Navigating diagnostic quandaries: A case series of diagnostic dilemmas in central nervous system (CNS) infections resolved by molecular sequencing

Central nervous system (CNS) infections present a significant diagnostic challenge due to their diverse etiologies and the limitations of conventional diagnostic methods. Standard cerebrospinal fluid (CSF) culture and polymerase chain reaction (PCR) assays often fail to identify causative pathogens, particularly in patients who have received prior antimicrobial therapy. The advent of 16S and 18S ribosomal RNA (rRNA) sequencing has revolutionized microbial identification by enabling the detection of a wide range of bacterial and fungal pathogens with high sensitivity and specificity. We present a retrospective case series of six patients with CNS infections that remained undiagnosed using conventional microbiological methods but were successfully identified using molecular sequencing. Clinical presentations, CSF findings, imaging studies, and treatment outcomes were analyzed to assess the impact of 16S/18S rRNA sequencing on diagnosis and patient management. Pathogens identified through sequencing included Klebsiella pneumoniae , Moraxella osloensis , Streptococcus intermedius , Candida albicans , Streptococcus pneumoniae , Brucella melitensis , and Brucella abortus . In all cases, sequencing enabled targeted antimicrobial therapy, leading to favorable clinical outcomes. This method proved particularly useful in cases of partially treated bacterial meningitis, fungal CNS infections, and neurobrucellosis, where standard diagnostics failed. Molecular sequencing serves as a powerful diagnostic tool for CNS infections, especially in culture-negative cases. Its implementation enhances pathogen detection, guides appropriate antimicrobial therapy, and improves clinical outcomes. As sequencing technology becomes more accessible, its integration into routine diagnostic workflows may redefine the approach to CNS infection management. • Molecular sequencing aids diagnosis in culture-negative CNS infections, resolving key diagnostic challenges. • Precise microbial identification enables targeted therapy and reduces reliance on empirical treatment. • Faster, accurate diagnosis can lead to earlier therapy, improving outcomes in CNS infections.