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Volume 23, Number 10—October 2017

Research

Investigation of Outbreaks of Salmonella enterica Serovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark

Pernille Gymoese, Gitte Sørensen, Eva Litrup, John Elmerdal Olsen, Eva Møller Nielsen, and Mia TorpdahlComments to Author 
Author affiliations: Statens Serum Institut, Copenhagen, Denmark (P. Gymoese, G. Sørensen, E. Litrup, E.M. Nielsen, M. Torpdahl); Technical University of Denmark, Lyngby, Denmark (G. Sørensen); University of Copenhagen, Frederiksberg, Denmark (J.E. Olsen)

Main Article

Table 2

New definitions of previously defined outbreaks based on core-genome SNP analysis in an outbreak investigation of Salmonella enterica serovar Typhimurium and its monophasic variants, Denmark*

Outbreak No. human cases Included/excluded compared with previously defined Food/veterinary isolates Sources No. SNPs Maximum SNP distance SNP distance from nearest neighbor
A 6 0 8 7 143
B 37 +2 2 Swine 11 4 34
C 7 0 0 0 64
D 7 +1/–2 4 Swine 2 (6) 2 (6) 3 (7)
E 20 +1/–5 13 Swine/cattle 6 (7) 3 (4) 3 (4)
F 22 +3 2 Cattle 4 3 20
G 9 −5 0 2 2 31
H 5 1 Swine 0 0 4 (7)

*Previous outbreaks shown in Table 1. SNPs in parentheses are derived from reanalysis of closely related clusters with an internal de novo assembled reference genome. SNP, single-nucleotide polymorphism.

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