A metagenomic DNA sequencing assay that is robust against environmental DNA contamination
Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse, Joan Sesing Lenz, Randy Longman, Amy Steadman, Luis G. Gómez-Escobar, Edward J. Schenck, Mirella Salvatore, Michael J. Satlin, Manikkam Suthanthiran, John R. Lee, Christopher E. Mason, Darshana M. Dadhania, Iwijn De Vlaminck
Abstract
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.