Development and validation of a multiplex-PCR based assay for the detection of 18 pathogens in the cerebrospinal fluid of hospitalized children with viral encephalitis

Background. The Applied Biosystems 3500 Genetic Analyzer (ABI3500) allows for automated capillary electrophoresis on multiple targets. So far, the application of this method for detecting cerebrospinal fluid pathogens has hardly been reported. Methods: To assess the performance of multiplex-PCR assay for 18 pathogens detection, 127 CSF samples from hospitalized children with suspected viral encephalitis were prospectively collected from April to November 2018. The Sanger sequencing was applied to verify this assay. Results: All of the 18 target pathogens can be identified by multiplex-PCR assay at 10(4) copies (or CFU/mL) of each virus, bacterium and fungus. In contrast, 10 control microorganisms failed to be amplified. Approximately 68.5 % of the cases tested had positive results, the enterovirus accounted for the majority of the positive cases (63.8 %). Agreement between multiplex-PCR and sequencing was 91.49 %. Conclusions: Our findings suggest that the ABI3500-based multiplex-PCR detection kit could be a valuable diagnostic tool for pathogen detection in CSF of children with suspected viral encephalitis.