ABSTRACT
We report here the closed genome sequence of one Salmonella enterica subsp. enterica serovar Bovismorbificans strain isolated from dried pork sausage consumed by a patient suffering from salmonellosis.
ANNOUNCEMENT
Salmonella enterica subsp. enterica serovar Bovismorbificans is responsible for an increased number of foodborne infections in Europe (1–3). We provide here the whole-genome sequence of S. Bovismorbificans strain 2020LSAL11867, which has been isolated (using the ISO6579-1:2017 method) from dried pork sausage associated with a Salmonella outbreak in France. The whole genome was sequenced using NovaSeq (Illumina, Inc., San Diego, CA, USA) and MinION (Nanopore, Oxford Science Park, Oxford, UK) technologies. Prior to genomic DNA isolation for Illumina and MinION sequencing, the strain was cultivated overnight at 37°C in brain heart infusion (BHI). Genomic DNA was prepared from 2 ml of BHI overnight cultures using the Wizard high-molecular-weight (HMW) DNA extraction kit (Promega, France) according to the manufacturer’s instructions. The Illumina paired-end sequencing (2 × 150-bp format) was performed as described (4). For MinION sequencing, the DNA was neither sheared nor size selected. The MinION library was prepared with 500 ng DNA using the ligation sequencing kit (SQK-LSK109; Oxford Nanopore Technologies, France) according to the manufacturer’s instructions, and long-read sequencing was performed using a Flongle (R9.4.1) flow cell on the Oxford Nanopore MinION sequencer for 24 h.
Default parameters were used for all software unless otherwise specified. The Illumina sequencing resulted in 8,856,638 raw reads, which were analyzed for quality control, normalization, and assembly using the ARTwork workflow (5). The raw reads were normalized (100×) using BBMap v38.22 and BBNorm v36.14 (6). The reads were trimmed (Phred score, 30×; trailing, >20; minimum length, 50 bp) using Trimmomatic v0.33 (7) and de novo assembled using SPAdes v3.13.0 (8) (minimum contig length, 200 bp), producing 15 contigs.
The raw fast5 files produced by the MinION sequencing were base called using the ONT Guppy v4.4.2 base caller with high accuracy mode. The sequencing output was 55,329 reads. The quality of the MinION read files as determined using NanoPlot v1.28.2 (9) passed the standard quality checks with a mean read quality of 11.0 and median read quality of 11.7. The read length N50 value was 20.9 kbp.
Hybrid assembly was performed using the Unicycler v0.4.8 assembler (10), combining the sequence data sets generated by both Illumina and Oxford Nanopore Technologies sequencing. Unicycler default parameters were used, except –min_fasta_length 1000, to obtain a genome of 4,676,102 bp with a GC content of 52.29%, divided into 3 circular contigs—the chromosome (4,667,486 bp) and two plasmids of 4,712 bp (GC content, 51.10%; GenBank accession number CP073716.1) and 3,904 bp (GC content, 51.10%; CP073717.1). Unicycler was used to circularize the replicons and search for dnaA or repA alleles. If such a sequence was found, the replicon as rotated so that it began with that gene encoded on the forward strand. S. Bovismorbificans was attributed using the SeqSero v1.2 application on the Center for Genomic Epidemiology website (https://cge.cbs.dtu.dk/services), and the multilocus sequence type (ST) was found to be ST142. The sequence was annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (PGAP) at http://www.ncbi.nlm.nih.gov/genome/annotation_prok. Sequencing metrics are provided in Table 1.
TABLE 1.
NCBI accession numbers and assembly metrics of the S. Bovismorbificans draft genome sequence
| Feature | Data |
|---|---|
| GenBank accession no. | GCF_018340585.1 |
| SRA accession no. | PRJNA722181 |
| Origin | Dried pork sausage |
| Yr | 2020 |
| No. of contigs | 3 |
| Genome size (Mbp) | 4.6675 |
| GC content (%) | 52.29 |
| N50 (kbp) | 4,667 |
| No. of coding sequences (per PGAP) | 4,308 |
Data availability.
The genome of this strain, which harbors 4,308 coding sequences, was deposited in NCBI/DDBJ/ENA/GenBank under the accession number GCF_018340585.1. The raw data were deposited in the SRA database under the accession number PRJNA722181.
Contributor Information
Patrick Fach, Email: patrick.fach@anses.fr.
Vincent Bruno, University of Maryland School of Medicine.
REFERENCES
- 1.Brandwagt D, van den Wijngaard C, Tulen AD, Mulder AC, Hofhuis A, Jacobs R, Heck M, Verbruggen A, van den Kerkhof H, Slegers-Fitz-James I, Mughini-Gras L, Franz E. 2018. Outbreak of Salmonella Bovismorbificans associated with the consumption of uncooked ham products, the Netherlands, 2016 to 2017. Euro Surveill 23:17-00335. doi: 10.2807/1560-7917.ES.2018.23.1.17-00335. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Rimhanen-Finne R, Niskanen T, Lienemann T, Johansson T, Sjoman M, Korhonen T, Guedes S, Kuronen H, Virtanen MJ, Makinen J, Jokinen J, Siitonen A, Kuusi M. 2011. A nationwide outbreak of Salmonella bovismorbificans associated with sprouted alfalfa seeds in Finland, 2009. Zoonoses Public Health 58:589–596. doi: 10.1111/j.1863-2378.2011.01408.x. [DOI] [PubMed] [Google Scholar]
- 3.Knoblauch AM, Bratschi MW, Zuske MK, Althaus D, Stephan R, Hachler H, Baumgartner A, Prager R, Rabsch W, Altpeter E, Jost M, Mausezahl M, Hatz C, Kiefer S. 2015. Cross-border outbreak of Salmonella enterica ssp. enterica serovar Bovismorbificans: multiple approaches for an outbreak investigation in Germany and Switzerland. Swiss Med Wkly 145:w14182. doi: 10.4414/smw.2015.14182. [DOI] [PubMed] [Google Scholar]
- 4.Sevellec Y, Granier SA, Radomski N, Felten A, Le Hello S, Feurer C, Mistou M-Y, Cadel-Six S. 2018. Complete genome sequence of Salmonella enterica subsp. enterica serotype Derby, associated with the pork sector in France. Microbiol Resour Announc 7:e01027-18. doi: 10.1128/MRA.01027-18. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Vila Nova M, Durimel K, La K, Felten A, Bessieres P, Mistou M-Y, Mariadassou M, Radomski N. 2019. Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale. BMC Genomics 20:814. doi: 10.1186/s12864-019-6188-x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Bushnell B, Rood J, Singer E. 2017. BBMerge—accurate paired shotgun read merging via overlap. PLoS One 12:e0185056. doi: 10.1371/journal.pone.0185056. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, 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. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.De Coster W, D'Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669. doi: 10.1093/bioinformatics/bty149. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.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]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome of this strain, which harbors 4,308 coding sequences, was deposited in NCBI/DDBJ/ENA/GenBank under the accession number GCF_018340585.1. The raw data were deposited in the SRA database under the accession number PRJNA722181.