PLoS Negl Trop Dis. 2016 Feb 29;10(2):e0004470. doi: 10.1371/journal.pntd.0004470. eCollection 2016 Feb.

Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach.

Decuypere S1, Meehan CJ2, Van Puyvelde S2, De Block T2, Maltha J3,4, Palpouguini L5, Tahita M5, Tinto H5, Jacobs J3,6, Deborggraeve S2.

1Telethon Kids Institute, University of Western Australia, Perth, Australia.

2Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.

3Clinical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerpen, Belgium.

4Center for Molecular and Vascular Biology, KU Leuven, Leuven, Belgium.

5Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso.

6Department of Immunology and Microbiology, KU Leuven, Leuven, Belgium.

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.

PMID:

26927306

PMCID:

PMC4771206

DOI:

10.1371/journal.pntd.0004470