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
Prokaryotes

Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts

Ran An, Pengpeng Lin, Salim Bougouffa, Magbubah Essack, David Boxrud, Vladimir B. Bajic, Sinisa Vidovic
Ran An
aDepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Pengpeng Lin
bDepartment of Mathematics, Statistics, and Computer Sciences, University of Wisconsin—Stout, Menomonie, Wisconsin, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Salim Bougouffa
cKing Abdullah University of Science and Technology (KAUST), Computational Biosciences Research Center, Thuwal, Kingdom of Saudi Arabia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Magbubah Essack
cKing Abdullah University of Science and Technology (KAUST), Computational Biosciences Research Center, Thuwal, Kingdom of Saudi Arabia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Boxrud
dPublic Health Laboratory, Minnesota Department of Health, Saint Paul, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vladimir B. Bajic
cKing Abdullah University of Science and Technology (KAUST), Computational Biosciences Research Center, Thuwal, Kingdom of Saudi Arabia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sinisa Vidovic
aDepartment of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.01550-17
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Salmonella enterica subsp. enterica serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four S. Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.

GENOME ANNOUNCEMENT

Salmonella enterica subsp. enterica serovar Enteritidis (here referred to as Salmonella Enteritidis) is a Gram-negative rod-shaped non-spore-forming bacterium capable of infecting a wide range of mammalian (1), bird (2), and reptile (3) species.

The S. Enteritidis strains 15-00488 and 16-03217, implicated in the infection of avian hosts, were obtained from Alabama and Wisconsin in 2015 and 2016, respectively. Two human S. Enteritidis strains, 2016010175 and 2011007870, were obtained from Minnesota in 2015 and 2011, respectively. The strain 2016010175 was isolated from a stool sample of a patient who suffered from gastrointestinal infection, and the 2011007870 strain was obtained from a patient who experienced bacteremia. The primary goal of this research project was to identify differences on the genome level between avian-associated (15-00488 and 16-03217) and human-associated (2016010175 and 2011007870) S. Enteritidis strains.

Genomic DNA was extracted using the Gentra Puregene kit (Qiagen, Inc., Valencia, CA). The whole-genome sequencing libraries were prepared using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA). The genomes were sequenced using an Illumina HiSeq 2500 platform with V4 125-bp paired-end sequencing chemistry. Sequencing reads were de novo assembled by the A5 pipeline version 5.0 (4). The draft genomes were annotated using the NCBI Prokaryotic Genome Automated Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/). PlasmidFinder 1.3 (5) and Mauve (6) were used for plasmid and single nucleotide polymorphism (SNP) identification, respectively.

The draft genomes of the avian strains, 15-00488 and 16-03217, were 4,699,188 bp and 4,771,079 bp, with average genome coverages of 60× and 183×, respectively. The genomes of the 15-00488 and 16-03217 strains resulted in 4,736 and 4,851 protein-coding sequences, respectively. The two draft genomes of the human strains, 2016010175 and 2011007870, resulted in 4,771,079 bp and 4,698,250 bp, with average genome coverages of 75× and 146×, respectively. The 2016010175 and 2011007870 strains contained 4,737 and 4,740 protein-coding regions, respectively.

Comparative genome analysis revealed that the S. Enteritidis strains of avian origin possessed all four genes, galK, galM, galT, and galE, that encode the enzymes galactokinase, galactose-1-epimerase, galactose-1-phosphate uridylyltransferase, and UDP-galactose 4-epimerase, respectively, which are necessary for conversion of galactose into glucose. Besides the enzymes of the Leloir pathway, the avian strains possessed the protein-coding sequences involved in acquisitions of molybdate (modFBAE) and iron (fepCD), as well as multidrug efflux (ybhT), and a protein of unknown function (DUF2167 domain-containing protein). Recently, it has been shown that molybdate uptake is important for anaerobic growth and multihost virulence in Pseudomonas aeruginosa (7, 8), which may indicate that the human-associated S. Enteritidis strains undergo a host restriction process compared to that of the avian strains.

In addition to loss of the genes involved in conversion of galactose into glucose and acquisition of molybdate, the human-associated strains showed a unique host-associated amino acid substitution at position 111, threonine (T) to isoleucine (I), in the gene lpfA, which encodes an adhesin “long polar fimbria protein A” that mediates bacterial attachment to the Peyer’s patches (9).

Accession number(s).The complete genome sequences of avian-associated (15-00488 and 16-03217) and human-associated (2016010175 and 2011007870) strains have been deposited in the NCBI GenBank database under the accession numbers NQNX00000000, NQUZ00000000, NQVA00000000, and NQVB00000000, respectively.

ACKNOWLEDGMENTS

This work was supported by the start-up fund provided to S.V. by the Department of Veterinary and Biomedical Sciences, University of Minnesota. S.B., M.E., and V.B.B. were supported by the KAUST research grants URF/1/2302-01-01, FCC/1/1976-02-01, and BAS/1/1606-01-01, respectively.

FOOTNOTES

    • Received 12 December 2017.
    • Accepted 19 December 2017.
    • Published 25 January 2018.
  • Copyright © 2018 An et al.

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

REFERENCES

  1. 1.↵
    1. Kingsley RA,
    2. Msefula CL,
    3. Thomson NR,
    4. Kariuki S,
    5. Holt KE,
    6. Gordon MA,
    7. Harris D,
    8. Clarke L,
    9. Whitehead S,
    10. Sangal V,
    11. Marsh K,
    12. Achtman M,
    13. Molyneux ME,
    14. Cormican M,
    15. Parkhill J,
    16. MacLennan CA,
    17. Heyderman RS,
    18. Dougan G
    . 2009. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res 19:2279–2287. doi:10.1101/gr.091017.109.
    OpenUrlAbstract/FREE Full Text
  2. 2.↵
    1. Han J,
    2. Gokulan K,
    3. Barnette D,
    4. Khare S,
    5. Rooney AW,
    6. Deck J,
    7. Nayak R,
    8. Stefanova R,
    9. Hart ME,
    10. Foley SL
    . 2013. Evaluation of virulence and antimicrobial resistance in Salmonella enterica serovar Enteritidis isolates from humans and chicken- and egg-associated sources. Foodborne Pathog Dis 10:1008–1015. doi:10.1089/fpd.2013.1518.
    OpenUrlCrossRefPubMed
  3. 3.↵
    1. Bosch S,
    2. Tauxe RV,
    3. Behravesh CB
    . 2016. Turtle-associated salmonellosis, United States, 2006–2014. Emerg Infect Dis 22:1149–1155. doi:10.3201/eid2207.150685.
    OpenUrlCrossRef
  4. 4.↵
    1. Coil D,
    2. Jospin G,
    3. Darling AE
    . 2015. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. doi:10.1093/bioinformatics/btu661.
    OpenUrlCrossRefPubMed
  5. 5.↵
    1. Carattoli A,
    2. Zankari E,
    3. García-Fernández A,
    4. Voldby Larsen M,
    5. Lund O,
    6. Villa L,
    7. Møller Aarestrup F,
    8. Hasman H
    . 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi:10.1128/AAC.02412-14.
    OpenUrlAbstract/FREE Full Text
  6. 6.↵
    1. Darling AE,
    2. Mau B,
    3. Perna NT
    . 2010. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147. doi:10.1371/journal.pone.0011147.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Pederick VG,
    2. Eijkelkamp BA,
    3. Ween MP,
    4. Begg SL,
    5. Paton JC,
    6. McDevitt CA
    . 2014. Acquisition and role of molybdate in Pseudomonas aeruginosa. Appl Environ Microbiol 80:6843–6852. doi:10.1128/AEM.02465-14.
    OpenUrlAbstract/FREE Full Text
  8. 8.↵
    1. Périnet S,
    2. Jeukens J,
    3. Kukavica-Ibrulj I,
    4. Ouellet MM,
    5. Charette SJ,
    6. Levesque RC
    . 2016. Molybdate transporter ModABC is important for Pseudomonas aeruginosa chronic lung infection. BMC Res Notes 9:23. doi:10.1186/s13104-016-1840-x.
    OpenUrlCrossRef
  9. 9.↵
    1. Bäumler AJ,
    2. Tsolis RM,
    3. Heffron F
    . 1996. The l.p.f. fimbrial operon mediates adhesion of Salmonella Typhimurium to murine Peyer’s patches. Proc Natl Acad Sci U S A 93:279–283. doi:10.1073/pnas.93.1.279.
    OpenUrlAbstract/FREE Full Text
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts
Ran An, Pengpeng Lin, Salim Bougouffa, Magbubah Essack, David Boxrud, Vladimir B. Bajic, Sinisa Vidovic
Genome Announcements Jan 2018, 6 (4) e01550-17; DOI: 10.1128/genomeA.01550-17

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.
Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts
(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
Draft Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts
Ran An, Pengpeng Lin, Salim Bougouffa, Magbubah Essack, David Boxrud, Vladimir B. Bajic, Sinisa Vidovic
Genome Announcements Jan 2018, 6 (4) e01550-17; DOI: 10.1128/genomeA.01550-17
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • 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