Abstract
The genome of Salmonella enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1 was sequenced. The genome sequence of this fresh-vegetable isolate from Scandinavia will be useful for the elucidation of plant host factors in comparison to other serovars of S. enterica subsp. enterica.
Food-borne Salmonella enterica subsp. enterica serovars are a major cause of human gastroenteritis worldwide. Outbreaks have been traced to consumption of meat, egg, dairy, and plant products that have been contaminated during the production or processing stage. A diversity of serovars has been implicated (5). Salmonella enterica subsp. enterica serovar Weltevreden has emerged as an important food-borne pathogen in Southeast Asia (2, 6, 8) and Europe. S. Weltevreden was identified as the cause of a recent gastroenteritis outbreak in Scandinavia associated with contaminated alfalfa sprouts and fresh salad (3). Here, we report the complete genome of this S. Weltevreden outbreak strain, 2007-60-3289-1 (1).
Whole-genome shotgun sequencing was performed with a combined strategy using 454 single-end sequencing technology and Illumina paired-end technology (GATC, Konstanz, Germany). Totals of 270,589 and 6,442,668 reads were used to generate a draft assembly using Lasergene NGen version 2.2.0 (DNASTAR, Madison, WI), with overall coverages of 19.0- and 47.1-fold, respectively. Contigs were linked using complementary information from the draft genome sequences of S. Weltevreden SL484 and Salmonella enterica subsp. enterica serovar Dublin CT_02021853, followed by realignment using both sets of reads to confirm linkage. Final genome assembly after linkage resulted in 67 contigs with, in total, 4,922,273 bp (N50 = 196,931 bp). The S. Weltevreden 2007-60-3289-1 genome has a G+C content of 52.1%, with an estimated 4,858 coding sequences (CDS). Putative functions of encoding genes were automatically assigned using the GenDB annotation pipeline (7).
Salmonella pathogenicity islands (SPI) 1 to 6, 9, 11, 13, 14, 17, and 19 were detected in this strain, containing genes necessary for host-cell invasion and intracellular pathogenesis (4). The genome contains several phage-gene-containing regions and genomic islands unique for S. Weltevreden. These genomic islands encode mainly hypothetical proteins or conserved proteins with unknown function. A novel Salmonella plasmid, pSW82 (81,965 bp, with 48.8% G+C content), which contains 93 CDS, including genes encoding typical plasmid maintenance and stability proteins, (remnants of) transposases and integrases, and a two-gene type II nonribosomal peptide synthase/polyketide synthase, was identified.
The genome sequence of S. Weltevreden strain 2007-60-3289-1 will be used for comparative genomic analysis of this fresh produce isolate with the scallop isolate S. Weltevreden SL484 and other publically available S. enterica subsp. enterica serovar genomes. Serovar-discriminatory sequences from the Salmonella pan-genome will be developed as targets for specific detection of S. Weltevreden strains.
Nucleotide sequence accession numbers.
The 66 contigs of the draft chromosome of S. enterica subsp. enterica serovar Weltevreden strain 2007-60-3289-1 were deposited in the EMBL database under accession numbers FR775188 through FR775253; the plasmid pSW82 sequence was deposited under accession number FR775255.
ACKNOWLEDGMENTS
Strain S. Weltevreden 2007-60-3289-1 was kindly provided by Annette Nygaard Jensen (Zoonosis Laboratorium, DTU-FOOD, Denmark). Funding was provided by the European FP7 CORE-Organic ERA-Net Pilot Project “PathOrganic” and the Swiss Federal Office of Agriculture.
Footnotes
Published ahead of print on 4 February 2011.
REFERENCES
- 1. Arthurson V., Sessitsch A., Jäderlund L. 2011. Persistence and spread of Salmonella enterica serovar Weltevreden in soil and on spinach plants. FEMS Microbiol. Lett. 314:67–74 [DOI] [PubMed] [Google Scholar]
- 2. Bangtrakulnonth A., et al. 2004. Salmonella serovars from humans and other sources in Thailand, 1993–2002. Emerg. Infect. Dis. 10:131–136 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Emberland K. E., et al. 2007. Outbreak of Salmonella Weltevreden infections in Norway, Denmark and Finland associated with alfalfa sprouts, July-October 2007. Euro Surveill. 12:389–390 [DOI] [PubMed] [Google Scholar]
- 4. Hensel M. 2004. Evolution of pathogenicity islands of Salmonella enterica. Int. J. Med. Microbiol. 294:95–102 [DOI] [PubMed] [Google Scholar]
- 5. Herikstad H., Motarjemi Y., Tauxe R. V. 2002. Salmonella surveillance: a global survey of public health serotyping. Epidemiol. Infect. 129:1–8 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Learn-Han L., et al. 2008. Analysis of Salmonella Agona and Salmonella Weltevreden in Malaysia by PCR fingerprinting and antibiotic resistance profiling. Antonie Van Leeuwenhoek 94:377–387 [DOI] [PubMed] [Google Scholar]
- 7. Meyer F., et al. 2003. GenDB—an open source genome annotation system for prokaryote genomes. Nucleic Acids Res. 31:2187–2195 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Sood L., Basu S. 1979. Bacteriophage typing of Salmonella Weltevreden. Antonie Van Leeuwenhoek 45:595–604 [DOI] [PubMed] [Google Scholar]