital PCR (dPCR) is a molecular tool that can detect nucleic acid targets with high sensitivity and resistance to inhibition. A 3 hour dPCR assay targeting the 16S gene was performed on archived synovial fluids. The assay detected the 16S gene directly from 4 µL of joint fluid without nucleic acid extraction. In 43 culture positive neat synovial fluids, the dPCR instrument detected 31 (72%) as positive, and 12 (28%) as indeterminate. In 49 culture negative specimens, dPCR was negative for 34 (69%), indeterminate for 14 (29%). The detection of bacteria was similar to real-time PCR performed on extracted specimens and demonstrated superior sensitivity to Gram stain. This technique shows potential as a rapid detection method for bacterial pathogens in synovial fluids, with optimization to improve specificity.