Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin-producing Escherichia coli

David Greig, Claire Jenkins, Saheer Gharbia, Tim Dallman*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

16 Citations (Scopus)

Abstract

Background: We aimed to compare Illumina and Oxford Nanopore Technology sequencing data from the 2 isolates of Shiga toxin-producing Escherichia coli (STEC) O157:H7 to determine whether concordant single-nucleotide variants were identified and whether inference of relatedness was consistent with the 2 technologies. Results: For the Illumina workflow, the time from DNA extraction to availability of results was ∼40 hours, whereas with the ONT workflow serotyping and Shiga toxin subtyping variant identification were available within 7 hours. After optimization of the ONT variant filtering, on average 95% of the discrepant positions between the technologies were accounted for by methylated positions found in the described 5-methylcytosine motif sequences, CC(A/T)GG. Of the few discrepant variants (6 and 7 difference for the 2 isolates) identified by the 2 technologies, it is likely that both methodologies contain false calls. Conclusions: Despite these discrepancies, Illumina and Oxford Nanopore Technology sequences from the same case were placed on the same phylogenetic location against a dense reference database of STEC O157:H7 genomes sequenced using the Illumina workflow. Robust single-nucleotide polymorphism typing using MinION-based variant calling is possible, and we provide evidence that the 2 technologies can be used interchangeably to type STEC O157:H7 in a public health setting.

Original languageEnglish
Article numbergiz104
JournalGigaScience
Volume8
Issue number8
DOIs
Publication statusPublished - 1 Aug 2019

Bibliographical note

Funding Information:
The research was part funded by the National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England (PHE), in collaboration with University of East Anglia, University of Oxford and the Quadram Institute. Claire Jenkins and Timothy Dallman are based at Public Health England. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England.

Funding Information:
This project was part funded by Oxford Nanopore Technologies.

Publisher Copyright:
© 2019 The Author(s) 2019. Published by Oxford University Press.

Keywords

  • Illumina
  • Oxford Nanopore
  • STEC
  • outbreak
  • variant calling

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