Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States.

A multistate outbreak of 11 Salmonella infections linked to pistachio nuts occurred in 2016. In this announcement, we report the complete genome sequences of four Salmonella enterica subsp. enterica serovar Senftenberg and S. enterica subsp. enterica serovar Montevideo isolates from pistachios collected during the 2016 outbreak investigation.

GENOME ANNOUNCEMENT

The Centers for Disease Control and Prevention estimates that there are 1.2 million illnesses, 23,000 hospitalizations, and 450 deaths in the United States due to Salmonella infection every year (https://www.cdc.gov/salmonella/index.html). Salmonella bacteria have been shown to persist in low-moisture environments and represent a potential hazard for a wide range of low-moisture foods and food materials (1). Salmonella enterica subsp. enterica serovar Senftenberg and S. enterica subsp. enterica serovar Montevideo have been isolated from pistachios since 2009. In March 2016, the Centers for Disease Control and Prevention (CDC) announced a 9-state outbreak of S. Senftenberg and S. Montevideo infections, which resulted in 11 identified cases and 2 hospitalizations (2). The collaborative investigation by federal, state, and local officials linked these illnesses to the consumption of pistachios and traced the pistachios to a single firm. The investigation led to a voluntary recall for a limited number of shelled and in-shell pistachios (2). Clinical isolates and isolates recovered from raw pistachios were found to be genetically related based on whole-genome sequencing (2).

In this report, we announce the availability of four complete closed genome sequences of S. Senftenberg (isolates CFSAN045763 and CFSAN047866) and S. Montevideo (isolates CFSAN045764 and CFSAN051296), which were isolated from pistachios. The U.S. Food and Drug Administration obtained these isolates as part of a federal public health investigation during the multistate outbreak.

The isolates were cultured in Trypticase soy broth (Becton, Dickinson, Franklin Lakes, NJ, USA) overnight at 37°C. Genomic DNA was sequenced based on previously reported procedures (3). The genomes were de novo assembled using the Hierarchical Genome Assembly Process version 4.0 (PacBio) (4). The assembled sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline and deposited at DDBJ/EMBL/GenBank.

Isolate CFSAN045764 was sequenced with 375× coverage; its genome size was 4,694,399 bp, and the G+C content was 52.2%. Isolate CFSAN051296 was sequenced with 204× coverage; its genome size was 4,694,373 bp, and the G+C content was 52.2%. Isolate CFSAN045763 was sequenced with 275× coverage; its genome size was 4,766,139, and the G+C content was 52.1%. Isolate CFSAN047866 was sequenced with 477× coverage; its genome size was 4,807,052, and the G+C content was 52.1%.

Accession number(s).

The complete genome sequences reported here are available in GenBank under the accession numbers CP029038, CP029039, CP029040, and CP029336.