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The objective of this study was to investigate the microbiome of blood from healthy donors from the Luzhou area in southwestern China. Potential pathogens and cytomegalovirus (CMV) infection in the donor blood were identified. Total plasma nucleic acids were extracted from one pool of 5734 samples and were constructed for metagenomics analysis using Illumina sequencing. The microbiome and potential emerging\/re-emerging pathogens were identified using bioinformatics analysis. Moreover, CMV antigen was measured via an enzyme-linked immunosorbent assay, and the CMV DNA level was assessed by quantitative RT-PCR. A total of 132 bacterial reads, 65 viral reads and 165 parasitic reads were obtained. The most frequent bacterium was <jats:italic>Escherichia coli<\/jats:italic> (95\/132, 72%) with 95 reads in 132 bacterial reads, and the most prevalent parasite was <jats:italic>Toxoplasma gondii<\/jats:italic> (131\/165, 79%). Among the viruses, <jats:italic>cytomegalovirus<\/jats:italic> (44\/65, 68%) accounted for the highest frequency<jats:italic>,<\/jats:italic> followed by <jats:italic>Hepatitis E Virus<\/jats:italic> (10\/65, 15%). Moreover, the positive rate of CMV-IgG was 46.25% (2652\/5734), and the positive rate of CMV-IgM was 5.82% (334\/5734). The positive rate of dual positive (IgG+ and IgM+) CMV was 0.07% (4\/5734). Twenty-one (0.37%) specimens from 5734 donated blood samples were positive for CMV DNA. The CMV DNA levels ranged from 7.56\u2009\u00d7\u200910<jats:sup>2<\/jats:sup> to 3.58\u2009\u00d7\u200910<jats:sup>3<\/jats:sup> copies\/mL. The current study elucidated the microbiome structure in blood from healthy\/qualified donors in the Luzhou area and identified emerging\/re-emerging pathogens. This preliminary study contributes to information regarding blood transfusion safety in China.<\/jats:p>","DOI":"10.1038\/s41598-020-72808-8","type":"journal-article","created":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T10:02:43Z","timestamp":1601028163000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Metagenomic analysis and identification of emerging pathogens in blood from healthy donors"],"prefix":"10.1038","volume":"10","author":[{"given":"Min","family":"Xu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Gao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shilin","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianming","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mao","family":"Luo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2020,9,25]]},"reference":[{"key":"72808_CR1","first-page":"420","volume":"13","author":"SL Stramer","year":"2015","unstructured":"Stramer, S. 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