Genome Sequence of the Salmonella enterica subsp. enterica Serovar Namur Strain 05-2929, Lacking the Salmonella Atypical Fimbrial Operon.

This paper announces the genome sequence and annotation of Salmonella enterica subsp. enterica serovar Namur strain 05-2929. S. Namur is a new serovar (39:z4,z23:-) that was isolated from a patient with salmonellosis in 2005 in Namur, Belgium, and has been identified as lacking the Salmonella atypical fimbrial (saf) operon.

GENOME ANNOUNCEMENT

Salmonella is one of the major causes of food-borne zoonoses. Between 90,000 and 135,000 cases per year of human salmonellosis were reported in Europe in the period 2008 to 2012 (1). The genus Salmonella includes 2 species, i.e., S. enterica and S. bongori, which are both pathogenic for humans (2). S. enterica is further divided into 6 subspecies and 2,587 serovars, which are often named according to the place of first isolation. The serovars are unequally distributed, since 1,547 belong to the subspecies S. enterica subsp. enterica (subsp. I) (2), which is most often found in human and food samples (1).

In 2005, a Salmonella strain (05-2929) was isolated at the Centre Hospitalier Régional de Namur, Belgium, from a stool sample of a patient with salmonellosis. The serotyping of this strain was performed at the Belgian National Reference Center for Salmonella and Shigella. It was characterized as a Salmonella enterica subsp. enterica (subsp. I) serovar, presenting a new antigenic formula, i.e., 39:z4,z23:−. This was confirmed by the World Health Organization (WHO) Collaborating Centre for Reference and Research on Salmonella, Pasteur Institute, Paris, France. This new serovar was added to the White-Kauffmann-Le Minor scheme in 2010 as the S. Namur serovar (2).

During the selectivity test of the validation of SYBR green real-time PCR (qPCR) assays for detection in food samples of Salmonella spp. based on genus-, species-, and subspecies-specific marker genes, genomic DNA isolated from this S. Namur serovar was identified as not amplified by two qPCR assays targeting safC (3). safC belongs to the Salmonella atypical fimbrial (saf) operon (4) and was reported to be specific for S. enterica subsp. enterica (5).

To further characterize this S. Namur 05-2929 strain, whole-genome sequencing was performed on an Illumina HiSeq 2000 run using a paired-end and a 4-kbp insert mate-pair library (performed by BaseClear B.V., Leiden, the Netherlands). Sequencing yielded 4,901,007 paired-end and 11,099,754 mate-pair reads (50 cycles, 439-fold coverage), which were assembled de novo using the de novo assembly option of the CLC Genomics Workbench version 5.1 (CLC bio). The assembly generated 21 scaffolds consisting of 95 contigs, with a maximum scaffold size of 3,131,320 bp and a minimum size of 323 bp. The total sequence length is 4,842,244 bp and has a G+C content of 51.96%.

Genome annotation was performed by the NCBI Prokaryotic Genome Annotation Pipeline (2013) and predicted 4,616 genes, including 4,501 protein-coding genes. This annotation confirmed the deletion of the entire saf operon in this S. Namur strain. Strains of other subspecies I serovars lacking safC have been reported previously (6). Moreover, based on the presence and absence of clade-specific genes and previously identified single nucleotide polymorphisms (7), this S. Namur strain can be further classified as an S. enterica subsp. enterica clade A strain.

It would be interesting to further investigate these deletion and diversification events using the newly available S. Namur sequence and to extend this analysis to other strains of the S. Namur serovar.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AWGG00000000. The version described in this paper is version AWGG01000000.