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 3
Statistical data from core-genome SNP analysis of different subgroups with complete genome of Salmonella enterica serovar Typhimurium 14028S or an internal de novo assembled genome as reference in an outbreak investigation of Salmonella Typhimurium and its monophasic variants, Denmark*
| Isolates within | Selection of isolates | Size of core-genome used, bp |
% Reference genome used |
Called SNPs |
|||||
|---|---|---|---|---|---|---|---|---|---|
| 14028S | Internal de novo | 14028S | Internal de novo | 14028S | Internal de novo | ||||
| All |
All |
3806685 |
– |
78.16 |
– |
14,326 (10,163) |
– |
||
| ST36 | All | 4527849 | 4494995 | 92.97 | 95.32 | 2,887 | 3,146 | ||
| Outbreak A |
4604894 |
4611321 |
94.55 |
97.78 |
8 |
8 |
|||
| ST19 | All | 4314989 | 4304908 | 88.60 | 90.34 | 6,596 | 6,549 (6,004) | ||
| Outbreak B | 4648245 | 4662681 | 95.44 | 97.85 | 16 | 16 | |||
| Outbreak C |
4711565 |
4720046 |
96.74 |
99.02 |
0 |
0 |
|||
| ST34 | All | 4055543 | 4034423 | 83.27 | 81.55 | 1,490 | 1,488 (1,091) | ||
| Outbreak D | 4665201 | 4771546 | 95.79 | 97.39 | 32 | 34 | |||
| Outbreak E | 4706675 | 4871858 | 96.64 | 98.48 | 7 | 7 | |||
| Outbreak F | 4705075 | 4836637 | 96.61 | 98.41 | 9 | 10 | |||
| Outbreak G | 4694550 | 4826771 | 96.39 | 98.00 | 2 | 3 | |||
| Outbreak H | 4734518 | 4886190 | 97.21 | 98.84 | 0 | 0 | |||
*SNPs in parentheses are called SNPs with inclusion of poor-quality sequences. SNP, single-nucleotide polymorphism; ST, sequence type.
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Page updated: September 18, 2017
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