High-Quality Whole-Genome Sequences for 21 Enterotoxigenic
            <i>Escherichia coli</i>
            Strains Generated with PacBio Sequencing

Smith, P. B.; Lindsey, Rebecca L.; Rowe, Lori A.; Batra, Dhwani; Stripling, Devon; Garcia-Toledo, Lisley; Drapeau, Daniel; Knipe, Kristen; Strockbine, Nancy

doi:10.1128/genomea.01311-17

Cited by 10 publications

(30 citation statements)

References 13 publications

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“…(pAvM_E925_4 and pAvM_E1649_8) are highly similar to several CS3 harbouring plasmids from O6:H16 strains collected from various geographical locations between 1975 and 2014, including Escherichia coli O6:H16 strain M9682-C1 plasmid unnamed2 (CP024277.1) and Escherichia coli strain O6:H16 F5656C1 plasmid unnamed2 (CP024262.1) PacBio sequenced by Smith et al[20] …”

mentioning

confidence: 72%

“…sul1 and tetA genes on a putative mobile plasmid. Since ATCC 43886/E2539C1, The ETEC O169:H41 isolate F8111-1SC3 plasmid unnamed 2 [20,70] is highly similar to pAvM_E1373_28 (Figure 1h). The F8111-ISC3 isolate is part of a CDC collection of ETEC isolates from cruise ship outbreaks and diarrheal cases in US 1996-2003.…”

Section: Prophages Present and Their Cargo Genesmentioning

confidence: 99%

“…There is currently one complete ETEC reference genome, H10407 [19], which has been manually annotated. Several additional complete ETEC genomes are available [20,21], some of which are annotated using automated annotation pipelines that often fail at correctly annotating ETEC specific genes such as CFs. The rapid adaptation of nextgeneration sequencing in public health, specifically within bacterial diseases [22,23] and a number of large-scale sequencing studies [18,[24][25][26][27][28] has led to a rapid increase in the number of publicly available ETEC genomes.…”

mentioning

confidence: 99%

“…Hence, it is important to identify lineage-specific reference genomes that are fully annotated and include both chromosome and plasmid(s). A number of fully complete genomes have been generated using long-read sequencing alone [20,28], however circularising some chromosomes and plasmids may be difficult due to repeat regions. This can be resolved using a hybrid assembly approach combining long-read and short-read sequencing data.…”

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confidence: 99%

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

Mentzer

Blackwell

Pickard

et al. 2020

Preprint

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BackgroundEnterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 fatalities per year, with the highest burden, ca 75 million cases per year, amongst children under five 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 world-wide.MethodsHere we have used PacBio long read sequencing in combination with Illumina sequencing to create high quality complete reference genomes for each of these lineages with manually curated chromosomes and plasmids. The plasmids carrying ETEC virulence genes were compared to other available long-read sequenced ETEC strains using blastn.ResultsThe ETEC reference strains harbour between two and five plasmids, including virulence, antibiotic resistance and phage-plasmids. The virulence plasmids carrying the colonization factors are highly conserved as shown by comparison with plasmids with other ETEC strains and confirm that the plasmids and chromosomes of ETEC are both crucial for ETEC virulence and superiority as pathogens.ConclusionWe confirm that the major ETEC lineages all harbor conserved plasmids that have been associated to their respective background genomes for decades. The in-depth analysis of gene content and order and correct annotations of plasmids will help to elucidate other plasmids with and without virulence factors in related bacterial species. These reference genomes allow for rapid and accurate comparison between different ETEC strains and these data will form the foundation of ETEC genomics research for years to come.

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mentioning

confidence: 72%

Section: Prophages Present and Their Cargo Genesmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Mentzer

Blackwell

Pickard

et al. 2020

Preprint

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“…The DNA of the isolates was extracted using the ArchivePure DNA extraction kit standard protocol (5 Prime, Gaithersburg, MD). Library construction and PacBio sequencing were conducted as previously described ( 3 ), and DNA was sheared to an approximate length of 20 kb via needle shearing. BluePippin (Sage Scientific, Beverly, MA) was used to size select the sheared DNA.…”

Section: Genome Announcementmentioning

confidence: 99%

High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated with PacBio Sequencing

et al. 2018

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

Mentzer

Blackwell

Pickard

et al. 2021

Sci Rep

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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.

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High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing

Abstract: Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here the high-quality whole-genome sequences of 21 ETEC strains isolated from patients in the United States, international diarrheal surveillance studies, and cruise ship outbreaks.

Cited by 10 publications

References 13 publications

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

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

High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated with PacBio Sequencing

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

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