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PLoS One. 2019 Oct 2;14(10):e0222915. doi: 10.1371/journal.pone.0222915. eCollection 2019.

Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples.

Author information

1
Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, United States of America.
2
Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America.
3
Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America.
4
Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, United States of America.

Abstract

BACKGROUND:

Vector-borne pathogens are a significant public health concern worldwide. Infections with these pathogens, some of which are emerging, are likely under-recognized due to the lack of widely-available laboratory tests. There is an urgent need for further advancement in diagnostic modalities to detect new and known vector-borne pathogens. We evaluated the utility of metagenomic shotgun sequencing (MGS) as a pathogen agnostic approach for detecting vector-borne pathogens from human blood samples.

METHODS:

Residual whole blood samples from patients with known infection with Babesia microti, Borrelia hermsii, Plasmodium falciparum, Mansonella perstans, Anaplasma phagocytophilum or Ehrlichia chaffeensis were studied. Samples underwent DNA extraction, removal of human DNA, whole genome amplification, and paired-end library preparation, followed by sequencing on Illumina HiSeq 2500. Bioinformatic analysis was performed using the Livermore Metagenomics Analysis Toolkit (LMAT), Metagenomic Phylogenetic Analysis (MetaPhlAn2), Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) and Kraken 2.

RESULTS:

Eight samples were included in the study (2 samples each for P. falciparum and A. phagocytophilum). An average of 27.5 million read pairs was generated per sample (range, 18.3-38.8 million) prior to removal of human reads. At least one of the analytic tools was able to detect four of six organisms at the genus level, and the organism present in five of eight specimens at the species level. Mansonella and Ehrlichia species were not detected by any of the tools; however, mitochondrial cytochrome c oxidase subunit I amino acid sequence analysis suggested the presence of M. perstans genetic material.

CONCLUSIONS:

MGS is a promising tool with the potential to evolve as a non-hypothesis driven diagnostic test to detect vector-borne pathogens, including protozoa and helminths.

PMID:
31577814
DOI:
10.1371/journal.pone.0222915
Free PMC Article

Conflict of interest statement

The authors have read the journal's policy and the authors of this manuscript have the following competing interests: RP reports grants from CD Diagnostics, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, ContraFect, TenNor Therapeutics Limited and Shionogi. RP is a paid consultant of Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, and Qvella; monies are paid to Mayo Clinic. RP receives travel reimbursement from ASM and IDSA, an editor’s stipend from ASM and IDSA, and honoraria from the NBME, Up-to-Date and the Infectious Diseases Board Review Course. The authors would like to declare the following patents/patent applications, none of which are associated with this research: Bordetella pertussis/parapertussis PCR issued [8507201], a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic [8076117], and a patent on an anti-biofilm substance issued [8802414]. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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