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; Mia Torpdahl

doi:10.3201/eid2310.161248

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, Mia Torpdahl^*

^*Corresponding author af dette arbejde

28 Citationer (Scopus)

36 Downloads (Pure)

Abstract

Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34).

Originalsprog	Engelsk
Tidsskrift	Emerging Infectious Diseases
Vol/bind	23
Udgave nummer	10
Sider (fra-til)	1631-1639
Antal sider	9
ISSN	1080-6040
DOI	https://doi.org/10.3201/eid2310.161248
Status	Udgivet - 2017

Adgang til dokumentet

10.3201/eid2310.161248Licens: CC BY

16-1248-combinedForlagets udgivne version, 2,59 MBLicens: CC BY

Citationsformater

@article{64f7b8df3522427fa6d02297a5257c70,

title = "Investigation of outbreaks of Salmonella enterica serovar typhimurium and its monophasic variants using whole-genome sequencing, Denmark",

abstract = "Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34).",

author = "Pernille Gymoese and Gitte S{\o}rensen and Eva Litrup and Olsen, {John Elmerdal} and Nielsen, {Eva M{\o}ller} and Mia Torpdahl",

year = "2017",

doi = "10.3201/eid2310.161248",

language = "English",

volume = "23",

pages = "1631--1639",

journal = "Emerging Infectious Diseases ",

issn = "1080-6040",

publisher = "CDC Centers for Disease Control and Prevention",

number = "10",

}

TY - JOUR

T1 - Investigation of outbreaks of Salmonella enterica serovar typhimurium and its monophasic variants using whole-genome sequencing, Denmark

AU - Gymoese, Pernille

AU - Sørensen, Gitte

AU - Litrup, Eva

AU - Olsen, John Elmerdal

AU - Nielsen, Eva Møller

AU - Torpdahl, Mia

PY - 2017

Y1 - 2017

N2 - Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34).

AB - Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34).

U2 - 10.3201/eid2310.161248

DO - 10.3201/eid2310.161248

M3 - Journal article

C2 - 28930002

AN - SCOPUS:85029768201

SN - 1080-6040

VL - 23

SP - 1631

EP - 1639

JO - Emerging Infectious Diseases

JF - Emerging Infectious Diseases

IS - 10

ER -

Investigation of outbreaks of Salmonella enterica serovar typhimurium and its monophasic variants using whole-genome sequencing, Denmark

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater