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Updated: Jul 17, 2026

Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens
Published on: April 17, 2026
Epidemiology of Potential Missed Diagnosis of Pediatric Central Nervous System Infections in the Emergency Department
Kaileen Jafari1,2, Yasaman Fatemi1,3, Apeksha Gupta1
1Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA.
Insights
One in 10 children with CNS infections (CNSi) experienced a potential missed diagnosis, often after an emergency department visit for flu-like symptoms. This risk was higher in older infants and children, and in those treated at lower-volume or non-academic emergency departments.
Area of Science:
- Pediatric Neurology
- Infectious Diseases
- Emergency Medicine
Background:
- Pediatric central nervous system infections (CNSi) are uncommon but serious conditions requiring prompt diagnosis.
- Timely emergency department (ED) diagnosis of CNSi is critical but challenging.
- This study investigated the epidemiology of potential missed diagnoses (PMD) of CNSi and their link to neurological complications.
Purpose of the Study:
- To characterize the epidemiology of potential missed diagnoses (PMD) in pediatric CNS infections (CNSi).
- To assess the association between PMD of CNSi and acute neurological complications.
- To identify risk factors for PMD in pediatric CNSi.
Main Methods:
- A cross-sectional analysis of 2018-2019 healthcare data from five US states.
- Included children aged 0-17 years admitted for CNSi, excluding specific cases.
- Defined PMD using a prior 7-day ED visit with a high-risk diagnosis and employed logistic regression.
Main Results:
- 10.6% of pediatric CNSi cases had a PMD, with a median revisit interval of 2 days.
- PMD was more common in children over 90 days old, minority racial/ethnic groups, and those treated at lower-volume or non-teaching EDs.
- Among bacterial CNSi cases, PMD was linked to a significantly increased risk of neurological complications (aOR 2.49).
Conclusions:
- A substantial proportion of pediatric CNSi cases involve a potential missed diagnosis, frequently following an initial ED visit for nonspecific symptoms.
- Children over 90 days old and those presenting to less specialized EDs face a higher risk of PMD.
- Improving diagnostic tools for pediatric CNS infections is crucial, especially for older infants and children, to prevent severe neurological outcomes.
Background:
Pediatric CNS infections (CNSi)-meningitis, encephalitis, and craniospinal abscess-are uncommon, high-morbidity conditions in which timely emergency department (ED) diagnosis is critical and challenging. This study aimed to characterize the epidemiology of potential missed diagnosis (PMD) of CNSi and assess its association with acute neurological complications.
Methods:
Cross-sectional analysis of 2018 to 2019 Healthcare Cost and Utilization Project State ED and Inpatient datasets from California, Florida, Maryland, New York, and Wisconsin. Children aged 0 to 17 years with an admission for CNSi were included; those missing the linkage variable, birth hospitalizations, and with pre-existing intracranial devices were excluded. PMD was defined as a prior 7-day ED visit with a high-risk diagnosis, defined using Symptom-Disease Pair Analysis of Diagnostic Error methodology. Descriptive statistics and multivariable logistic regression were used to assess predictors of PMD and neurological complications.
Results:
Among 2686 CNSi cases, 284 (10.6%) had PMD with a median revisit interval of 2 days (IQR 1 to 3). In children >90 days with PMD, over 75% had isolated ED diagnoses of flu-like symptoms (fever, headache, vomiting, or fatigue), while 6% had CNSi "red flags" of altered mental status or neck pain. Potential missed diagnosis was more common in all age groups >90 days of age (aOR range: 4.19 to 4.78) and patients who were Asian (aOR 1.83, 95% CI: 1.06-3.16), Black (aOR 1.87, 95% CI: 1.30-2.70), and Hispanic (aOR 1.53, 95% CI: 1.1-2.13) relative to White children. In addition, patients initially presenting to lower annual pediatric volume quartile EDs (aOR 3.7, 95% CI: 2.6-5.3) and minor (aOR 1.49, 95% CI: 1.11-1.98) or nonteaching hospitals (aOR 2.08, 95% CI: 1.27-3.41) had higher risk of PMD. Among the subset of bacterial CNSi cases, PMD was associated with increased risk of neurological complications (aOR 2.49, 95% CI: 1.41-4.39).
Conclusions:
One in 10 children with CNSi had a potential missed diagnosis, most often after an initial ED visit for nonspecific flu-like symptoms. Risk of PMD was greater in children >90 days of age and those seen at lower-pediatric volume and nonacademic EDs. In addition, PMD in bacterial CNSi was associated with increased risk of severe neurological complications. These findings highlight the need for targeted diagnostic support tools to improve timely recognition of pediatric CNS infections, particularly in older infants and children.
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