Abstract
BACKGROUND: Encephalitis is a significant global cause of morbidity and often causes permanent neurological deficits. It can stem from diverse viral and bacterial infections, with the mortality rate varying by region due to differences in prevalent pathogens. In Bangladesh, the Nipah virus, an endemic zoonotic pathogen in the region, has an alarming case fatality rate exceeding 75% and causes recurrent encephalitis outbreaks. Many encephalitis cases associated with a history of consuming raw date palm sap remain undiagnosed, suggesting that pathogens other than Nipah virus - including Streptococcus pneumoniae - may also play important roles. Conventional diagnostic methods for S. pneumoniae are time-consuming and costly, and handling samples that may contain potentially high-risk pathogens such as Nipah virus remains challenging in low-resource settings. The recent expansion of molecular biology infrastructure post-COVID-19 offers new opportunities for rapid, non-culture-based diagnostics. [Figure: see text] [Figure: see text] METHODS: We developed a real-time qPCR-based approach for the detection and characterization of viral and bacterial pathogens and antimicrobial resistance (AMR) genes in cerebrospinal fluid (CSF) samples of suspected encephalitic cases. A total of 520 CSF samples were considered for this study, collected between June 2024 and January 2025. RESULTS: Out of 520 samples, 35 tested positive forS. pneumoniae through detection of the lytA gene, with 22 serotypes (considering PCV-10, 13, and 23) accurately identified. Additionally, we characterized 33 AMR genes associated with resistance to beta-lactams, macrolides, glycopeptides, fluoroquinolones, and tetracyclines. CONCLUSION: Our findings highlight the importance of rapid, cost-effective molecular diagnostics in resource-limited settings. This approach facilitates early therapeutic decision- making by bypassing traditional culture-based methods. It also underscores the need for strengthened antibiotic stewardship and timely clinical intervention for critically ill patients in Bangladesh and similar contexts. DISCLOSURES: All Authors: No reported disclosures