Pathogen detection in acellular cerebrospinal fluid: diagnostic insights from a pediatric cohort in Colombia

The diagnosis of pediatric meningoencephalitis has traditionally relied on the detection of inflammatory markers in cerebrospinal fluid (CSF), particularly pleocytosis, as an indirect indicator of infection. This assumption presumes that microbial invasion of the central nervous system consistently triggers a measurable immune response. In this prospective observational study conducted in Cartagena, Colombia, we enrolled 166 pediatric patients with suspected meningoencephalitis. All patients underwent testing with the FilmArray Meningitis/Encephalitis (FA-M/E) panel for direct pathogen detection in CSF, and results were compared to conventional CSF cytochemical analysis and culture. The FA-M/E panel identified a pathogen in 21 of 166 patients (12.6%), whereas CSF cultures were negative in all cases. Detected pathogens included 16 viruses (76.2%), most frequently Enterovirus and Human Herpesvirus 6 and five bacteria (23.8%), including Escherichia coli K1 and Streptococcus agalactiae . Remarkably, 100% (21/21) of the FA-M/E-positive samples exhibited complete absence of pleocytosis (0 white blood cells/µL). Additionally, 33.3% (7/21) showed entirely normal CSF biochemistry. Among these cases with a normal CSF profile, the panel identified two clinically significant bacterial infections and five viral infections that would have otherwise gone undetected. These findings demonstrate that traditional CSF parameters are poor predictors of infection in patients with a positive molecular result. Routine reliance on cytochemical analysis alone may therefore delay diagnosis and treatment. Our results support the use of molecular diagnostics as a frontline tool, even in the absence of classical inflammatory CSF markers. IMPORTANCE This study challenges the long-standing paradigm that abnormal cerebrospinal fluid (CSF) findings are required to justify molecular testing in pediatric meningoencephalitis. We show that critical central nervous system (CNS) infections can present with entirely normal CSF profiles, including cases caused by high-risk pathogens such as E. coli K1 and Streptococcus agalactiae . By highlighting the limitations of pleocytosis and biochemical markers in detecting early CNS infection, our data underscore the importance of incorporating molecular diagnostics into routine clinical evaluation, particularly for high-risk pediatric populations. Failure to do so may result in missed or delayed diagnoses and suboptimal treatment.