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Mycobacteriology and Aerobic Actinomycetes

Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis

Carol Smith, Tanya A. Halse, Joseph Shea, Herns Modestil, Randal C. Fowler, Kimberlee A. Musser, Vincent Escuyer, Pascal Lapierre
Geoffrey A. Land, Editor
Carol Smith
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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Tanya A. Halse
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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Joseph Shea
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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Herns Modestil
bNew York City Bureau of Tuberculosis Control, New York City, New York, USA
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Randal C. Fowler
cNew York City Public Health Laboratory, Department of Health and Mental Hygiene, New York City, New York, USA
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Kimberlee A. Musser
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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  • ORCID record for Kimberlee A. Musser
Vincent Escuyer
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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Pascal Lapierre
aWadsworth Center, New York State Department of Health, Albany, New York, USA
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Geoffrey A. Land
Carter BloodCare & Baylor University Medical Center
Roles: Editor
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DOI: 10.1128/JCM.00583-20
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ABSTRACT

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of Mycobacterium tuberculosis isolates for species identification, in silico spoligotyping, detection of mutations associated with antimicrobial resistance (AMR) to accurately predict drug susceptibility profiles, and phylogenetic analysis to detect transmission between cases. The results were compared prospectively in real time to those obtained with our current clinically validated Illumina MiSeq sequencing assay for M. tuberculosis and phenotypic drug susceptibility testing results when available. Our assessment of 431 sequenced samples over a 32-week period demonstrates that, when using the proper quality controls and thresholds, the MinION can achieve levels of genotyping analysis and phenotypic resistance predictions comparable to those of the Illumina MiSeq at a very competitive cost per sample. Our results indicate that nanopore sequencing can be a suitable alternative to, or complement, currently used sequencing platforms in a clinical setting and has the potential to be widely adopted in public health laboratories in the near future.

FOOTNOTES

    • Received 26 March 2020.
    • Returned for modification 11 June 2020.
    • Accepted 6 October 2020.
    • Accepted manuscript posted online 14 October 2020.
  • Supplemental material is available online only.

  • Copyright © 2020 American Society for Microbiology.

All Rights Reserved.

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Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis
Carol Smith, Tanya A. Halse, Joseph Shea, Herns Modestil, Randal C. Fowler, Kimberlee A. Musser, Vincent Escuyer, Pascal Lapierre
Journal of Clinical Microbiology Dec 2020, 59 (1) e00583-20; DOI: 10.1128/JCM.00583-20

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Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis
Carol Smith, Tanya A. Halse, Joseph Shea, Herns Modestil, Randal C. Fowler, Kimberlee A. Musser, Vincent Escuyer, Pascal Lapierre
Journal of Clinical Microbiology Dec 2020, 59 (1) e00583-20; DOI: 10.1128/JCM.00583-20
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KEYWORDS

clinical study
MinION
Mycobacterium tuberculosis
nanopore
public health laboratories
whole-genome sequence

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