ABSTRACT
We present the genome sequence of Staphylococcus aureus CI/BAC/25/13/W, which was isolated in 2013 as a contaminant of a platelet concentrate with abnormal clotting at the National Health Service Blood and Transplant. Assessment of the genome sequence showed the presence of one chromosome (2,719,347 bp) and one plasmid (1,533 bp).
ANNOUNCEMENT
Staphylococcus aureus is naturally present in the mucosa of healthy humans, and it is responsible for community- and health care-associated infections (1, 2). A major platelet concentrate (PC) contaminant (3), it is introduced into donated blood during venipuncture and is predominant in PCs due to the growth-promoting storage conditions for this blood product (4). S. aureus often escapes detection during routine PC screening with culture methods, sometimes causing septic transfusion reactions (3, 5).
Here, we announce the whole-genome sequence of S. aureus strain CI/BAC/25/13/W, part of hemovigilance studies in the United Kingdom. PC samples isolated by the National Health Service Blood and Transplant (NHSBT) from a 5-day-old contaminated split apheresis PC unit were cultured in the BacT/Alert system and yielded positive results within 3 h (6). For DNA isolation, S. aureus CI/BAC/25/13/W was streaked on blood agar plates from frozen stocks at −80°C, and single colonies were cultured at 35°C in 5 ml Trypticase soy broth with 0.6% yeast extract (7). Cells were collected by centrifugation and resuspended in DNA/RNA Shield tubes (Cedarlane), and DNA was extracted using the Quick-DNA high-molecular-weight (HMW) MagBead kit (Zymo Research Corp.) with lysozyme and RNAse A treatment according to the manufacturer’s manual. The same DNA extraction was used for both Nanopore and Illumina libraries.
Paired-end Illumina sequencing was performed using the Nextera XT DNA library preparation kit and a MiSeq instrument (v3 chemistry, 2 × 300-bp reads; Illumina Inc.) according to the manufacturer’s instructions. Nanopore sequencing libraries were constructed using the rapid barcoding sequencing kit (SQK-RBK004) and run using a FLO-MIN106 flow cell (R9.4) and a 1D MinION system (Oxford Nanopore Technologies) for 16 h according to the manufacturer’s protocol. Signal processing, base calling, demultiplexing, and adapter trimming were performed using Guppy (Guppy GPU v3.3.3+fa743ab).
Illumina reads (987,908 reads) were processed using fastp v0.20.0 (8) to remove adapter and barcode sequences, to correct mismatched bases in overlaps, and to filter low-quality reads, resulting in 971,430 filtered reads. From the Nanopore data (28,406 raw reads), reads of <1 kb were removed using Filtlong v0.2.0 (https://github.com/rrwick/Filtlong), resulting in 21,886 filtered reads with an N50 value of 11,786 bp. Hybrid assembly using Illumina and Nanopore filtered reads was performed using Unicycler v0.4.8 (cluster, reconcile, partition, and consensus functions, with default circularization and rotation) (9) in normal mode, yielding a closed, circular genome comprising a 2,719,347-bp chromosome and a circular 1,533-bp plasmid, with a GC content of 32.88% and average coverage of 96.2× and 61.5× for Illumina and Nanopore data, respectively. Genome annotation was performed using PGAP (release 2020-09-24.build4894; best-placed reference protein set) with GeneMarkS-2+ (https://github.com/ncbi/pgap) and analyzed with QUAST v5.0.2 (https://github.com/ablab/quast) (10). Default parameters were used for computational tools except where otherwise noted.
A total of 2,699 features were identified, including 2,537 genes, 79 pseudogenes, 0 CRISPR arrays, 19 rRNAs, 60 tRNAs, and 4 noncoding RNAs. PC storage conditions facilitate S. aureus proliferation and virulence enhancement, posing a serious health risk. S. aureus CI/BAC/25/13/W was assigned to sequence type 12 (ST12) based on the PubMLST database (11).
Data availability.
This genome is available in GenBank and the Sequence Read Archive (SRA) under the accession numbers indicated in Table 1.
TABLE 1.
Provenance and NCBI accession numbers for the CI/BAC/25/13/W isolate
| Parameter | Details |
|---|---|
| Isolate | CI/BAC/25/13/W |
| BioProject accession no. | PRJNA703973 |
| GenBank accession no. | |
| Chromosome | CP071102 |
| Plasmid | CP071103 |
| SRA accession no. | |
| Illumina reads | SRR13745244 |
| Nanopore reads | SRR13745250 |
| Country (region) | United Kingdom (England) |
| Year | 2013 |
ACKNOWLEDGMENTS
Funding for this study was provided by Canadian Blood Services and Health Canada.
We thank Nicholas Petronella (Health Canada, Bureau of Food Surveillance and Science Integration) and the bioinformatics team for providing infrastructure and data support.
Contributor Information
Franco Pagotto, Email: franco.pagotto@hc-sc.gc.ca.
David A. Baltrus, University of Arizona
REFERENCES
- 1.Jenul C, Horswill AR. 2019. Regulation of Staphylococcus aureus virulence. Microbiol Spectr 7:GPP3-0031-2018. doi: 10.1128/microbiolspec.GPP3-0031-2018. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Sato A, Yamaguchi T, Hamada M, Ono D, Sonoda S, Oshiro T, Nagashima M, Kato K, Okazumi S, Katoh R, Ishii Y, Tateda K. 2019. Morphological and biological characteristics of Staphylococcus aureus biofilm formed in the presence of plasma. Microb Drug Resist 25:668–676. doi: 10.1089/mdr.2019.0068. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Loza-Correa M, Kou Y, Taha M, Kalab M, Ronholm J, Schlievert PM, Cahill MP, Skeate R, Cserti-Gazdewich C, Ramirez-Arcos S. 2017. Septic transfusion case caused by a platelet pool with visible clotting due to contamination with Staphylococcus aureus. Transfusion 57:1299–1303. doi: 10.1111/trf.14049. [DOI] [PubMed] [Google Scholar]
- 4.Ramirez-Arcos S, Evans S, McIntyre T, Pang C, Yi QL, DiFranco C, Goldman M. 2020. Extension of platelet shelf life with an improved bacterial testing algorithm. Transfusion 60:2918–2928. doi: 10.1111/trf.16112. [DOI] [PubMed] [Google Scholar]
- 5.Chen L, Tang ZY, Cui SY, Ma ZB, Deng H, Kong WL, Yang LW, Lin C, Xiong WG, Zeng ZL. 2020. Biofilm production ability, virulence and antimicrobial resistance genes in Staphylococcus aureus from various veterinary hospitals. Pathogens 9:264. doi: 10.3390/pathogens9040264. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Brailsford SR, Tossell J, Morrison R, McDonald CP, Pitt TL. 2018. Failure of bacterial screening to detect Staphylococcus aureus: the English experience of donor follow-up. Vox Sang 113:540–546. doi: 10.1111/vox.12670. [DOI] [PubMed] [Google Scholar]
- 7.U.S. Food and Drug Administration. 1998. BAM media M157: Trypticase soy broth with 0.6% yeast extract (TSBYE). https://www.fda.gov/food/laboratory-methods-food/bam-media-m157-trypticase-soy-broth-06-yeast-extract-tsbye.
- 8.Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. doi: 10.1093/bioinformatics/bty560. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Wick RR, Judd LM, Gorrie CL, 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Jolley KA, Bray JE, Maiden MC. 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:124. doi: 10.12688/wellcomeopenres.14826.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
This genome is available in GenBank and the Sequence Read Archive (SRA) under the accession numbers indicated in Table 1.
TABLE 1.
Provenance and NCBI accession numbers for the CI/BAC/25/13/W isolate
| Parameter | Details |
|---|---|
| Isolate | CI/BAC/25/13/W |
| BioProject accession no. | PRJNA703973 |
| GenBank accession no. | |
| Chromosome | CP071102 |
| Plasmid | CP071103 |
| SRA accession no. | |
| Illumina reads | SRR13745244 |
| Nanopore reads | SRR13745250 |
| Country (region) | United Kingdom (England) |
| Year | 2013 |