Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time

Abstract Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with the highest rates of burden, ca 75 million cases per year, amongst children under 5 years of age in r...

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Autores principales:	Astrid von Mentzer, Grace A. Blackwell, Derek Pickard, Christine J. Boinett, Enrique Joffré, Andrew J. Page, Ann-Mari Svennerholm, Gordon Dougan, Åsa Sjöling
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2495dd11c7b24f429b1cf99eae01a99b
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spelling	oai:doaj.org-article:2495dd11c7b24f429b1cf99eae01a99b2021-12-02T16:55:34ZLong-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time10.1038/s41598-021-88316-22045-2322https://doaj.org/article/2495dd11c7b24f429b1cf99eae01a99b2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88316-2https://doaj.org/toc/2045-2322Abstract Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with the highest rates of burden, ca 75 million cases per year, amongst children under 5 years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Previous large-scale sequencing studies have found seven major ETEC lineages currently in circulation worldwide. We used PacBio long-read sequencing combined with Illumina sequencing to create high-quality complete reference genomes for each of the major lineages with manually curated chromosomes and plasmids. We confirm that the major ETEC lineages all harbour conserved plasmids that have been associated with their respective background genomes for decades, suggesting that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and success as pathogens. The in-depth analysis of gene content, synteny and correct annotations of plasmids will elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for fast and accurate comparison between different ETEC strains, and these data will form the foundation of ETEC genomics research for years to come.Astrid von MentzerGrace A. BlackwellDerek PickardChristine J. BoinettEnrique JoffréAndrew J. PageAnn-Mari SvennerholmGordon DouganÅsa SjölingNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-16 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Astrid von Mentzer Grace A. Blackwell Derek Pickard Christine J. Boinett Enrique Joffré Andrew J. Page Ann-Mari Svennerholm Gordon Dougan Åsa Sjöling Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
description	Abstract Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with the highest rates of burden, ca 75 million cases per year, amongst children under 5 years of age in resource-poor countries. It is also the leading cause of diarrhoea in travellers. Previous large-scale sequencing studies have found seven major ETEC lineages currently in circulation worldwide. We used PacBio long-read sequencing combined with Illumina sequencing to create high-quality complete reference genomes for each of the major lineages with manually curated chromosomes and plasmids. We confirm that the major ETEC lineages all harbour conserved plasmids that have been associated with their respective background genomes for decades, suggesting that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and success as pathogens. The in-depth analysis of gene content, synteny and correct annotations of plasmids will elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for fast and accurate comparison between different ETEC strains, and these data will form the foundation of ETEC genomics research for years to come.
format	article
author	Astrid von Mentzer Grace A. Blackwell Derek Pickard Christine J. Boinett Enrique Joffré Andrew J. Page Ann-Mari Svennerholm Gordon Dougan Åsa Sjöling
author_facet	Astrid von Mentzer Grace A. Blackwell Derek Pickard Christine J. Boinett Enrique Joffré Andrew J. Page Ann-Mari Svennerholm Gordon Dougan Åsa Sjöling
author_sort	Astrid von Mentzer
title	Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
title_short	Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
title_full	Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
title_fullStr	Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
title_full_unstemmed	Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time
title_sort	long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic escherichia coli (etec) circulating in modern time
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/2495dd11c7b24f429b1cf99eae01a99b
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Long-read-sequenced reference genomes of the seven major lineages of enterotoxigenic Escherichia coli (ETEC) circulating in modern time

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