Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain

• Published in: PloS one Vol. 16; no. 11; p. e0259471
• Main Authors: Haendiges, Julie, Davidson, Gordon R., Pettengill, James B., Reed, Elizabeth, Ramachandran, Padmini, Blessington, Tyann, Miller, Jesse D., Anderson, Nathan, Myoda, Sam, Brown, Eric W., Zheng, Jie, Tikekar, Rohan, Hoffmann, Maria
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04.11.2021; Public Library of Science (PLoS)
• Subjects: Biology and Life Sciences; Biopesticides; Computer and Information Sciences; Contamination; Data analysis; Diagnosis; DNA, Environmental - analysis; Earth Sciences; Epidemics; Food; Food contamination & poisoning; Food Contamination - analysis; Food safety; Food science; Food Storage - methods; Genetics; Genomic analysis; Genomic islands; Health aspects; Homeostasis; Humans; Medicine and Health Sciences; Metagenomics; Metagenomics - methods; Multilocus Sequence Typing; Nucleotide sequence; Nucleotides; Nut industry; Nutrition; Pathogens; Patient outcomes; Phylogeny; Pistachio; Pistachio nuts; Pistacia; Pistacia - microbiology; Polymorphism; Polymorphism, Single Nucleotide; Product recalls; Public health; Relative humidity; Retrospective Studies; Risk factors; Safety and security measures; Salmonella; Salmonella - genetics; Salmonella - isolation & purification; Salmonella food poisoning; Salmonellosis; Single-nucleotide polymorphism; Supply chains; Survivability; Survival; United States; Whole Genome Sequencing; United States; United Kingdom; United States > US; Maryland; California
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0259471

Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed an in-depth retrospective data analysis of Salmonella associated with pistachios as well as a storage study to evaluate the survivability of Salmonella on inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed utilizing short-read and long-read sequencing technologies. The sequence data were analyzed using two methods: the FDA’s Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multilocus Sequence Typing (wgMLST). The year-long storage study evaluated the survival of five strains of Salmonella on pistachios stored at 25 °C at 35% and 54% relative humidity (RH). Our results demonstrate: i) evidence of persistent Salmonella Senftenberg and Salmonella Montevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) in Salmonella Senftenberg and Montevideo strains in the pistachio supply chain; and iii) the use of metagenomic analysis is a novel tool for determining the composition of serovar survival in a cocktail inoculated storage study.