Complete and Assembled Genome Sequence of Salmonella enterica subsp. enterica Serotype Senftenberg N17-509, a Strain Lacking Salmonella Pathogen Island 1

ABSTRACT

The genome of Salmonella enterica subsp. enterica serotype Senftenberg N17-509, a strain isolated from desiccated coconut, was sequenced using single-molecule real-time sequencing. It consists of a 5.1-Mbp chromosome and a 29-kb linear plasmid.

GENOME ANNOUNCEMENT

The Salmonella enterica subsp. enterica serotype Senftenberg strain N17-509 was isolated from desiccated coconut and provided different identification and typing challenges. The biochemical tests performed to confirm the Salmonella genus were inconclusive. A commercial real-time PCR identification system (Assurance GDS Salmonella kit; BioControl Systems, Bellevue, WA, USA) based on the invA gene yielded a negative result. A further rRNA-based fast method (VIT Salmonella kit; vermicon AG, Munich, Germany) and the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS)-based identification were positive for Salmonella. According to the Kauffmann-White scheme (Institut Pasteur, Paris, France), the strain was serotyped as Salmonella enterica subsp. enterica serovar 1,3,19:nt.

Genomic DNA was extracted using the Wizard genomic DNA purification kit, according to the manufacturer’s protocol (Promega AG, Dübendorf, Switzerland). The genome was sequenced using two single-molecule real-time (SMRT) cells on a PacBio RS II (Pacific Biosciences, Menlo Park, CA, USA) and was performed at the Functional Genomics Center Zurich (Zurich, Switzerland). The raw reads were filtered using the RS_Filter_Only protocol in the SMRT Portal (Pacific Biosciences) with 0.75 as polymerase read quality cutoff and a minimal length of 500 bp. A total of 91,709 reads with an average length of 11,001 bp were selected, corresponding to 1,008,898,178 sequenced base pairs and 197-fold coverage. The reads were assembled using the Canu assembler 1.6 (1) with the option “pacbio-raw” and an estimated genome size of 5.1 Mbp. The Canu output consisted of 3 contigs, which were further polished in CLC Workbench 7 (CLC, Aarhus, Denmark). Two contigs were combined and formed the chromosomal sequence. The third contig contained a plasmid-like sequence. The start of the chromosome was set at the origin of replication, determined using Ori-Finder (2).

A blastN search with the complete chromosome against all Enterobacteriales genomes in the NCBI nucleotide database revealed a highest identity of 99% and a coverage of 91% with the genome of Salmonella enterica subsp. enterica serotype Senftenberg 775W (=ATCC 43845). Hence, strain N17-509 was classified as belonging to Salmonella enterica subsp. enterica serotype Senftenberg. The genome of N17-509 consists of a 5,121,989-bp chromosome and a 29,600-bp extrachromosomal element designated pN17-509. The GC contents of the chromosome and pN17-509 are 52.2% and 36.5%, respectively. The genome was annotated using the NCBI Prokaryotic Genomes Annotation Pipeline and contains 5,361 genes, of which 5,241 encode proteins. Further, 84 tRNA genes and 7 rRNA operons are present. Remarkably, the Salmonella pathogen island 1 (SPI-1), harboring, e.g., the invA gene, is absent in this strain. The plasmid pN17-509 has 97% identity at 87% coverage with the linear plasmid pBSSB1 from Salmonella enterica subsp. enterica serovar Typhi that mediates flagellar variation (3).

Accession number(s).

The sequence and annotation data of the complete genome of Salmonella enterica subsp. enterica serovar Senftenberg strain N17-509 are deposited in the GenBank database with the accession numbers CP026379 for the chromosome and CP026380 for the plasmid.