Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages

Abstract

Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th-18th centuries and diversified during the 1920s and 1950s.

Figure 1

Comparison of Salmonella enterica serotype Enteritidis phylogenies inferred from Illumina data and combined data of Illumina (San Diego, CA, USA) and Roche 454 (Indianapolis, IN, USA). The tree on the right incudes 80 Illumina sequenced isolates and the reference genome (PT4). The tree on the left includes both the 80 Illumina and the 44 454 sequenced isolates in addition to the reference. Isolates were numbered (online Technical Appendix Table 1, http://wwwnc.cdc.gov/EID/article/20/9/13-1095-Techapp-s1.pdf). Lineages I, II, III, IV, and V are highlighted in purple, green, yellow, red, and blue, respectively. Branches representing 454 sequenced isolates are labeled in red. Arrows on the left tree indicate the 3 serotype Nitra isolates. MRCA, most recent common ancestor. Scale bar indicates 10 single-nucleotide polymorphisms.

Figure 2

Inferred number of Salmonella enterica serotype Enteritidis lineages over time based on a constant effective population size model using BEAST (16). Blue shading indicates 95% CIs.

Figure 3

Salmonella enterica serotype Enteritidis genetic lineage III. Isolates from human blood and stool samples are indicated by red and blue, respectively. Four clades are highlighted and designated A–D, representing individual outbreak clades identified from clinical cases in Thailand in 2008. Branches with bootstrap value >0.9 are indicated by thickened lines. Age of the ancestral node (median most recent common ancestor) is labeled. Inset indicates the location of the highlighted lineage on the global phylogenetic tree.

Figure 4

Salmonella enterica serotype Enteritidis clades associated with the 2010 US shelled eggs outbreak. Red indicates isolates sequenced as part of the outbreak investigation using Roche 454 technology (Indianapolis, IN, USA); blue indicates isolates associated with chicken or chicken products; asterisk (*) indicates the isolate was traced back to the implicated egg production facility. Five outbreak clades are highlighted and designated as A–E, of which A and B are definite and C, D, and E are putative. Isolates ascribed to the egg outbreak in this study are underlined. Branches with bootstrap values >0.9 are shown by thickened lines. Age of the ancestral node (median most recent common ancestor) is labeled. Scale bar indicates single-nucleotide polymorphisms. Inset indicates the location of the highlighted lineage on the global phylogenetic tree.