Abstract
Salmonella enterica is a bacterial species that is a major cause of illness in humans and food-producing animals. S. enterica exhibits considerable inter-serovar diversity, as evidenced by the large number of host adapted serovars that have been identified. The development of methods to assess genome diversity in S. enterica will help to further define the limits of diversity in this foodborne pathogen. Thus, we evaluated a PCR assay, which targets prophage integrase genes, as a rapid method to investigate S. enterica genome diversity. To evaluate the PCR prophage integrase assay, 49 isolates of S. enterica were selected, including 19 clinical isolates from clonal serovars (Enteritidis and Heidelberg) that commonly cause human illness, and 30 isolates from food-associated Salmonella serovars that rarely cause human illness. The number of integrase genes identified by the PCR assay was compared to the number of integrase genes within intact prophages identified by whole genome sequencing and phage finding program PHASTER. The PCR assay identified a total of 147 prophage integrase genes within the 49 S. enterica genomes (79 integrase genes in the food-associated Salmonella isolates, 50 integrase genes in S. Enteritidis, and 18 integrase genes in S. Heidelberg). In comparison, whole genome sequencing and PHASTER identified a total of 75 prophage integrase genes within 102 intact prophages in the 49 S. enterica genomes (44 integrase genes in the food-associated Salmonella isolates, 21 integrase genes in S. Enteritidis, and 9 integrase genes in S. Heidelberg). Collectively, both the PCR assay and PHASTER identified the presence of a large diversity of prophage integrase genes in the food-associated isolates compared to the clinical isolates, thus indicating a high degree of diversity in the food-associated isolates, and confirming the clonal nature of S. Enteritidis and S. Heidelberg. Moreover, PHASTER revealed a diversity of 29 different types of prophages and 23 different integrase genes within the food-associated isolates, but only identified four different phages and integrase genes within clonal isolates of S. Enteritidis and S. Heidelberg. These results demonstrate the potential usefulness of PCR based detection of prophage integrase genes as a rapid indicator of genome diversity in S. enterica.
Highlights
Salmonella enterica is a Gram-negative pathogen that infects humans and animals
In order to determine whether prophage integrase genes could be used to assess genome diversity in S. enterica, we chose isolates from serovars that are consistently implicated in outbreaks of salmonellosis and that are clonal in nature as well as isolates from rare serovars that were isolated from diverse food sources
To investigate the potential for the polymerase chain reaction (PCR) assay to be used as a rapid screening tool to determine genome diversity in Salmonella, we compared the results of the PCR assay with core genome Single-nucleotide polymorphisms (SNPs) sequence alignments for a population of clonal and diverse S. enterica isolates chosen from the Salmonella Foodborne Syst-OMICS Database (SalFoS) database
Summary
Salmonella enterica is a Gram-negative pathogen that infects humans and animals. S. enterica is divided into six sub-species on the basis of genetic content (Wain and O’Grady, 2017), and contains more than 2,500 serovars. In Canada, salmonellosis accounts for 87,510 human cases, and 17 deaths each year (Thomas et al, 2013, 2015). While there are more than 2,500 serovars of S. enterica subspecies I, the majority (75%) of all salmonellosis cases in Canada are caused by only 10 serovars. In the United States, where Salmonella accounts for 1.2 million illnesses and 450 deaths annually (Scallan et al, 2011), the top 10 serovars cause approximately 57% of illnesses. While the implementation of Hazard Analysis and Critical Control Point (HACCP) programs in the food industry has reduced contamination of foods of animal origin, there has been increased recognition of Salmonella contamination associated with fresh produce, which accounts for approximately half of all fresh produce outbreaks due to bacteria in the United States and European Union (Callejón et al, 2015)
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