Scientific Publications by FDA Staff

J Clin Microbiol 2014 May;52(5):1490-500

Genetic diversity and evolution of Salmonella enterica serovar Enteritidis strains with different phage types.

Zheng J, Pettengill J, Strain E, Allard MW, Ahmed R, Zhao S, Brown EW

Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis (S. Enteritidis) for over two decades. However, knowledge of the genetic and evolutionary relationships between phage types is very limited, making differences difficult to interpret. Here, single nucleotide polymorphisms (SNPs) identified from whole genome comparisons were used to determine the relationships between some S. Enteritidis phage types (PTs) commonly associated with foodborne outbreaks in the United States. Emphasis was placed on predominant phage types PT8, PT13a, and PT13 in North America. With greater than 89,400 base pairs surveyed across 98 S. Enteritidis isolates representing 14 distinct phage types, 55 informative SNPs were discovered within 23 chromosomally anchored loci. To maximize the discriminatory and evolutionary partitioning of these highly homogenous strains, sequences comprising informative SNPs were concatenated into a single combined data matrix and subjected to phylogenetic analysis. The resultant phylogeny allocated most S. Enteritidis isolates into two distinct clades (I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs were identified capable of distinguishing the individual clade/subclade. However, individual phage types appeared to be evolutionarily disjunct when mapped to this phylogeny, suggesting that phage typing may not be valid for making phylogenetic inferences. Furthermore, the set of SNPs identified here represent useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provide core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.