Abstract
Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.
GENOME ANNOUNCEMENT
Staphylococcus epidermidis is a Gram-positive bacterium naturally found on human skin (1) and an important opportunistic pathogen linked with neonatal blood sepsis (2–5).
Preterm neonates are a highly susceptible patient group for bacterial infections, due to their naive immune status and the invasive procedures to which they are often subjected to in neonatal ICU settings (2, 6, 7). Rapid detection of blood sepsis and characterization of the causative pathogen are critical first steps to enable appropriate treatment and improved prognostic outcomes (8–10). As part of the ClouDx-i project consortium, we aim to extend our knowledge of currently circulating pathogenic strains linked with neonatal blood sepsis to inform the continued development of new and improved molecular diagnostic assays (11). Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis strains, isolated from preterm neonates at the Royal Infirmary, Edinburgh, United Kingdom, in 2014. Positivity for blood sepsis and species of each isolate was confirmed by classical microbiological identification and characterization techniques.
Isolates were grown overnight at 37°C on Luria broth (LB) agar, and genomic DNA was isolated using Qiagen genomic tips (Venlo, Limburg, Netherlands). Genomic DNA fragments, ranging in size from 2 to 10 kb, were generated by sonication. Fragments were subsequently used to produce a non-size-selected genome library using the Nextera mate-pair kit (Illumina, San Diego, CA). The resulting libraries were then sequenced on an Illumina MiSeq using MiSeq Reagent kit v3. Genomic sequence assembly, analysis, and automated reporting were carried out using the Simplicity software pipeline (12). The results of this analysis are summarized in Table 1. Sequence assembly was achieved using a de-novo assembly pipeline based on the Spades 3.10 assembly tool, with k-mers K21, K33, K55, K77, K99, and K127 nucleotides in length. Each genome was initially annotated with the Prokka tool (13) and the identified 16S rRNA genes were used to confirm the species as S. epidermidis in each case. Each genome was then screened using the Glimmer 3 tool (14). The predicted open reading frames (ORFs) were compared to the Uniprot Trembl database (15) using BLASTp.
TABLE 1 .
Genomic sequence assembly overview
| Strain | Total no. of reads |
Fold coverage | G+C content (%) | Total contigs (>1,000 bp) | Largest contig (bp) | No. of ORFs |
Accession no. |
|---|---|---|---|---|---|---|---|
| NGS-ED-1107 | 2,599,368 | 135.2 | 32.0 | 53 | 207,733 | 2,570 | JZUK00000000 |
| NGS-ED-1109 | 2,436,309 | 114.6 | 32.0 | 51 | 360,587 | 2,252 | JZUL00000000 |
| NGS-ED-1110 | 4,476,721 | 223.5 | 32.0 | 45 | 207,733 | 2,515 | JZUM00000000 |
| NGS-ED-1111 | 5,197,793 | 163.5 | 32.0 | 44 | 250,293 | 2,583 | JZUN00000000 |
| NGS-ED-1117 | 1,607,705 | 76.0 | 32.0 | 48 | 206,303 | 2,459 | JZUO00000000 |
| NGS-ED-1118 | 1,681,207 | 94.1 | 31.9 | 48 | 206,303 | 2,444 | JZUP00000000 |
Samples were handled in accordance with local ethical approval by the ethics committees of the NHS Lothian SAHSC Bioresource and NHS R&D office (project 2011/R/NE/01) and the HSS BioResource (request 13/ES/0126).
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1.
ACKNOWLEDGMENT
This work was supported by the ClouDx-i IAPP EU FP7 project, coordinated by RDS.
Footnotes
Citation Walsh P, Bekaert M, Carroll J, Manning T, Kelly B, O’Driscoll A, Lu X, Smith C, Dickinson P, Templeton K, Ghazal P, Sleator RD. 2015. Draft genome sequences of six different Staphylococcus epidermidis clones, isolated individually from preterm neonates presenting with sepsis at Edinburgh’s Royal Infirmary. Genome Announc 3(3):e00471-15. doi:10.1128/genomeA.00471-15.
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