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Molecular Virology & Microbiology - Alkek Center for Metagenomics and Microbiome Research

Houston, Texas

A BCM research lab.
Department of Molecular Virology and Microbiology
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Project: Meningitis Etiologic Agent Discovery and Diagnosis

University Association: UT Health
Collaborator Name: Rodrigo Hasbun, M.D.
Email: Rodrigo.Hasbun@uth.tmc.edu

This is a prospective observational study of adults and children admitted to four hospitals in the Texas Medical Center with aseptic meningoencephalitis. Up to 705 of cases do not have an etiology despite the currently available standard evaluation with cultures, serologies and PCR.
The purpose of this study is to attempt to identify infectious bacteria, viruses, and eukaryotes from this meningoencephalitis samples using 3 metagenomic approaches. The following outlines the these methodologies which will be applied to each sample.

  • Nucleic acids from primary samples will be extracted for subsequent metagenomic sequencing of the bacterial, eukaryote, and viral components. Standard genomic DNA kits are used for the isolation of bacterial and eukaryotic nucleic acids, and a filtration/detergent/protease based lysis protocol is used to isolate viral nucleic acids
  • Each sample is then subjected to either random (viral) or targeted (bacteria: 16S rRNA gene, eukaryotes: 18S intergenic spacer region) PCR amplification to augment the appropriate nucleic acids needed to determine the presence of these organisms
  • The Illumina HiSeq platform will be used for viral metagenomic sequencing, and 454 will be used for multiplexed sequencing of the bacterial and eukaryote samples

All sequence data will be analyzed using standard DNA analysis tools for identification of 16S, 18S, and viral sequences. Human data will be filtered and removed.