Uncovering Hidden Pathogens in Culture Negative Cases: Enhancing Diagnostic Utility in Post-Neurosurgical Meningitis/Ventriculitis Using 16S Metagenomics

Post-neurosurgical Meningitis/Ventriculitis remains a major clinical challenge, particularly in cases where conventional microbiological cultures yield negative results. Delayed or improper diagnosis can lead to sepsis or even death in patients. 16S metagenomics next-generation sequencing (mNGS) techniques have higher sensitivity and specificity than gold-standard techniques. This prospective study aimed to evaluate the ability of mNGS to detect pathogens in cerebrospinal fluid (CSF) in culture-negative cases. Forty-four CSF specimens collected from 44 patients with suspected central nervous system (CNS) infection were subjected to mNGS and microbial culture analysis in parallel. Among the 44 CSF specimens, 27 (79%) were NGS positive, which was higher than microbial culture 4 (9%). The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were 75%, 20%, 11%, and 85%, respectively. A high NPV aids in ruling out infection, and mNGS substantially improves pathogen detection in culture-negative cases. Further advances in sample processing methods are required to improve sensitivity and specificity. ImportanceThis study aimed to evaluate the ability of mNGS to detect pathogens in the cerebrospinal fluid in cases of post-neurosurgical meningitis, which can have high mortality rates and severe sequelae. This prospective study of patients with suspected CNS infection found that mNGS has a higher sensitivity for detecting bacterial pathogens than the current gold standard microbial culture. It was the first time combining mNGS and microbial culture to verify the results using 16S mNGS. Although microbial culture was thought to be the gold standard for pathogen detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing (CNS) infection. NGS should be recommended to be used in CSF for diagnosing CNS infection.