First Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Worthington Strain CFSAN051295, Isolated from Pistachio.

We report here, using third-generation, single-molecule, real-time DNA sequencing, the first complete genome sequence of Salmonella enterica serovar Worthington CFSAN051295, isolated from pistachios in the United States. The genome consists of a single 4.9-Mb chromosome.

ANNOUNCEMENT

The presence of Salmonella spp. in low-moisture foods, such as tahini, cereal, black pepper, and pistachios, has led to a number of multistate outbreaks (https://wwwn.cdc.gov/norsdashboard/), and in recent years, the incidence of these outbreaks has increased (1). Pistachios have been linked to outbreaks of salmonellosis in the United States, with a limited range of Salmonella enterica serovars (Montevideo and Senftenberg), but other serovars, such as Salmonella enterica serovar Worthington, were isolated during a study looking at the prevalence of Salmonella spp. in pistachios (2). S. Worthington is very common among pigs and poultry, with few documented incidences of contamination in low-moisture foods (https://www.ncbi.nlm.nih.gov/pathogens/). Here, we report the complete genome sequence of strain CFSAN051295, which is one of a few occurrences of this serovar in a low-moisture food.

Using the Sequel system (Pacific Biosciences [PacBio], Menlo Park, CA), we fully closed the first genome sequence of Salmonella Worthington CFSAN051295, which was isolated from raw pistachio in 2016 in the United States. The isolate was cultured in Trypticase soy broth (Becton, Dickinson, Franklin Lakes, NJ) overnight at 37°C. The S. Worthington genomic DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Inc., Valencia, CA). A single SMRTbell 20-kb library was prepared according to the 20-kb PacBio sample preparation protocol using a BluePippin size selection system (Sage Science, Beverly, MA). The genome was sequenced using a single-molecule real-time (SMRT) cell with the PacBio Sequel sequencing platform, following the manufacturer’s specifications. The total number of reads was 256,718, with an insert read length of 7,810 bp. Analysis of the data was performed using PacBio SMRT Link version 5.1. The genome was de novo assembled using the Hierarchical Genome Assembly Process version 4.0 (HGAPv4) with default parameters (3). The assembly resulted in a single contig. The final sequence was uploaded into SMRT Link, and the final polished sequence was obtained using the resequencing analysis with default parameters. The assembled sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and deposited in DDBJ/EMBL/GenBank. Isolate CFSAN051295 was sequenced with 449× coverage, with a genome size of 4,914,635 bp and a GC content of 52.2%. Base modification analysis of strain CFSAN051296 was also performed and submitted to NCBI.

Prophage analysis using PHASTER, an upgraded version of the PHAST Web server, identified the presence of four intact prophages (4). The first prophage has sequence similarity to Sal_SPN3UB (GenBank accession number NC_019545) and contained the recT gene, which is involved in recombination and repair. The other three prophages show sequence similarity to Sal_vB_SosS (NC_018279), Entero_I2_2 (NC_001332), and Gifsy_1 (NC_010392).

Data availability.

The complete genome sequence of strain CFSAN051295 has been deposited in DDBJ/ENA/GenBank under the accession number CP029041. The raw reads have been submitted to the SRA under BioProject number PRJNA186035 and accession number SRR8106747.