Stratified survey of the most prevalent infectious agents in meningitis and encephalitis diagnosed by rapid automated multiplex PCR: experience from Rio de Janeiro, Brazil

Abstract

Background: Infectious meningitis and encephalitis (ME) are neurological emergencies associated with high morbidity and mortality, in which rapid etiological diagnosis is essential for appropriate clinical management. Cerebrospinal fluid (CSF) analysis remains central to diagnosis; however, conventional methods such as culture and serology are limited by long turnaround times and reduced sensitivity, particularly after antimicrobial exposure. In recent years, rapid and fully automated multiplex polymerase chain reaction (PCR) panels have emerged as powerful tools for the simultaneous detection of the most clinically relevant central nervous system (CNS) pathogens. Their optimal use, however, requires integration into diagnostic algorithms that consider epidemiological background and differentiate community-acquired from healthcare-associated infections. Objective: To perform a stratified evaluation of the most prevalent infectious agents associated with suspected meningitis and encephalitis using an automated multiplex PCR panel applied to CSF samples, and to highlight the importance of a diagnostic algorithm based on epidemiological history and appropriate panel selection, drawing on the experience of a reference diagnostic center in Rio de Janeiro, Brazil. Methods: This retrospective observational study included CSF samples from patients with clinical suspicion of meningitis and/or encephalitis submitted for molecular testing at a specialized laboratory in Rio de Janeiro. Samples were analyzed using a rapid, fully automated multiplex PCR platform capable of detecting a broad spectrum of bacterial, viral, and fungal CNS pathogens. Results were stratified according to age group, clinical presentation, CSF cytochemical profile, epidemiological background, and suspected infection setting (community-acquired versus nosocomial). Diagnostic turnaround time and concordance with initial clinical hypotheses were descriptively assessed. Results: The multiplex PCR panel enabled rapid etiological identification in a substantial proportion of cases, with viral pathogens predominating in community-acquired infections and CSF samples showing lymphocytic profiles, while bacterial agents were more frequently detected in cases with inflammatory patterns suggestive of bacterial meningitis. The use of a stratified diagnostic algorithm, incorporating epidemiological data and tailored panel selection, improved diagnostic efficiency and avoided unnecessary testing. Molecular testing significantly reduced turnaround time compared with conventional methods and identified pathogens not routinely detected by standard laboratory techniques, leading to changes in clinical management in several cases. Conclusion: The implementation of rapid automated multiplex PCR panels, integrated into epidemiology-driven diagnostic algorithms, represents an effective strategy for the investigation of meningitis and encephalitis. The experience from Rio de Janeiro underscores the importance of individualized panel selection.