Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Eukaryotic Cell
    • Microbiology Resource Announcements
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Microbiology Resource Announcements
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Latest Articles
    • Archive
  • Types of Resources
    • Amplicon Sequence Collections
    • Culture Collections/Mutant Libraries
    • Databases and Software
    • Omics Data Sets
    • Other Genetic Resources
    • Genome Sequences
  • For Authors
    • Getting Started
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About MRA
    • Editor in Chief
    • Board of Editors
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
Genome Sequences

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada

Shari Tyson, Christy-Lynn Peterson, Adam Olson, Shaun Tyler, Natalie Knox, Emma Griffiths, Damion Dooley, William Hsiao, Jennifer Cabral, Roger P. Johnson, Chad Laing, Victor Gannon, Tarah Lynch, Gary Van Domselaar, Fiona Brinkman, Morag Graham
Julie C. Dunning Hotopp, Editor
Shari Tyson
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christy-Lynn Peterson
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adam Olson
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shaun Tyler
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Natalie Knox
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
dDepartment of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emma Griffiths
eDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia, Canada
fBritish Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Damion Dooley
fBritish Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
William Hsiao
fBritish Columbia Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer Cabral
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Roger P. Johnson
bNational Microbiology Laboratory, Public Health Agency of Canada, Guelph, Ontario, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chad Laing
cNational Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Victor Gannon
cNational Microbiology Laboratory, Public Health Agency of Canada, Lethbridge, Alberta, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tarah Lynch
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gary Van Domselaar
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
dDepartment of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fiona Brinkman
eDepartment of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Morag Graham
aNational Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
dDepartment of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Julie C. Dunning Hotopp
University of Maryland School of Medicine
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/MRA.00625-19
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

ABSTRACT

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

ANNOUNCEMENT

Shiga toxin (Stx)-producing Escherichia coli (STEC) strains cause significant human enteric disease (1–3). Among >129 O serogroups, O157, O26, O45, O111, O103, O121, and O145 cause most infections (4–6). Non-O157 STEC strains are increasingly reported (5–7), with recent widespread STEC O121 and O103 outbreaks in Canada and the United States sourced to flour (8) and ground beef, respectively (https://www.cdc.gov/ecoli/2019/o103-04-19/).

To catalogue pangenomic diversity, we generated closed reference genomes for 11 routinely used lab control strains from the “top seven” STEC O serogroups, plus O91 and O104, and 360 draft assemblies for 129 distinct O serogroups from STEC culture collections (1980 to 2013) originating from watersheds, farms or foods (n = 238), human infections (n = 74), proficiency panels (n = 27), and unknown sources (n = 32). Prior to selection, isolates were traditionally serotyped at national or provincial reference labs, and stx gene presence/subtype was assessed by preestablished generic and differentiating stx PCR assays (9–11).

DNA extracted from 1-ml Luria-Bertani broth cultures grown overnight at 37°C using MasterPure complete DNA purification kits (Epicentre Technologies Corp., Chicago, IL, USA) was fragmented by an E210 ultrasonicator (Covaris, Inc., Woburn, MA, USA). TruSeq DNA library preparation v2 kit (Illumina, San Diego, CA, USA) libraries were shotgun sequenced using an Illumina GAIIx system (2 × 150-bp paired-end cluster generation kit v4 and TruSeq SBS kit v5) or MiSeq platform (2 × 300 bp; v3 chemistry). Illumina reads were managed in the Integrated Rapid Infectious Disease Analysis (IRIDA) platform (12), assessed for quality (Q > 30) using FastQC (13), and trimmed using Trimmomatic v0.34 (14). Overlapping reads merged with FLASH v1.2.11 (15) were de novo assembled using SPAdes v3.8.2 (16)/Shovill 0.9.0 (17). Postassembly quality control was achieved using QUAST v5.0.0 (number of contigs, < 500; reference coverage, 70% [closest polished genome of FWSEC0001-0011]) (18). Reference strains were augmented with 2 × 300-bp MiSeq (v3 chemistry) reads from mate pair (∼8 kb) TruSeq libraries and with MinION Mk1b long reads from the rapid barcoding sequencing kit (SQK-RBK004; Oxford Nanopore Technologies Ltd., Oxford, UK) libraries. Albacore v2.3.0 base-called/quality-filtered long reads were de novo assembled using Canu v1.7 (19) and with quality-controlled Illumina mate pair reads as hybrid assemblies using Unicycler v0.4.4.0 (20). When assemblies appeared congruent in Mauve v20150226Build10 (21), Unicycler assemblies were used. Otherwise, mate pair reads were mapped to both assemblies using Bowtie 2 v2.3.4.1 (22) and BAM files assessed for coverage/connections using GAP5 v.1.2.14-r (23); long reads were mapped with BWA-MEM v0.7.17.1 (24) and assessed using Tablet v1.17.08.17 (25). Canu contigs were employed to scaffold/correct Unicycler contigs using the Staden package GAP4 (26, 27); all contigs were circularized and trimmed. Assemblies were Illumina read polished (5 rounds) using Bowtie 2/Pilon v1.20.1 (28). NCBI’s default Web BLASTN (29) identified plasmid contigs and confirmed that in silico O-serogroup determinations were congruent with traditional lab determinations. Read depth was assessed using SAMtools idxstats (30). After functional annotation using NCBI’s Prokaryotic Genome Annotation Pipeline (31), assemblies were reoriented to replication origin (dnaA) using Circlator v1.1.5 (32).

Illumina reference genome coverage ranged from 65.6× to 130.7× (average, 96.1×); MinION coverage ranged from 51.2× to 325.1× (average, 149.6×) (Table 1). Of 360 draft assemblies, 357 yielded scaffolds (average contigs, 153.0; average coverage depth, 111.7×). Eleven reference chromosomes and all plasmids but one were circularized (0 to 3 plasmids per strain). The reference chromosomes (4,955,402 to 5,697,154 bp) contained 4,967 to 5,833 coding sequences (CDS), 22 rRNAs, 90 to 103 tRNAs, and 8 to 11 noncoding RNAs (ncRNAs), as well as bacteriophages. These genomic resources augment available data and are ideal for pathogenomics applications and machine learning.

View this table:
  • View inline
  • View popup
TABLE 1

Characteristics and accession numbers for 11 high-quality STEC reference genomes and 360 STEC draft genome assemblies from 129 distinct serogroups sequenced for this study

Data availability.The standardized strain descriptions and accession numbers are presented in Table 1; the genomic data are publicly available in DDBJ/ENA/GenBank under BioProject no. PRJNA287560 and in the Sequence Read Archive under accession no. SRP155537. The versions described are the first versions.

ACKNOWLEDGMENTS

Many strains were actively collected during the Genomics Research and Development Initiative national shared priorities project on Food and Water Safety (GRDI-FWS); otherwise, they were acquired from the culture collections of T. Alexander, P. Delaquis, T. Edge, A. Gill, C. Gyles, C. Nadon, A. Scott, E. Topp, L. Tschetter, G. Wang, and the GRDI-FWS project partner organizations (namely, Agriculture and Agri-Food Canada, the Canadian Food Inspection Agency, Environment and Climate Change Canada, Health Canada, and the Public Health Agency of Canada [PHAC]). The National Microbiology Laboratory (NML)-Division of Enteric Diseases performed STEC serotyping (under direction by K. Tabor and K. Ziebell). C. Jokinen and R. Wang provided lab support. The NML Genomics Core (C. Bonner, B. Kaplen, V. Laminman, E. Landry, K. Melnychuk, T. Murphy, and G. Peters) performed sequencing. F. Pollari and K. Pintar collated metadata for FoodNet Canada isolates. IRIDA’s development team provided data management. The NML’s Bioinformatics Core and Scientific Informatics Services Division provided analysis capacity and infrastructure, respectively.

We thank the NCBI for all data assistance.

A.O. and T.L. were supported by the Government of Canada’s Federal Genomics Research and Development Initiative (GRDI) national shared priorities project on Food and Water Safety (GRDI-FWS). The work was funded by GRDI-FWS and an intramural GRDI to V.G. (for a portion of STEC draft genome assemblies and strain metadata), the Public Health Agency of Canada (for STEC reference genome closures), and Genome Canada/Genome BC (for metadata standardization).

The funders had no role in the study design, data collection, interpretation, public repository submission, or the decision to submit the work for publication.

FOOTNOTES

    • Received 28 May 2019.
    • Accepted 31 August 2019.
    • Published 10 October 2019.
  • © Crown copyright 2019.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

REFERENCES

  1. 1.↵
    1. Cray WC,
    2. Moon HW
    . 1995. Experimental infection of calves and adult cattle with Escherichia coli O157:H7. Appl Environ Microbiol 61:1586–1590. 10113/34422.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Karmali MA,
    2. Gannon V,
    3. Sargeant JM
    . 2010. Verocytotoxin-producing Escherichia coli (VTEC). Vet Microbiol 140:360–370. doi:10.1016/j.vetmic.2009.04.011.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    1. Valilis E,
    2. Ramsey A,
    3. Sidiq S,
    4. DuPont HL
    . 2018. Non-O157 Shiga toxin-producing Escherichia coli—a poorly appreciated enteric pathogen: systematic review. Int J Infect Dis 76:82–87. doi:10.1016/j.ijid.2018.09.002.
    OpenUrlCrossRef
  4. 4.↵
    1. Johnson KE,
    2. Thorpe CM,
    3. Sears CL
    . 2006. The emerging clinical importance of non-O157 Shiga toxin-producing Escherichia coli. Clin Infect Dis 43:1587–1595. doi:10.1086/509573.
    OpenUrlCrossRefPubMedWeb of Science
  5. 5.↵
    1. Hadler JL,
    2. Clogher P,
    3. Hurd S,
    4. Phan Q,
    5. Mandour M,
    6. Bemis K,
    7. Marcus R
    . 2011. Ten-year trends and risk factors for non-O157 Shiga toxin-producing Escherichia coli found through Shiga toxin testing, Connecticut, 2000–2009. Clin Infect Dis 53:269–276. doi:10.1093/cid/cir377.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Gould LH,
    2. Mody RK,
    3. Ong KL,
    4. Clogher P,
    5. Cronquist AB,
    6. Garman KN,
    7. Lathrop S,
    8. Medus C,
    9. Spina NL,
    10. Webb TH,
    11. White PL,
    12. Wymore K,
    13. Gierke RE,
    14. Mahon BE,
    15. Griffin PM, Emerging Infections Program FoodNet Working Group
    . 2013. Increased recognition of non-O157 Shiga toxin-producing Escherichia coli infections in the United States during 2000–2010: epidemiologic features and comparison with E. coli O157 infections. Foodborne Pathog Dis 10:453–460. doi:10.1089/fpd.2012.1401.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Bettelheim KA
    . 2007. The non-O157 Shiga-toxigenic (verocytotoxigenic) Escherichia coli; under-rated pathogens. Crit Rev Microbiol 33:67–87. doi:10.1080/10408410601172172.
    OpenUrlCrossRefPubMedWeb of Science
  8. 8.↵
    1. Morton V,
    2. Cheng JM,
    3. Sharma D,
    4. Kearney A
    . 2017. Notes from the field: an outbreak of Shiga toxin-producing Escherichia coli O121 infections associated with flour–Canada, 2016–2017. MMWR Morb Mortal Wkly Rep 66:705–706. doi:10.15585/mmwr.mm6626a6.
    OpenUrlCrossRef
  9. 9.↵
    1. Lin Z,
    2. Kurazono H,
    3. Yamasaki S,
    4. Takeda Y
    . 1993. Detection of various variant verotoxin genes in Escherichia coli by polymerase chain reaction. Microbiol Immunol 37:543–548. doi:10.1111/j.1348-0421.1993.tb01675.x.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Paton AW,
    2. Paton JC
    . 1998. Detection and characterization of Shiga toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2, eaeA, enterohemorrhagic E. coli hlyA, rfbO111, and rfbO157. J Clin Microbiol 36:598–602.
    OpenUrlAbstract/FREE Full Text
  11. 11.↵
    1. Ziebell KA,
    2. Read SC,
    3. Johnson RP,
    4. Gyles CL
    . 2002. Evaluation of PCR and PCR-RFLP protocols for identifying Shiga toxins. Res Microbiol 153:289–300. doi:10.1016/S0923-2508(02)01322-0.
    OpenUrlCrossRefPubMed
  12. 12.↵
    1. Matthews TC,
    2. Bristow FR,
    3. Griffiths EJ,
    4. Petkau A,
    5. Adam J,
    6. Dooley D,
    7. Kruczkiewicz P,
    8. Curatcha J,
    9. Cabral J,
    10. Fornika D,
    11. Winsor GL,
    12. Courtot M,
    13. Bertelli C,
    14. Roudgar A,
    15. Feijao P,
    16. Mabon P,
    17. Enns E,
    18. Thiessen J,
    19. Keddy A,
    20. Isaac-Renton J,
    21. Gardy JL,
    22. Tang P, the IRIDA Consortium
    , Carrico JA, Chindelevitch L, Chauve C, Graham MR, McArthur AG, Taboada EN, Beiko RG, Brinkman FS, Hsiao WW, Van Domselaar G. 2018. The Integrated Rapid Infectious Disease Analysis (IRIDA) platform. bioRxiv. doi:10.1101/381830.
    OpenUrlCrossRef
  13. 13.↵
    1. Andrews S
    . 2010. FastQC: a quality control tool for high throughput sequence data. FastQC: a quality control tool for high throughput sequence data (v11.8). http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 15 September 2017.
  14. 14.↵
    1. Bolger AM,
    2. Lohse M,
    3. Usadel B
    . 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:10.1093/bioinformatics/btu170.
    OpenUrlCrossRefPubMedWeb of Science
  15. 15.↵
    1. Magoč T,
    2. Salzberg SL
    . 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. doi:10.1093/bioinformatics/btr507.
    OpenUrlCrossRefPubMedWeb of Science
  16. 16.↵
    1. Bankevich A,
    2. Nurk S,
    3. Antipov D,
    4. Gurevich AA,
    5. Dvorkin M,
    6. Kulikov AS,
    7. Lesin VM,
    8. Nikolenko SI,
    9. Pham S,
    10. Prjibelski AD,
    11. Pyshkin AV,
    12. Sirotkin AV,
    13. Vyahhi N,
    14. Tesler G,
    15. Alekseyev MA,
    16. Pevzner PA
    . 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi:10.1089/cmb.2012.0021.
    OpenUrlCrossRefPubMed
  17. 17.↵
    1. Seeman T
    . 2018. Shovill: faster SPAdes assembly of Illumina reads (v0.9.0). https://github.com/tseemann/shovill. Accessed 15 March 2018.
  18. 18.↵
    1. Gurevich A,
    2. Saveliev V,
    3. Vyahhi N,
    4. Tesler G
    . 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi:10.1093/bioinformatics/btt086.
    OpenUrlCrossRefPubMedWeb of Science
  19. 19.↵
    1. Koren S,
    2. Walenz BP,
    3. Berlin K,
    4. Miller JR,
    5. Bergman NH,
    6. Phillippy AM
    . 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi:10.1101/gr.215087.116.
    OpenUrlAbstract/FREE Full Text
  20. 20.↵
    1. Wick RR,
    2. Judd LM,
    3. Gorrie CL,
    4. Holt KE
    . 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. doi:10.1371/journal.pcbi.1005595.
    OpenUrlCrossRefPubMed
  21. 21.↵
    1. Rissman AI,
    2. Mau B,
    3. Biehl BS,
    4. Darling AE,
    5. Glasner JD,
    6. Perna NT
    . 2009. Reordering contigs of draft genomes using the Mauve aligner. Bioinformatics 25:2071–2073. doi:10.1093/bioinformatics/btp356.
    OpenUrlCrossRefPubMedWeb of Science
  22. 22.↵
    1. Langmead B,
    2. Salzberg SL
    . 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. doi:10.1038/nmeth.1923.
    OpenUrlCrossRefPubMedWeb of Science
  23. 23.↵
    1. Bonfield JK,
    2. Whitwham A
    . 2010. Gap5—editing the billion fragment sequence assembly. Bioinformatics 26:1699–1703. doi:10.1093/bioinformatics/btq268.
    OpenUrlCrossRefPubMedWeb of Science
  24. 24.↵
    1. Houtgast EJ,
    2. Sima V-M,
    3. Bertels K,
    4. Al-Ars Z
    . 2018. Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths. Comput Biol Chem 75:54–64. doi:10.1016/j.compbiolchem.2018.03.024.
    OpenUrlCrossRef
  25. 25.↵
    1. Milne I,
    2. Stephen G,
    3. Bayer M,
    4. Cock PJA,
    5. Pritchard L,
    6. Cardle L,
    7. Shaw PD,
    8. Marshall D
    . 2013. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinformatics 14:193–202. doi:10.1093/bib/bbs012.
    OpenUrlCrossRefPubMed
  26. 26.↵
    1. Bonfield JK,
    2. Smith KF,
    3. Staden R
    . 1995. A new DNA sequence assembly program. Nucleic Acids Res 23:4992–4999. doi:10.1093/nar/23.24.4992.
    OpenUrlCrossRefPubMedWeb of Science
  27. 27.↵
    1. Staden R,
    2. Beal KF,
    3. Bonfield JK
    . 2000. The Staden package, 1998. Methods Mol Biol 132:115–130. doi:10.1385/1-59259-192-2:115.
    OpenUrlCrossRefPubMed
  28. 28.↵
    1. Walker BJ,
    2. Abeel T,
    3. Shea T,
    4. Priest M,
    5. Abouelliel A,
    6. Sakthikumar S,
    7. Cuomo CA,
    8. Zeng Q,
    9. Wortman J,
    10. Young SK,
    11. Earl AM
    . 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi:10.1371/journal.pone.0112963.
    OpenUrlCrossRefPubMed
  29. 29.↵
    1. Camacho C,
    2. Coulouris G,
    3. Avagyan V,
    4. Ma N,
    5. Papadopoulos J,
    6. Bealer K,
    7. Madden TL
    . 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421. doi:10.1186/1471-2105-10-421.
    OpenUrlCrossRefPubMed
  30. 30.↵
    1. Li H,
    2. Handsaker B,
    3. Wysoker A,
    4. Fennell T,
    5. Ruan J,
    6. Homer N,
    7. Marth G,
    8. Abecasis G,
    9. Durbin R, 1000 Genome Project Data Processing Subgroup
    . 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. doi:10.1093/bioinformatics/btp352.
    OpenUrlCrossRefPubMedWeb of Science
  31. 31.↵
    1. Tatusova T,
    2. DiCuccio M,
    3. Badretdin A,
    4. Chetvernin V,
    5. Nawrocki EP,
    6. Zaslavsky L,
    7. Lomsadze A,
    8. Pruitt KD,
    9. Borodovsky M,
    10. Ostell J
    . 2016. NCBI Prokaryotic Genome Annotation Pipeline. Nucleic Acids Res 44:6614–6624. doi:10.1093/nar/gkw569.
    OpenUrlCrossRefPubMed
  32. 32.↵
    1. Hunt M,
    2. Silva ND,
    3. Otto TD,
    4. Parkhill J,
    5. Keane JA,
    6. Harris SR
    . 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol 16:294. doi:10.1186/s13059-015-0849-0.
    OpenUrlCrossRefPubMed
  33. 33.
    1. Ashton PM,
    2. Perry N,
    3. Ellis R,
    4. Petrovska L,
    5. Wain J,
    6. Grant KA,
    7. Jenkins C,
    8. Dallman TJ
    . 2015. Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing. PeerJ 3:e739. doi:10.7717/peerj.739.
    OpenUrlCrossRef
  34. 34.
    1. Joensen KG,
    2. Tetzschner AMM,
    3. Iguchi A,
    4. Aarestrup FM,
    5. Scheutz F
    . 2015. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol 53:2410–2426. doi:10.1128/JCM.00008-15.
    OpenUrlAbstract/FREE Full Text
  35. 35.
    1. Inouye M,
    2. Dashnow H,
    3. Raven L-A,
    4. Schultz MB,
    5. Pope BJ,
    6. Tomita T,
    7. Zobel J,
    8. Holt KE
    . 2014. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6:90. doi:10.1186/s13073-014-0090-6.
    OpenUrlCrossRefPubMed
  36. 36.
    1. Mapleson D,
    2. Garcia Accinelli G,
    3. Kettleborough G,
    4. Wright J,
    5. Clavijo BJ
    . 2017. KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies. Bioinformatics 33:574–576. doi:10.1093/bioinformatics/btw663.
    OpenUrlCrossRef
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada
Shari Tyson, Christy-Lynn Peterson, Adam Olson, Shaun Tyler, Natalie Knox, Emma Griffiths, Damion Dooley, William Hsiao, Jennifer Cabral, Roger P. Johnson, Chad Laing, Victor Gannon, Tarah Lynch, Gary Van Domselaar, Fiona Brinkman, Morag Graham
Microbiology Resource Announcements Oct 2019, 8 (41) e00625-19; DOI: 10.1128/MRA.00625-19

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print
Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Microbiology Resource Announcements article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada
(Your Name) has forwarded a page to you from Microbiology Resource Announcements
(Your Name) thought you would be interested in this article in Microbiology Resource Announcements.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada
Shari Tyson, Christy-Lynn Peterson, Adam Olson, Shaun Tyler, Natalie Knox, Emma Griffiths, Damion Dooley, William Hsiao, Jennifer Cabral, Roger P. Johnson, Chad Laing, Victor Gannon, Tarah Lynch, Gary Van Domselaar, Fiona Brinkman, Morag Graham
Microbiology Resource Announcements Oct 2019, 8 (41) e00625-19; DOI: 10.1128/MRA.00625-19
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About MRA
  • Editor in Chief
  • Board of Editors
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • Getting Started
  • Submit a Manuscript
  • Author Warranty
  • Ethics
  • Contact Us
  • ASM Author Center

Follow #MRAJournal

@ASMicrobiology

       

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Online ISSN: 2576-098X