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 R. Greig, Claire Jenkins, Saheer Gharbia, Timothy J. Dallman*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

28 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

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

Keywords

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

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