The effect of contaminated reference genomes in clinical metagenomics (Item B)

The importance of using curated microbial reference genome databases. <br> Classifying unfiltered quality trimmed reads using a Kraken database composed of non-curated microbial reference genomes and the human reference results in the identification of many reads that are mapping to <i>Toxoplasma gondii</i> and <i>Plasmodium vivax</i>. In fact, these genomes recruit more reads than the causing agent <i>Enterococcus faecalis</i>. The classification is improved when human DNA sequences are filtered out prior to classification and a cleaned reference database is used.<br>The sankey diagrams were created using Pavian (https://www.biorxiv.org/content/early/2016/10/31/084715). <br><br><p><b>Reference</b></p> <p><b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b><b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.</p