A Rapid high-throughput sequencing-based Approach for the Identification of Unknown Bacterial Pathogens in Whole Blood | Zendy

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

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A Rapid high-throughput sequencing-based Approach for the Identification of Unknown Bacterial Pathogens in Whole Blood

Author(s) -

Ofir Israeli,

Efi Makdasi,

Inbar Cohen-Gihon,

Anat Zvi,

Shirley Lazar,

Ohad Shifman,

Haim Levy,

David Gur,

Orly Laskar,

Adi Beth-Din

Publication year - 2020

Publication title -

future science oa

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.825

H-Index - 23

ISSN - 2056-5623

DOI - 10.2144/fsoa-2020-0013

Subject(s) - biology , metagenomics , pathogen , microbiology and biotechnology , nucleic acid , dna sequencing , bacteria , dna , dna extraction , whole blood , computational biology , polymerase chain reaction , gene , genetics , immunology

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 10 3 –10 5 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.

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