title: Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Telethon Kids Institute, University of Western Australia, Perth, Australia.
authors.forename: Saskia
authors.initials: S
authors.lastname: Decuypere
authors.affiliation: Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.
authors.forename: Conor J
authors.initials: CJ
authors.lastname: Meehan
authors.affiliation: Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.
authors.forename: Sandra
authors.initials: S
authors.lastname: Van Puyvelde
authors.affiliation: Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.
authors.forename: Tessa
authors.initials: T
authors.lastname: De Block
authors.affiliation: Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.|Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium.
authors.forename: Jessica
authors.initials: J
authors.lastname: Maltha
authors.affiliation: Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso.
authors.forename: Lompo
authors.initials: L
authors.lastname: Palpouguini
authors.affiliation: Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso.
authors.forename: Marc
authors.initials: M
authors.lastname: Tahita
authors.affiliation: Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso.
authors.forename: Halidou
authors.initials: H
authors.lastname: Tinto
authors.affiliation: Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.|Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Jacobs
authors.affiliation: Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.
authors.forename: Stijn
authors.initials: S
authors.lastname: Deborggraeve
mesh_terms: D016470:Bacteremia / Q000175:diagnosis* / Q000382:microbiology; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D001424:Bacterial Infections / Q000175:diagnosis* / Q000382:microbiology; D002675:Child, Preschool; D004269:DNA, Bacterial / Q000235:genetics*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D056186:Metagenomics / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S