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. 2019 Jan;24(4):1800186.
doi: 10.2807/1560-7917.ES.2019.24.4.1800186.

Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016

Lotta Siira  1   2 , Umaer Naseer  1 , Kristian Alfsnes  1 , Nils Olav Hermansen  1   3 , Heidi Lange  1 , Lin T Brandal  1
Affiliations

Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016

Lotta Siira et al. Euro Surveill. 2019 Jan.

Abstract

IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.

Keywords: Norway; Salmonella; Salmonella Chester; WGS; bacterial genomes; bacterial infections; food-borne infections; laboratory surveillance; molecular methods; outbreak detection; salmonellosis; typing; whole genome sequencing.

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Conflict of interest statement

Conflict of interest: LS is a co-investigator in an unrelated study, for which the National Institute for Health and Welfare, Finland, received research funding from GlaxoSmithKline Biologicals SA.

Figures

Figure 1
Figure 1
Salmonella Chester cases, by travel history and year, Norway, 2000–2016 (n = 86)
Figure 2
Figure 2
Neighbour-joining tree of Salmonella Chester isolates, based on 3,009 core genes included in core genome multilocus sequence typing Norway, 2000–2016 (n = 51)
Figure 3
Figure 3
Molecular phylogenetic analysis of Salmonella Chester isolates, based on single nucleotide polymorphism differences, Norway, 2000–2016 (n = 51)
See this image and copyright information in PMC

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