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Volume 7, Issue 11

Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Open Access

Abstract

Whole-genome sequencing (WGS) of (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performance of long-read (LR) and/or short-read (SR) sequencing for anti-TB drug-resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core-genome SNP (cgSNP) typing and core-genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic drug-susceptibility testing (DST) and drug-resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR- and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (<0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug-resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): cgMLST , cgSNP typing , de novo assembly , drug-resistance prediction , Mycobacterium tuberculosis and nanopore sequencing
Funding
This study was supported by the:
  • Stichting Beatrixoord Noord-Nederland
    • Principle Award Recipient: NotApplicable
  • H2020-MSCA-COFUND-2015 (Award 713660)
    • Principle Award Recipient: LeonardSchuele
  • H2020-MSCA-COFUND-2015 (Award 713660)
    • Principle Award Recipient: NilayPeker
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis
M Gen 7, 000695 (2021); https://doi.org/10.1099/mgen.0.000695
/content/journal/mgen/10.1099/mgen.0.000695
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