Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing

Matthew Thoendel, Patricio R. Jeraldo, Kerryl E. Greenwood-Quaintance, Janet Z. Yao, Nicholas D Chia, Arlen D. Hanssen, Matthew Abdel, Robin Patel

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.

Original languageEnglish (US)
Pages (from-to)141-145
Number of pages5
JournalJournal of Microbiological Methods
Volume127
DOIs
StatePublished - Aug 1 2016

Fingerprint

Metagenomics
Genome
Bacterial DNA
DNA
Microbiota
Arthroplasty
Staphylococcus aureus
Joints
Infection

Keywords

  • Clinical samples
  • Enrichment
  • Metagenomics
  • Pathogen detection
  • Whole genome sequencing

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology
  • Microbiology (medical)

Cite this

Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. / Thoendel, Matthew; Jeraldo, Patricio R.; Greenwood-Quaintance, Kerryl E.; Yao, Janet Z.; Chia, Nicholas D; Hanssen, Arlen D.; Abdel, Matthew; Patel, Robin.

In: Journal of Microbiological Methods, Vol. 127, 01.08.2016, p. 141-145.

Research output: Contribution to journalArticle

Thoendel, Matthew ; Jeraldo, Patricio R. ; Greenwood-Quaintance, Kerryl E. ; Yao, Janet Z. ; Chia, Nicholas D ; Hanssen, Arlen D. ; Abdel, Matthew ; Patel, Robin. / Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing. In: Journal of Microbiological Methods. 2016 ; Vol. 127. pp. 141-145.
@article{2c39ccfa059c411cb7ba61c2a3c929a8,
title = "Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing",
abstract = "Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59{\%} of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.",
keywords = "Clinical samples, Enrichment, Metagenomics, Pathogen detection, Whole genome sequencing",
author = "Matthew Thoendel and Jeraldo, {Patricio R.} and Greenwood-Quaintance, {Kerryl E.} and Yao, {Janet Z.} and Chia, {Nicholas D} and Hanssen, {Arlen D.} and Matthew Abdel and Robin Patel",
year = "2016",
month = "8",
day = "1",
doi = "10.1016/j.mimet.2016.05.022",
language = "English (US)",
volume = "127",
pages = "141--145",
journal = "Journal of Microbiological Methods",
issn = "0167-7012",
publisher = "Elsevier",

}

TY - JOUR

T1 - Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing

AU - Thoendel, Matthew

AU - Jeraldo, Patricio R.

AU - Greenwood-Quaintance, Kerryl E.

AU - Yao, Janet Z.

AU - Chia, Nicholas D

AU - Hanssen, Arlen D.

AU - Abdel, Matthew

AU - Patel, Robin

PY - 2016/8/1

Y1 - 2016/8/1

N2 - Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.

AB - Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing.

KW - Clinical samples

KW - Enrichment

KW - Metagenomics

KW - Pathogen detection

KW - Whole genome sequencing

UR - http://www.scopus.com/inward/record.url?scp=84973915626&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84973915626&partnerID=8YFLogxK

U2 - 10.1016/j.mimet.2016.05.022

DO - 10.1016/j.mimet.2016.05.022

M3 - Article

C2 - 27237775

AN - SCOPUS:84973915626

VL - 127

SP - 141

EP - 145

JO - Journal of Microbiological Methods

JF - Journal of Microbiological Methods

SN - 0167-7012

ER -