Abstract 107: Exploring Non-Human DNA Content in Cerebral Thrombi Using Shotgun Metagenomic Sequencing

Stroke, Volume 55, Issue Suppl_1, Page A107-A107, February 1, 2024. Introduction:Prior studies that use 16S rRNA amplicon sequencing to profile bacterial components of cerebral thrombi do not provide species-level taxonomic information or functional gene content, which are critical for the development of subsequent clinical applications. To determine the amount and taxonomic nature of non-human DNA in cerebral thrombi, shotgun metagenomic sequencing was performed on specimens retrieved from ischemic stroke patients.Methods:Thrombi were retrieved during standard of care thrombectomy and preserved in DNA/RNA Shield (Zymo), alongside environmental controls. DNA was extracted per manufacturer instructions, using Zymo kits. Quality control was carried out using Bowtie2 and the bbtools suite. To clump reads, bbmap was applied. Sequencing adapter contamination was removed with bbduk. Data was aligned to the human reference genome (hg38) using Bowtie2. Tadpole (mode=correct, ecc=t, ecco=t) was used to correct sequencing errors. MetaSPAdes was used to assemble quality-controlled sequencing reads into contigs. CAT/BAT was then applied to annotate contigs and their Open Reading Frames (ORF) taxonomically using the Lowest Common Ancestor approach.Results:Of the 41 specimens, N = 31 met quality control. The preponderance of DNA sequencing reads mapped to the human genome. An average of 7,559,292 +/- 1,615,7061 (9.1%) reads per sample did not align (Fig 1A). Contigs resulting fromde novoassemblies of these potentially non-human reads contained sequences consistent with bacterial ORFs. The number of these ORFs varied per sample (Fig 1B) and correlated with the number of non-human reads.ProteobacteriaandFirmicutesdominated. (Fig 1C).Conclusion:While much work remains to optimize sequencing techniques and controls, the potential to recover near-complete bacterial genomes from thrombus presents an opportunity to further explore the human host-microbiota interactions in acute ischemic stroke.

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Febbraio 2024

LIQUID-BIOPSY FOR ASSESSING SEVERITY OF INFLAMMATORY BOWEL DISEASE VIA PLASMA MICROBIAL CELL-FREE DNA

Plasma cell-free DNA (cfDNA) has emerged as a robust biomarker utilized in multiple applications that span cancer screening, diagnosis and monitoring, prenatal testing, and characterization of organ health post-transplantation. Cell-free DNA-based assays leverage the occurrence of processed extracellular DNA that produce unique signatures to discern a variety of biological states, disease manifestations, as well as forms of cell death. Similar to human cells, microbes produce cfDNA when they turnover, providing evident clinical utility in diagnosing and treating deep-seated infections in immunocompromised patients.

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Gennaio 2024