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    Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach

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    DecuyepreMeehan_BloodMetagenomics_PLOSNTD_2016.PDF (491.6Kb)
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    Publication date
    2016-02-29
    Author
    Decuypere, S.
    Meehan, Conor J.
    Van Puyvelde, S.
    De Block, T.
    Maltha, J.
    Palpouguini, L.
    Tahita, M.
    Tinto, H.
    Jacobs, J.
    Deborggraeve, S.
    Keyword
    Bacterial bloodstream infections
    bBSI
    Diagnosis
    16S metagenomics
    Rights
    © 2016 Decuypere et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. http://creativecommons.org/licenses/by/4.0/
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    Abstract
    Background. Bacterial bloodstream infection (bBSI) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial. We here report a 16S metagenomics approach for diagnosing and understanding bBSI. Methodology/Principal Findings. The proof-of-concept was delivered in 75 children (median age 15 months) with severe febrile illness in Burkina Faso. Standard blood culture and malaria testing were conducted at the time of hospital admission. 16S metagenomics testing was done retrospectively and in duplicate on the blood of all patients. Total DNA was extracted from the blood and the V3–V4 regions of the bacterial 16S rRNA genes were amplified by PCR and deep sequenced on an Illumina MiSeq sequencer. Paired reads were curated, taxonomically labeled, and filtered. Blood culture diagnosed bBSI in 12 patients, but this number increased to 22 patients when combining blood culture and 16S metagenomics results. In addition to superior sensitivity compared to standard blood culture, 16S metagenomics revealed important novel insights into the nature of bBSI. Patients with acute malaria or recovering from malaria had a 7-fold higher risk of presenting polymicrobial bloodstream infections compared to patients with no recent malaria diagnosis (p-value = 0.046). Malaria is known to affect epithelial gut function and may thus facilitate bacterial translocation from the intestinal lumen to the blood. Importantly, patients with such polymicrobial blood infections showed a 9-fold higher risk factor for not surviving their febrile illness (p-value = 0.030). Conclusions/Significance. Our data demonstrate that 16S metagenomics is a powerful approach for the diagnosis and understanding of bBSI. This proof-of-concept study also showed that appropriate control samples are crucial to detect background signals due to environmental contamination.
    URI
    http://hdl.handle.net/10454/17303
    Version
    Published version
    Citation
    Decuypere S, Meehan CJ, Van Puyvelde S et al (2016) Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach. PLoS Neglected Tropical Diseases. 10(2): e0004470.
    Link to publisher’s version
    https://doi.org/10.1371/journal.pntd.0004470
    Type
    Article
    Notes
    This paper has been subject to a correction. Please see Correction file above.
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