A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood

Ofir Israeli; Efi Makdasi; Inbar Cohen-Gihon; Anat Zvi; Shirley Lazar; Ohad Shifman; Haim Levy; David Gur; Orly Laskar; Adi Beth-Din

doi:10.2144/fsoa-2020-0013

A rapid high-throughput sequencing-based approach for the identification of unknown bacterial pathogens in whole blood

Future Sci OA. 2020 Apr 29;6(6):FSO476. doi: 10.2144/fsoa-2020-0013.

Authors

Affiliations

¹ Department of Biochemistry & Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel.
² Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel.

Abstract

High-throughput DNA sequencing (HTS) of pathogens in whole blood samples is hampered by the high host/pathogen nucleic acids ratio. We describe a novel and rapid bacterial enrichment procedure whose implementation is exemplified in simulated bacteremic human blood samples. The procedure involves depletion of the host DNA, rapid HTS and bioinformatic analyses. Following this procedure, Y. pestis, F. tularensis and B. anthracis spiked-in samples displayed an improved host/pathogen DNA ratio of 2.5-5.9 orders of magnitude, in samples with bacteria spiked-in at 10³-10⁵ CFU/ml. The procedure described in this study enables rapid and detailed metagenomic profiling of pathogens within 8-9 h, circumventing the challenges imposed by the high background present in the bacteremic blood and by the unknown nature of the sample.

Keywords: B. anthracis; F. tularensis; Y. pestis; bacteremia; high-throughput DNA sequencing; host/pathogen DNA ratio; whole blood samples.