Abstract Details

Title Shallow-depth Metagenomic Sequencing of Cerebrospinal Fluid for CNS Infection Diagnosis in Lima, Peru

Topic Infectious Disease

Presentation(s) S22 - Neuroinfectious Disease: Basic Sciences (2:48 PM-3:00 PM)

Poster/Presentation
Number 010

Objective To assess the diagnostic value of shallow-depth cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) for central nervous system (CNS) infections in Lima, Peru.

Background CNS infections remain diagnostically challenging, particularly in low- and middle-income countries. mNGS enables broad-range pathogen detection with a single test. Shallow-depth mNGS offers a cost-effective approach that could facilitate wider adoption, but its diagnostic performance remains unknown.

Design/Methods Adult patients with suspected CNS infection and surplus CSF (after routine clinical testing) were enrolled at Hospital Nacional Dos de Mayo. Patients who received antibiotics for >7 days before lumbar puncture were excluded. DNA/RNA extraction, library preparation, pooling, and sequencing (Illumina NextSeq 500/550) were preformed locally at Universidad Peruana Cayetano Heredia. Sequencing data were processed using the open-source Chan-Zuckerberg ID software for pathogen detection via computational filtering and manual review.

Results Forty-three patients were included (32.6% female; median age 47.5). RNA libraries were sequenced in one run with mean depth of 13,033,943 reads per sample (SD 9,110,614), while DNA libraries were sequenced in two runs with mean depth of 30,203,814 reads per sample (SD 18,643,933). Pathogens were detected via mNGS in 51.1% of patients (n=22), including 41.2% diagnosed exclusively by mNGS. Nine patients with probable or possible tuberculous meningitis were found to have alternative non-tuberculous infections. Many pathogens detected exclusively via mNGS represent treatable conditions with medications available through the Peruvian public health system, including cerebral toxoplasmosis, neurocysticercosis, neurosyphilis, and varicella zoster virus.

Conclusions Shallow-depth CSF mNGS demonstrated substantial diagnostic utility in a resource-limited setting, identifying pathogens in over half of cases and providing exclusive diagnostic information in over 40% of patients, supporting its potential for broader implementation in CNS infection diagnosis. Further validation of these results is underway, including direct comparison to deeper sequencing depths more traditionally used in clinically available mNGS assays.

Authors/Disclosures
Sumanth Reddy, MD PRESENTER	Dr. Reddy has nothing to disclose.
Michael R. Wilson, MD, FAAN (University of California San Francisco)	Dr. Wilson has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Pfizer. Dr. Wilson has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Ouro Medicines. Dr. Wilson has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Vertex Pharmaceuticals. Dr. Wilson has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Indapta Therapeutics. Dr. Wilson has received personal compensation in the range of $50,000-$99,999 for serving as an officer or member of the Board of Directors for Delve Bio. Dr. Wilson has received personal compensation in the range of $500-$4,999 for serving as an Expert Witness for Cambridge Medical Experts. Dr. Wilson has received personal compensation in the range of $5,000-$9,999 for serving as an Expert Witness for Dunham Hallmark. Dr. Wilson has stock in Delve Bio. The institution of Dr. Wilson has received research support from Genentech / Roche. The institution of Dr. Wilson has received research support from NIH. The institution of Dr. Wilson has received research support from Novartis. The institution of Dr. Wilson has received research support from National Multiple Sclerosis Society. The institution of Dr. Wilson has received research support from Fanconi Anemia Research Foundation. The institution of Dr. Wilson has received research support from Department of Defense. The institution of Dr. Wilson has received research support from Chan Zuckerberg Initiative. The institution of Dr. Wilson has received research support from Kyverna Therapeutics. Dr. Wilson has received intellectual property interests from a discovery or technology relating to health care. Dr. Wilson has received intellectual property interests from a discovery or technology relating to health care. Dr. Wilson has received personal compensation in the range of $10,000-$49,999 for serving as a Expert Witness with US Dept of Justice.
Renzo J. Villanueva Villegas, Sr., MD	Dr. Villanueva Villegas has nothing to disclose.

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