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Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbrea...

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Autores principales: Hawkey, Jane, Paranagama, Kalani, Baker, Kate S., Bengtsson, Rebecca J., Weill, François-Xavier, Thomson, Nicholas R., Baker, Stephen, Cerdeira, Louise, Iqbal, Zamin, Hunt, Martin, Ingle, Danielle J., Dallman, Timothy J., Jenkins, Claire, Williamson, Deborah A., Holt, Kathryn E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113504/
https://www.ncbi.nlm.nih.gov/pubmed/33976138
http://dx.doi.org/10.1038/s41467-021-22700-4
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author Hawkey, Jane
Paranagama, Kalani
Baker, Kate S.
Bengtsson, Rebecca J.
Weill, François-Xavier
Thomson, Nicholas R.
Baker, Stephen
Cerdeira, Louise
Iqbal, Zamin
Hunt, Martin
Ingle, Danielle J.
Dallman, Timothy J.
Jenkins, Claire
Williamson, Deborah A.
Holt, Kathryn E.
author_facet Hawkey, Jane
Paranagama, Kalani
Baker, Kate S.
Bengtsson, Rebecca J.
Weill, François-Xavier
Thomson, Nicholas R.
Baker, Stephen
Cerdeira, Louise
Iqbal, Zamin
Hunt, Martin
Ingle, Danielle J.
Dallman, Timothy J.
Jenkins, Claire
Williamson, Deborah A.
Holt, Kathryn E.
author_sort Hawkey, Jane
collection PubMed
description Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.
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spelling pubmed-81135042021-05-14 Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei Hawkey, Jane Paranagama, Kalani Baker, Kate S. Bengtsson, Rebecca J. Weill, François-Xavier Thomson, Nicholas R. Baker, Stephen Cerdeira, Louise Iqbal, Zamin Hunt, Martin Ingle, Danielle J. Dallman, Timothy J. Jenkins, Claire Williamson, Deborah A. Holt, Kathryn E. Nat Commun Article Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales. Nature Publishing Group UK 2021-05-11 /pmc/articles/PMC8113504/ /pubmed/33976138 http://dx.doi.org/10.1038/s41467-021-22700-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Hawkey, Jane
Paranagama, Kalani
Baker, Kate S.
Bengtsson, Rebecca J.
Weill, François-Xavier
Thomson, Nicholas R.
Baker, Stephen
Cerdeira, Louise
Iqbal, Zamin
Hunt, Martin
Ingle, Danielle J.
Dallman, Timothy J.
Jenkins, Claire
Williamson, Deborah A.
Holt, Kathryn E.
Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title_full Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title_fullStr Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title_full_unstemmed Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title_short Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei
title_sort global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, shigella sonnei
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8113504/
https://www.ncbi.nlm.nih.gov/pubmed/33976138
http://dx.doi.org/10.1038/s41467-021-22700-4
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