Abstract
Salmonella bongori is a close relative of the highly virulent members of S. enterica subspecies enterica, encompassing more than 2,500 serovars, most of which cause human salmonellosis, one of the leading food-borne illnesses. S. bongori is only very rarely implicated in infections. We here present the sequence of a clinical isolate from Switzerland, S. bongori strain N268-08.
GENOME ANNOUNCEMENT
The complete genome sequence of Salmonella bongori strain N268-08 was determined de novo using the Pacific Biosciences SMRT sequencing technology (Functional Genomics Center, Zurich, Switzerland). Assembly was carried out using the SMRT-Analysis software (version 2.0, HGAP assembly protocol), and the sequence was automatically annotated using RAST (http://rast.nmpdr.org/) (1). It was aligned and compared to that of S. bongori NCTC12419 (2) by progressive Mauve (3, 4).
Sequence information for N268-08 is provided in comparison to NCTC12419 (2). The sequence of N268-08 is 4.7 Mbp (NCTC12419, 4.5 Mbp) long, and the G+C content is 51.3% (NCTC12419, 51.3%). A total of 4,642 coding sequences (CDS) (NCTC12419, 4,054 CDS), 22 rRNAs (NCTC12419, 22 rRNAs), and 86 tRNAs (NCTC12419, 84 tRNAs) were identified. Mauve alignment revealed that a prophage (~30 kb) seemed to be inverted and inserted at another location in N268-08 (2,769,647 to 2,738,043 versus 3,084,741 to 3,115,162 in NCTC12419).
N268-08 features two major deletions (>20 kb) compared to NCTC12419, in a 23.2-kb prophage (304,635 to 327,860) and a 27.6-kb region (2,013,350 to 2,040,915) encoding two putative phage integrases, transcriptional regulators, and membrane transport proteins. N268-08 features 6 insertions (>20 kb). Four are putative prophages: 37.8 kb (478,064 to 515,915) with similarities to phage Mu; 20.0 kb (1,022,461 to 1,042,491); 55.3 kb (1,317,949 to 1,373,269); and 50.8 kb (1,985,799 to 2,036,593) with two Gifsy-2-like proteins. The other insertions are 21.7 kb (1,721,254 to 1,742,938) with hypothetical proteins and 62.2 kb (4,528,603 to 4,590,835) featuring genes associated with fimbriae and type IV secretory-pathway-associated proteins VirB4/D4 (5, 6).
De novo assembly yielded a 90.0-kb plasmid featuring the tra operon of incompatibility group F. The best hits (BLASTn) are to Salmonella plasmids p14-120 (accession no. JQ418538) and pSGSC3045-121 (accession no. JQ418541).
The sequence type (as proposed in reference 7) of N268-08 is novel (aroC132 dnaN30 hemD103 hisD134 purE126 sucA133 thrA129) (http://mlst.ucc.ie/mlst/mlst/dbs/Senterica/).
Nucleotide sequence accession numbers.
The genome and plasmid sequences of N268-08 have been deposited under the accession numbers CP006608 and CP006609 at NCBI.
ACKNOWLEDGMENTS
We are thankful for the gift of S. bongori N268-08 by Herbert Hächler of the National Center for Enterobacteria (NENT, Zurich, Switzerland).
This work was not supported by any external funding.
Footnotes
Citation Marti R, Hagens S, Loessner MJ, Klumpp J. 2013. Genome sequence of Salmonella bongori strain N268-08, a rare clinical isolate. Genome Announc. 1(4):e00580-13. doi:10.1128/genomeA.00580-13.
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