Complex Microbiome in Brain Abscess Revealed by Whole-Genome Culture-Independent and Culture-Based Sequencing

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Brain abscess is a serious infection with significant mortality and morbidity.
• Traditional culture-based methods for identifying microbes in brain abscess are limited and biased.
• Previous studies using 16S ribosomal sequencing highlighted bacterial complexity but missed fungal and viral pathogens.

Purpose of the Study:

• To comprehensively investigate the microbial composition and genomic characteristics of brain abscess using both culture-independent and culture-based sequencing methods.
• To identify novel microbial species and antibiotic resistance genes within brain abscess samples.
• To expand the understanding of the full spectrum of microorganisms involved in brain abscess.

Main Methods:

• Utilized culture-independent nanopore metagenomic sequencing to analyze microbial communities.
• Employed culture-based whole-genome sequencing on both Illumina and Nanopore platforms.
• Investigated genomic characterization, including novel species identification and antibiotic resistance gene detection.

Main Results:

• Culture-independent sequencing revealed greater bacterial diversity and identified fungal and viral communities.
• Culture-based sequencing identified a novel *Prevotella* species and reconstructed a *Streptococcus constellatus* genome.
• Detected antibiotic resistance genes (*CfxA*, *ErmF*) conferring resistance to penicillin and clindamycin in both sequencing approaches.

Conclusions:

• Brain abscess involves a more diverse range of microorganisms than previously recognized, including bacteria, fungi, and viruses.
• Genomic analysis provides insights into novel species and antibiotic resistance mechanisms.
• Current understanding of brain abscess pathogenesis and treatment should incorporate this broader microbial diversity.