Diagnostic Performance of a Multiplex PCR Assay for Meningitis in an HIV-Infected Population in Uganda

Background: Meningitis remains a worldwide problem, and rapid diagnosis is essential to optimize survival. Delay in diagnosis leads to excess morbidity, mortality and healthcare costs related to unnecessary empiric treatment and isolation procedures.

Methods: From January-April 2014, cerebrospinal fluid (CSF) from 39 HIV-infected persons with suspected meningitis in Kampala, Uganda was collected at time of diagnosis (n=18) and among persons with cryptococcal meningitis at therapeutic lumbar punctures (n=53). Standard bacterial, mycobacterial and fungal CSF diagnostics were performed on site.  Cryopreserved CSF specimens (200 mcL) were then analyzed on the FilmArray™ System using a Meningitis/Encephalitis PCR panel (BioFire Diagnostics, Salt Lake City, UT; research use only). The panel targets 16 common pathogens: 6 bacterial, 8 viral, and Cryptococcus neoformans/gattii speciation.  Operators were blinded to microbiology results. We assessed the diagnostic performance of the panel.

Results: The FilmArray™ multiplex PCR panel detected Cryptococcus in the CSF of all patients diagnosed with a first episode of cryptococcal meningitis by quantitative fungal cultures (n=14) with 100% sensitivity and specificity.  In second episodes, the FilmArray™ system was able to differentiate between fungal relapse (n=2) vs paradoxical immune reconstitution syndrome (IRIS) and/or sterile cultures (n=4).  In patients receiving antifungal therapy, FilmArray™ predicted follow up culture sterility with 67% negative predictive value.  The first possible case of C. gattii meningitis in Uganda was detected. EBV was frequently detected in this HIV-infected population regardless of whether or not they had active cryptococcal infection [77% with (n=35) and 100% without (n=4) cryptococcosis].  Other pathogens detected included CMV (n=3), HSV-2 (n=2), HHV-6 (n=2), VZV (n=1), Streptococcus pneumoniae (n=1).

Conclusion: The FilmArray™ multiplex PCR panel offers a promising platform for the rapid diagnosis of CNS infections.  PCR testing appears to be particularly useful in cryptococcal disease, distinguishing species, predicting culture sterility, and differentiating IRIS from culture-positive cryptococcal relapse in patients with recurrent symptoms.