Genetic Diversity and Evolution of Salmonella enterica Serovar Enteritidis Strains with Different Phage Types

Abstract

c Phage typing has been used for the epidemiological surveillance of Salmonella enterica serovar Enteritidis for over 2 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 food-borne outbreaks in the United States. Emphasis was placed on the predominant phage types PT8, PT13a, and PT13 in North America. With >89,400 bp 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 homogeneous 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 (clades I and II) and four subclades. Synapomorphic (shared and derived) sets of SNPs capable of distinguishing individual clades/subclades were identified. 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 represents useful genetic markers for strain differentiation of more clonal S. Enteritidis strains and provides core genotypic markers for future development of a SNP typing scheme with S. Enteritidis.

Identification of Genetic Features for Attenuation of Two Salmonella Enteritidis Vaccine Strains and Differentiation of These From Wildtype Isolates Using Whole Genome Sequencing

“…Over the last few decades the Colindale phage typing (PT) scheme has played a central role in epidemiological studies of S. Enteritidis while there are limitations regarding Pulsed-field Gel Electrophoresis (PFGE) and Multilocus Variable-Number Tandem Repeat Analysis (MLVA) methods and "neither PFGE nor MLVA could distinguish all of the S. Enteritidis PT30 from various sources, " for example (3)(4)(5). Recent phylogenetic studies based on whole genome sequencing (WGS) have revealed the presence of two separate clonal lineages of S. Enteritidis (6,7). Phage types that dominated in western Europe and Asia, including PT1, PT4, and PT21 occurred in clonal lineage I, while PTs that were most common in North America (i.e., PT8, PT13a, and PT13) comprised the majority of clonal lineage II (6).…”

“…Recent phylogenetic studies based on whole genome sequencing (WGS) have revealed the presence of two separate clonal lineages of S. Enteritidis (6,7). Phage types that dominated in western Europe and Asia, including PT1, PT4, and PT21 occurred in clonal lineage I, while PTs that were most common in North America (i.e., PT8, PT13a, and PT13) comprised the majority of clonal lineage II (6).…”

Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s

“…Salmonella enterica serovar Enteritidis (SE) is a long-standing public health concern in the US (1); salmonellosis can result in hospitalization or death of infants, the elderly, and those with compromised immune systems (2, 3). This pathogen has been strongly associated with poultry farms, eggs, and egg products (4, 5).…”

“…Whole genome sequencing (WGS) methods have identified variations across otherwise indistinguishable isolates from eggs and egg products (6, 12), SE associated with reptile feeder mice (13), S. Montevideo from red and black pepper (14). Genome-wide single nucleotide polymorphisms (SNPs) detected by WGS are considered as the most valuable genetic markers for investigating the evolutionary relationships among SE homogeneous isolates (1, 7, 15). Application of WGS have also been useful in other microorganisms, including E. coli (16), Vibrio cholera (17), and Staphylococcus aureus (18).…”

Salmonella entericaSerotype Enteritidis in French Polynesia, South Pacific, 2008–2013

“…Given the signatures offered by the polymorphism of the 2 CRISPR loci in our study and in previous works ( 8 , 9 , 13 ), we are convinced that CRISPR DNA targets might be very helpful for subtyping Salmonella , including serotype Enteritidis. Furthermore, because the CRISPR spacer content can be extracted easily from short-read DNA sequences, in contrast to MLVA loci, it could be used to define particular Salmonella Enteritidis strains together with, or as an alternative to, core genome single nucleotide polymorphisms when whole-genome sequencing for foodborne pathogen surveillance and investigation are implemented in public health and veterinary laboratories ( 14 ).…”