P-1994. Faster than Culture. Use of 16/ITS Next-Generation Sequencing for Rapid Identification of Pathogens Directly from Brain/Cerebellar Samples

TL;DR

This study shows that next-generation sequencing can identify brain abscess pathogens faster and more effectively than traditional culture methods.

Contribution

The study demonstrates the clinical utility of 16S/ITS NGS as a rapid diagnostic tool for brain and cerebellar abscesses.

Findings

NGS identified pathogens in 63.3% of brain samples within 3 days, outperforming culture results.

NGS detected organisms in culture-negative cases, including Streptococcus intermedius and Klebsiella pneumoniae.

Resistance markers like mecA and CTX-M were not detected in identified pathogens.

Abstract

It is of critical importance to accurately and timely provide organism identification for brain and cerebellar abscess. Rapid and appropriate identification of causative organisms is crucial for guiding effective treatment strategies and improving patient outcomes. However, traditional culture-based diagnostic methods often face significant challenges, including low sensitivity, extended turnaround times, and inability to detect fastidious or anaerobic pathogens, leading to delayed or inappropriate treatment. Next-generation sequencing (NGS) can detect a wide range of organisms, including bacteria, mycobacteria, and fungi, even in culture-negative cases. In this study, we compare the result of NGS performed directly on brain aspirate/tissue samples against traditional culture.

A total of 11 tissues or swabs from brain or cerebellar cortex were sent for 16S/ITS NGS (MicroGenDX) testing by AdventHealth Orlando from June 2023 to September 2024. This test is based on a qPCR (Level 1) that includes antimicrobial resistance genes and 16S/ITS (Level 2) with a 3-day turnaround time. All samples were cultured in aerobic and anaerobic conditions in-house on tissue/surgical culture and held for 5 days.

7/11 (63.3%) samples were positive by 16S/ITS. Four Streptococcus intermedius, one Cutibacterium acnes, one Staphylococcus aureus, and one Klebsiella pneumoniae. 5/11 (45.6%) samples were also positive on culture for two S. intermedium, S. aureus, and K. pneumoniae. Resistance markers were performed by PCR along with 16S/ITS. mecA gene for S. aureus and CTX-M, KPC and NDM for K. pneumoniae were not detected.

16S/ITS NGS identified an infectious organism in 63.3% (7/11) of brain samples directly from the specimen, 45.6% (5/11) of the samples were also positive on culture. The absences of mecA, CTX-M, KPC, and NDM were confirmed by phenotypical susceptibility of the S. aureus and K. pneumoniae. NGS turnaround time of 3 days returned a clinically significant and correlating result faster when compared to culture, with an average of 5.5 days. For rapid organism identification, NGS seamlessly complements culture, offering faster and clinically actionable results for brain samples enabling prompt antimicrobial intervention.

All Authors: No reported disclosures