EVALUATION OF THE COPPER HOMEOSTASIS AND SILVER RESISTANCE ISLAND AND ITS ROLE IN PERSISTENCE OF SALMONELLA ENTERICA

Abstract

Salmonella enterica is one of the leading bacterial cause of foodborne illness in the UnitedStates. Although there are many serovars, only a small subset causes human illness. Since Salmonella is ubiquitous in the environment, the Food and Drug Administration has established regulations for food processors to ensure that the products are free of contamination. Low-moisture foods are commonly ready-to-eat, and due to the low water activity do not promote growth of bacteria. However, Salmonella has been shown to persist in these foods. There havebeen two outbreaks and multiple recalls in the United States due to contaminated pistachios. Based on a retrospective study, results show that there is evidence of a contamination in the growing orchard and a significant number of Salmonella isolates from the environments contain the Copper Homeostasis and Silver Resistance Island (CHASRI) cassette. This raises several questions: what is the prevalence of CHASRI among different Salmonella isolates from food and environmental sources? Does presence of CHASRI enable Salmonella to survive better against copper stress? And whether presence of CHASRI provide cross-protection against other stresses such as desiccation and thermal treatment? This dissertation attempts to answer those questions. The prevalence of the CHASRI in Salmonella was determined by the use of publicly availablewhole genome sequencing data. The CHASRI was found in 61 different serovars and types of sources. The presence of the CHASRI in isolates from low-moisture foods that have caused previous outbreaks (peanut butter, nuts, spices) was interesting to note, and leads to future studies on correlations between this island and virulence. Based on results of phylogenetic analysis of CHASRI sequences from closed genomes, we determined there were four types of CHASRI found in Salmonella. Traditionally, the Salmonella Genomic Island-4 (SGI-4) is found but in addition the CHASRI can incorporate by itself, within a variant of SGI-4, or via a rare plasmid. Interestingly, the sequence of the CHASRI from SGI-4 and the variant SGI-4 were highly different. The high SNP differences in sequence along with the difference in the arsenic operon led to the conclusion that these variants arose independently. A Salmonella Senftenberg strain (CFSAN047523), isolated from pistachios, was used to createthree knockouts (∆cus, ∆pco, and ∆CHASRI). Previous studies have looked at the minimum inhibitory concentration (MIC) of strains with and without the CHASRI but have omitted the minimum bactericidal concentration (MBC). In this study, we used the knockouts to test for both MIC and MBC. While the MIC was similar for the strains, the MBC was greater in the wild type and partial CHASRI knockouts. Growth and inactivation kinetics were measured in different concentrations of copper sulfate. At higher levels of copper sulfate, the presence of the CHASRI made cells more resilient to inactivation by copper sulfate. Evidence shows that the stress response in Salmonella has the ability to crosstalk and provideprotection against multiple stresses. To investigate this phenomenon further, our isolates were tested against a multitude of stresses to evaluate for cross-protection that may be due to theCHASRI. Cells undergoing copper stress were better equipped to survive lethal copper concentrations and desiccation if the CHASRI was present. The presence of Salmonella in final pistachio products that have been fully processed identifies that some adaptation and stress response is occurring in the processing facility. Inoculated pistachios with the wild type and ∆CHASRI strain were thermally processed to test for survivors. This study showed that the presence of the CHASRI gave the isolate an advantage to survive thermal processing after desiccation. Overall, this study presents the prevalence of the CHASRI in Salmonella enterica as well as theimportant role it plays in copper tolerance. The evidence of cross-protection and tolerance to copper leads to future research regarding gene expression and virulence assessment.