16S metagenomics for diagnosis of bloodstream infections: opportunities and pitfalls

ABSTRACT

Introduction: Bacterial bloodstream infections (BSI) form a large public health threat worldwide. Current routine diagnosis is based on blood culture (BC) but this technique suffers from limited sensitivity. Molecular diagnostic tools have been developed for identification of bacteria in the blood of BSI patients. 16S metagenomics is an open-ended technique that can detect simultaneously all bacteria in a given sample based on PCR amplification of the 16S ribosomal RNA gene (rDNA) followed by sequencing of the PCR amplicons and taxonomic labeling of the sequence reads at genus or species level.

Areas covered: Here we review the studies that have used 16S metagenomics for the identification of bacteria in human blood samples. We also discuss the potential added value of 16S metagenomics in the diagnosis of BSI, challenges as well as future directions for implementation in clinical settings.

Expert commentary: 16S metagenomics has the potential to complement conventional BC; however, the technique currently suffers from several technical limitations jeopardizing implementation in routine clinical microbiology laboratories. Further studies are required to assess the cost-efficiency and clinical impact of 16S metagenomics in comparison to BC which remains the gold standard diagnostic method for BSI.

KEYWORDS:

• Bacterial bloodstream infections
• molecular diagnosis
• sepsis
• 16S metagenomics
• 16S rRNA gene

Declaration of interest

JP Rutanga has a PhD fellowship of the Belgian Directorate General for Development (DGD) and AS Heroes has a FWO-SB PhD fellowship of the Research Foundation Flanders (FWO). S Deborggraeve is a member of the Bacterial Infections in the Tropics (BIT) research cluster at ITM Antwerp, supported by the InBev-Baillet Latour (IBL) Fund. S Van Puyvelde has received postdoctoral scientist fellowship supported by the Department of Economy, Science and Innovation in Flanders (EWI funding, ITM Antwerp). J Jacobs is a member of the Bacterial Infections in the Tropics (BIT) research cluster at ITM Antwerp, supported by the InBev-Baillet Latour (IBL) Fund. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. Peer reviewers on this manuscript have no relevant financial or other relationships to disclose.

Additional information

Funding

This work was financially supported by the InBev-Baillet Latour (IBL) Fund for the Bacterial Infections in the Tropics (BIT) research cluster at the Institute of Tropical Medicine (ITM), Antwerp, Belgium, and the Department of Economy, Science and Innovation in Flanders (EWI funding ITM Antwerp).