{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T06:31:55Z","timestamp":1791354715917,"version":"4.3.1"},"reference-count":28,"publisher":"American Society for Microbiology","issue":"4","license":[{"start":{"date-parts":[[2016,4,1]],"date-time":"2016-04-01T00:00:00Z","timestamp":1459468800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"BC Children's Hospital Foundation","award":["KRZ28061"],"award-info":[{"award-number":["KRZ28061"]}]},{"name":"BC Clinical Genomics Network","award":["BCCGN00032"],"award-info":[{"award-number":["BCCGN00032"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2016,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (&gt;95%;\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.05) and improved the sensitivity of pathogen detection (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.\n          <\/jats:p>","DOI":"10.1128\/jcm.03050-15","type":"journal-article","created":{"date-parts":[[2016,1,14]],"date-time":"2016-01-14T09:57:12Z","timestamp":1452765432000},"page":"919-927","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":238,"title":["Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing"],"prefix":"10.1128","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4658-7949","authenticated-orcid":false,"given":"Mohammad R.","family":"Hasan","sequence":"first","affiliation":[{"name":"Department of Pathology, Sidra Medical and Research Center, Doha, Qatar"},{"name":"Weill Cornell Medical College in Qatar, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arun","family":"Rawat","sequence":"additional","affiliation":[{"name":"Division of Biomedical Informatics Research, Sidra Medical and Research Center, Doha Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sidra Medical and Research Center, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Puthen V.","family":"Jithesh","sequence":"additional","affiliation":[{"name":"Division of Biomedical Informatics Research, Sidra Medical and Research Center, Doha Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Thomas","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sidra Medical and Research Center, Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rusung","family":"Tan","sequence":"additional","affiliation":[{"name":"Department of Pathology, Sidra Medical and Research Center, Doha, Qatar"},{"name":"Children's and Women's Health Centre of BC, PHSA, Vancouver, British Columbia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Tilley","sequence":"additional","affiliation":[{"name":"Children's and Women's Health Centre of BC, PHSA, Vancouver, British Columbia, Canada"},{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3068"},{"key":"e_1_3_2_3_2","volume-title":"Manual of clinical microbiology","author":"Nolte FS","year":"2010","unstructured":"Nolte FS, Caliendo AM. 2010. Molecular microbiology. In Versalovic J, Carroll KC, Jorgensen JH, Funke G, Landry ML, Warnock DW (ed), Manual of clinical microbiology, vol 1. ASM Press, Washington, DC."},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0130378"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cll.2015.02.006"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2014.08.010"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00352-14"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00032-09"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/9781555815455"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00273-11"},{"key":"e_1_3_2_11_2","first-page":"493","article-title":"A simple method of estimating fifty percent endpoints","volume":"27","author":"Reed LJ","year":"1938","unstructured":"Reed LJ, Muench H. 1938. A simple method of estimating fifty percent endpoints. Am J Hygiene 27:493\u2013497.","journal-title":"Am J Hygiene"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02464-09"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1006\/meth.2001.1262"},{"key":"e_1_3_2_14_2","unstructured":"Andrews S. 2010. FastQC: a quality control tool for high-throughput sequence data. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0110915"},{"key":"e_1_3_2_17_2","first-page":"1","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li H","year":"2013","unstructured":"Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio.GN] 00:1\u20133.","journal-title":"arXiv:1303.3997 [q-bio.GN] 00"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02498-06"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1513\/AnnalsATS.201406-288FR"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2015.07.004"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1097\/PAT.0000000000000235"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2014.00025"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2013.10.006"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2013.03.003"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.anaerobe.2009.04.009"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.06087-11"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/763128"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.20365"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1002\/jmv.10382"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.03050-15","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.03050-15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T09:50:53Z","timestamp":1646473853000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.03050-15"}},"subtitle":[],"editor":[{"given":"N. 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