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Jul 02, 2024;12 (7): e0050924.

The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of and serovar Enteritidis.

Yu-Ping Hong, Bo-Han Chen, You-Wun Wang, Ru-Hsiou Teng, Hsiao-Lun Wei, Chien-Shun Chiou
Author Information
  1. Yu-Ping Hong: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan.
  2. Bo-Han Chen: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan.
  3. You-Wun Wang: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan.
  4. Ru-Hsiou Teng: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan.
  5. Hsiao-Lun Wei: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan.
  6. Chien-Shun Chiou: Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Taichung, Taiwan. ORCID
PMID: 38809017 DOI: 10.1128/spectrum.00509-24

Abstract

Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of and serovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations.
IMPORTANCE: This study unveils that Oxford Nanopore Technologies sequencing, by itself, holds the potential to serve as a whole-genome sequencing-based genotyping tool in public health laboratories, enabling routine subtyping of bacterial isolates for disease surveillance and outbreak investigations.

Keywords

Listeria monocytogenes ONT sequencing Salmonella enterica serovar Enteritidis cgMLST genotyping wgSNP whole-genome sequencing

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Grants

  1. MOHW110-CDC-C-315-113107, MOHW111-CDC-C-315-123108, MOHW112-CDC-C-315-133116, MOHW113-CDC-C-315-144316/Ministry of Health and Welfare (MOHW)

MeSH Term

Listeria monocytogenes
Salmonella enteritidis
Whole Genome Sequencing
Nanopore Sequencing
Genome, Bacterial
Humans
Listeriosis
Genotype
Disease Outbreaks
Genotyping Techniques
Salmonella Infections
Journal Article
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