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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 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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