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 Torpdahl
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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