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 Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom

K. A. Kropp, A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, C. Smith, P. Dickinson, A. O'Driscoll, K. Templeton, P. Ghazal, R. D. Sleator
K. A. Kropp
aDepartment of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A. Lucid
aDepartment of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
J. Carroll
bNSilico Lifescience Ltd., Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
V. Belgrudov
cDepartment of Computing, Cork Institute of Technology, Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
P. Walsh
bNSilico Lifescience Ltd., Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
B. Kelly
bNSilico Lifescience Ltd., Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
C. Smith
dDivision of Pathway Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
P. Dickinson
dDivision of Pathway Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
A. O'Driscoll
cDepartment of Computing, Cork Institute of Technology, Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
K. Templeton
dDivision of Pathway Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
eMicrobiological Diagnostic Unit, Royal Infirmary, University of Edinburgh, Edinburgh, Scotland, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
P. Ghazal
dDivision of Pathway Medicine, University of Edinburgh, Edinburgh, Scotland, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
R. D. Sleator
aDepartment of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/genomeA.00908-14
  • Article
  • Info & Metrics
  • PDF
Loading

ABSTRACT

Herein, we report the draft genome sequence for isolate ED-NGS-1015 of Serratia marcescens, cultivated from a blood sample obtained from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.

GENOME ANNOUNCEMENT

Serratia marcescens is a Gram-negative, rare, but clinically important nosocomial pathogen that causes meningitis and blood sepsis (1–3). Preterm neonates are a highly susceptible patient group for bacterial infections (4–6) and rapid detection of blood sepsis and the causative agent are critical first steps to enable proper treatment (7–9). The ClouDx-i project aims to extend our knowledge of currently circulating pathogenic strains linked with blood sepsis in neonates to inform the development of new molecular diagnostic assays. Herein, we present the draft genome of a Serratia marcescens strain isolated from a preterm neonate in Edinburgh in 2013. Positivity for blood sepsis and species identification were confirmed by classical microbiological techniques.

The isolate was grown overnight at 37°C on Luria broth (LB) agar, and genomic DNA was isolated using Qiagen genomic tips (Venlo, Limburg, Netherlands). Genomic DNA was fragmented (fragments 2 to 10 kb) using sonication and a non-size-selected genome library was produced using the Nextera mate pair kit (Illumina, San Diego, CA). This library was then sequenced on an Illumina MiSeq using MiSeq Reagent kit version 3. Genomic sequence assembly, analysis, and automated reporting were carried out using Simplicity (10). This approach produced 1,969,069 total reads, resulting in an average 117-fold coverage. The average G+C content was 59.91%. For sequence assembly, we used a de novo assembly pipeline based on the SPAdes version 3.10 assembly tool with k-mer sizes from K21, K33, K55, K77, K99 to K127, resulting in 166 contigs, of which 7 were >1,000 bp, representing 98.60% of the total sequence information, with the largest contig being 3,811,471 bp. Postassembly processing was performed using SPAdes, and only scaffolds of >1,000 bp were considered when estimating the genome length as 5,128,447 bp. We annotated the genome with Prokka (11) and used the identified 16S rRNA gene to confirm the species as Serratia marcescens. A scaffold of the genome was produced with Contiguator2, and we identified the closest related strain by BLASTing the scaffold, returning strains S. marcescens SM39 and FS14 as closely related but not identical, as was evidenced by a large inversion and numerous small insertions and deletions in the genome. The genome was then screened using GLIMMER3 (12) identifying 4,887 open reading frames (ORFs). The predicted ORFs were compared to the UniProt TrEMBL database (13) using BLASTp, mapping 3,885 of the ORFs to the database. To identify potential virulence factors, we compared the assembled genome to a local database built from the VFDB (14) and Victors databases with BLASTp. Using a 75% amino-acid sequence identity cutoff, while only considering alignments longer than 100 amino-acids, we identified 115 potential virulence factors.

Samples were handled in accordance with local ethical approval by the ethics committees of the NHS Lothian SAHSC Bioresource and NHS Research and Development Office, Project ID 2011/R/NE/01, and the HSS BioResource Request ID 13/ES/0126.

Nucleotide sequence accession numbers.This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JPWM00000000. The version described in this paper is version JPWM01000000.

ACKNOWLEDGMENT

This work was supported by the ClouDx-i IAPP EU FP7 project, coordinated by R. D. Sleator.

FOOTNOTES

    • Received 11 August 2014.
    • Accepted 20 August 2014.
    • Published 11 September 2014.
  • Copyright © 2014 Kropp et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

REFERENCES

  1. 1.↵
    1. Wu Y-M,
    2. Hsu P-C,
    3. Yang C-C,
    4. Chang H-J,
    5. Ye JJ Jr.,
    6. Huang C-T,
    7. Lee M-H
    . 2013. Serratia marcescens meningitis: epidemiology, prognostic factors and treatment outcomes. J. Microbiol. Immunol. Infect. 46:259–265. doi:10.1016/j.jmii.2012.07.006.
    OpenUrlCrossRefPubMed
  2. 2.↵
    1. Samuelsson A,
    2. Isaksson B,
    3. Hanberger H,
    4. Olhager E
    . 2014. Late-onset neonatal sepsis, risk factors and interventions: an analysis of recurrent outbreaks of Serratia marcescens, 2006–2011. J. Hosp. Infect. 86:57–63. doi:10.1016/j.jhin.2013.09.017.
    OpenUrlCrossRef
  3. 3.↵
    1. Iosifidis E,
    2. Farmaki E,
    3. Nedelkopoulou N,
    4. Tsivitanidou M,
    5. Kaperoni M,
    6. Pentsoglou V,
    7. Pournaras S,
    8. Athanasiou-Metaxa M,
    9. Roilides E
    . 2012. Outbreak of bloodstream infections because of Serratia marcescens in a pediatric department. Am. J. Infect. Control 40:11–15. doi:10.1016/j.ajic.2011.03.020.
    OpenUrlCrossRefPubMed
  4. 4.↵
    1. Kaufman D,
    2. Fairchild KD
    . 2004. Clinical microbiology of bacterial and fungal sepsis in very-low-birth-weight infants. Clin. Microbiol. Rev. 17:638–680. doi:10.1128/CMR.17.3.638-680.2004.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    1. Shah BA,
    2. Padbury JF
    . 2014. Neonatal sepsis: an old problem with new insights. Virulence 5:170–178. doi:10.4161/viru.26906.
    OpenUrlCrossRefPubMed
  6. 6.↵
    1. Ghazal P,
    2. Dickinson P,
    3. Smith CL
    . 2013. Early life response to infection. Curr. Opin. Infect. Dis. 26:213–218. doi:10.1097/QCO.0b013e32835fb8bf.
    OpenUrlCrossRefPubMed
  7. 7.↵
    1. Labib AZ,
    2. Mahmoud AB,
    3. Eissa N,
    4. El Gendy FM,
    5. Soliman MA,
    6. Aly AA
    . 2013. Early diagnosis of neonatal sepsis: a molecular approach and detection of diagnostic markers versus conventional blood culture. Int. J. Microbiol. Res. 4:77–85.
    OpenUrl
  8. 8.↵
    1. Mancini N,
    2. Carletti S,
    3. Ghidoli N,
    4. Cichero P,
    5. Burioni R,
    6. Clementi M
    . 2010. The era of molecular and other non-culture-based methods in diagnosis of sepsis. Clin. Microbiol. Rev. 23:235–251. doi:10.1128/CMR.00043-09.
    OpenUrlAbstract/FREE Full Text
  9. 9.↵
    1. Sibley CD,
    2. Peirano G,
    3. Church DL
    . 2012. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology. Infect. Genet. Evol. 12:505–521. doi:10.1016/j.meegid.2012.01.011.
    OpenUrlCrossRefPubMed
  10. 10.↵
    1. Walsh P,
    2. Carroll J,
    3. Sleator RD
    . 2013. Accelerating in silico research with workflows: a lesson in simplicity. Comput. Biol. Med. 43:2028–2035. doi:10.1016/j.compbiomed.2013.09.011.
    OpenUrlCrossRefPubMed
  11. 11.↵
    1. Seemann T
    . 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics Bioinformatics 30:2068–2069. doi:10.1093/bioinformatics/btu153.
    OpenUrlCrossRefPubMedWeb of Science
  12. 12.↵
    1. Delcher AL,
    2. Harmon D,
    3. Kasif S,
    4. White O,
    5. Salzberg SL
    . 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27:4636–4641. doi:10.1093/nar/27.23.4636.
    OpenUrlCrossRefPubMedWeb of Science
  13. 13.↵
    1. Boeckmann B,
    2. Bairoch A,
    3. Apweiler R,
    4. Blatter M-C,
    5. Estreicher A,
    6. Gasteiger E,
    7. Martin MJ,
    8. Michoud K,
    9. O'Donovan C,
    10. Phan I,
    11. Pilbout S,
    12. Schneider M
    . 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365–370. doi:10.1093/nar/gkg095.
    OpenUrlCrossRefPubMedWeb of Science
  14. 14.↵
    1. Chen L,
    2. Yang J,
    3. Yu J,
    4. Yao Z,
    5. Sun L,
    6. Shen Y,
    7. Jin Q
    . 2005. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res. 33:D325–D328. doi:10.1093/nar/gki008.
    OpenUrlCrossRefPubMedWeb of Science
View Abstract
PreviousNext
Back to top
Download PDF
Citation Tools
Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom
K. A. Kropp, A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, C. Smith, P. Dickinson, A. O'Driscoll, K. Templeton, P. Ghazal, R. D. Sleator
Genome Announcements Sep 2014, 2 (5) e00908-14; DOI: 10.1128/genomeA.00908-14

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 Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom
(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 Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom
K. A. Kropp, A. Lucid, J. Carroll, V. Belgrudov, P. Walsh, B. Kelly, C. Smith, P. Dickinson, A. O'Driscoll, K. Templeton, P. Ghazal, R. D. Sleator
Genome Announcements Sep 2014, 2 (5) e00908-14; DOI: 10.1128/genomeA.00908-14
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • GENOME ANNOUNCEMENT
    • ACKNOWLEDGMENT
    • 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