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Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing

Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic related...

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Autores principales: Greig, David R., Jenkins, Claire, Gharbia, Saheer E., Dallman, Timothy J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190617/
https://www.ncbi.nlm.nih.gov/pubmed/33683192
http://dx.doi.org/10.1099/mgen.0.000545
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author Greig, David R.
Jenkins, Claire
Gharbia, Saheer E.
Dallman, Timothy J.
author_facet Greig, David R.
Jenkins, Claire
Gharbia, Saheer E.
Dallman, Timothy J.
author_sort Greig, David R.
collection PubMed
description Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen.
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spelling pubmed-81906172021-06-10 Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing Greig, David R. Jenkins, Claire Gharbia, Saheer E. Dallman, Timothy J. Microb Genom Outbreak Reports Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen. Microbiology Society 2021-03-08 /pmc/articles/PMC8190617/ /pubmed/33683192 http://dx.doi.org/10.1099/mgen.0.000545 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
spellingShingle Outbreak Reports
Greig, David R.
Jenkins, Claire
Gharbia, Saheer E.
Dallman, Timothy J.
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title_full Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title_fullStr Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title_full_unstemmed Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title_short Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing
title_sort analysis of a small outbreak of shiga toxin-producing escherichia coli o157:h7 using long-read sequencing
topic Outbreak Reports
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190617/
https://www.ncbi.nlm.nih.gov/pubmed/33683192
http://dx.doi.org/10.1099/mgen.0.000545
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