Purpose: The objective of this study was to assess if a PCR assay designed to detect tyrosine phage integrases of the Enterobacteriaceae family could be used as a rapid screening tool to assess genome diversity in Salmonellae.
Methods: A PCR assay designed against thirty-two enteric phage tyrosine integrase sequences located in GenBank was used to assess the presence of phages within thirty rare serotypes of Salmonella (one isolate per serotype) of foodborne origin and ten clinical isolates of Salmonella Enteritidis. The whole genomes of the Salmonella isolates were sequenced and the bioinformatics tools PHAST and PhiSpy were used to detect phages within the genomes.
Results: Within the 40 Salmonella isolates, the PCR assay detected 120 phage integrases compared to the bioinformatics programs PHAST and PhiSpy, which detected 161 and 183 phages, respectively. The PCR assay detected more numerous and diverse phage integrases within the rare Salmonella isolates than within Salmonella Enteritidis isolates. This was validated by PHAST, which identified 48 different phages, within the forty isolates, originating from Escherichia coli, Salmonella spp., Shigella spp., Klebsiella spp., Burkholderia spp., and phage elements with homology to Vibrio spp. Only four of these phages were present in each of the ten Salmonella Enteritidis isolates.
Significance: This study demonstrates the potential use of this PCR assay as a rapid screening tool to assess the diversity of temperate phages in Salmonella spp. isolated from food sources. This study also highlights Salmonella Enteritidis as a highly conserved serotype with little genetic diversity.