MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

Shaoyuan Tan, Cheryl M.T. Dvorak, April A. Estrada, Connie Gebhart, Douglas G. Marthaler, Michael P. Murtaugh

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information. The Oxford Nanopore MinION sequencer has unparalleled potential as a rapid disease diagnostic tool due to its high mobility, accessibility, and short turnaround time. However, there is a lack of rigorous quality assessment and control processes standardizing the testing on the MinION, which is necessary for incorporation into a diagnostic workflow. Thus, our study examined the use of the MinION sequencer for bacterial whole genome generation and characterization. Using Streptococcus suis as a model, we optimized DNA isolation and treatments to be used for MinION sequencing and standardized de novo assembly to quickly generate a full-length consensus sequence achieving a 99.4% average accuracy. The consensus genomes from MinION sequencing were able to accurately predict the multilocus sequence type in 8 out of 10 samples and identified antimicrobial resistance profiles for 100% of the samples, despite the concern of a high error rate. The inability to unequivocally predict sequence types was due to difficulty in differentiating high identity alleles, which was overcome by applying additional error correction methods to increase consensus accuracy. This manuscript provides methods for the use of MinION sequencing for identification of S. suis genome sequence, sequence type, and antibiotic resistance profile that can be used as a framework for identification and classification of other pathogens.

Original languageEnglish (US)
Article number105817
JournalJournal of Microbiological Methods
Volume169
DOIs
StatePublished - Feb 2020

Bibliographical note

Funding Information:
National Pork Board Grant number 18-040 , Boehringer Ingelheim Vetmedica, Inc. Grant, MnDRIVE Global Food Ventures Fellowship awarded to ST, and University of Minnesota Veterinary Population Medicine Department Leman China student support awarded to ST.

Funding Information:
The authors would like to thank the University of Minnesota Veterinary Diagnostic Laboratory for providing samples for testing. The authors acknowledge the Minnesota Supercomputing Institute (MSI) at the University of Minnesota for providing resources that contributed to the research results reported within this paper. URL: http://www.msi.umn.edu. National Pork Board Grant number 18-040, Boehringer Ingelheim Vetmedica, Inc. Grant, MnDRIVE Global Food Ventures Fellowship awarded to ST, and University of Minnesota Veterinary Population Medicine Department Leman China student support awarded to ST. MPM conceived the idea. MPM and CMTD supervised and administered the project. ST conducted all the research, and was responsible for experiments, analysis, visualization and preparing the original draft. CMTD revised the manuscript. AE provided S. suis isolates and Illumina raw sequencing data. DGM and CG provided important suggestions for S. suis MLST and AMR analysis. Funding acquisition: MPM, CMTD and ST. All authors have edited and commented on the manuscript. All authors have read and approved the final version of the manuscript. The authors declare that there are no conflicts of interest.

Publisher Copyright:
© 2019 Elsevier B.V.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Keywords

  • Antimicrobial resistance (AMR)
  • MinION
  • Oxford nanopore
  • S. suis
  • Sequence typing
  • Sequencing

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't

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