Outbreaks Open Access
Like 0


In autumn 2019, the Public Health Agency of Sweden identified a cluster of Newport cases by whole genome sequencing (WGS). Cases’ distribution in place and time indicated a nation-wide ongoing outbreak. An investigation was initiated to identify the source and prevent further cases. We conducted a case–case study based on notified salmonellosis cases and a trawling questionnaire, comparing 20 outbreak cases and 139 control cases. Food exposures were compared by adjusted odds ratios (aOR) with 95% confidence interval (CI) using logistic regression. Implicated foods were sampled. Outbreak cases were more likely to have consumed crayfish (aOR = 26; 95% CI: 6.3–105). One specific brand of imported frozen, pre-cooked whole crayfish in dill brine was identified as the source. Newport was later detected in different batches from retail and in one sample from border control. Isolates from food samples clustered with the human outbreak strain by WGS. Although the retailer made a complete recall, two more cases were identified long afterwards. This investigation demonstrated the successful use of a case–case study and targeted microbiological testing to identify the source. The immediate action taken by the retailer was important to confirm the source and stop the outbreak.


Article metrics loading...

Loading full text...

Full text loading...



  1. European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC). The European Union One Health 2019 zoonoses report. EFSA J. 2021;19(2):e06406.  https://doi.org/10.2903/j.efsa.2021.6406 
  2. European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC). The European Union One Health 2020 zoonoses report. EFSA J. 2021;19(12):e06971.  https://doi.org/10.2903/j.efsa.2021.6971 
  3. Public Health Agency of Sweden (PHAS). Salmonella 2019. Solna: PHAS [Accessed: 10 Jun 2021]. Swedish. Available from: https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistik-a-o/sjukdomsstatistik/salmonellainfektion
  4. Swedish National Veterinary Institute (SVA). Surveillance of infectious diseases in animals and humans in Sweden 2018. Uppsala: SVA; 2019. Available from: https://www.sva.se/vi-erbjuder/publikationer/surveillance-of-infectious-diseases-in-animals-and-humans-2018/c-28/c-83/p-105
  5. Plumb ID, Schwensohn CA, Gieraltowski L, Tecle S, Schneider ZD, Freiman J, et al. Outbreak of Salmonella Newport infections with decreased susceptibility to azithromycin linked to beef obtained in the United States and soft cheese obtained in Mexico - United States, 2018-2019. MMWR Morb Mortal Wkly Rep. 2019;68(33):713-7.  https://doi.org/10.15585/mmwr.mm6833a1  PMID: 31437141 
  6. Marshall KEH, Tewell M, Tecle S, Leeper M, Sinatra J, Kissler B, et al. Protracted outbreak of Salmonella Newport infections linked to ground beef: possible role of dairy cows - 21 States, 2016-2017. MMWR Morb Mortal Wkly Rep. 2018;67(15):443-6.  https://doi.org/10.15585/mmwr.mm6715a2  PMID: 29672479 
  7. Byrne L, Fisher I, Peters T, Mather A, Thomson N, Rosner B, et al. A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012. Euro Surveill. 2014;19(31):20866.  https://doi.org/10.2807/1560-7917.ES2014.19.31.20866  PMID: 25138971 
  8. Bayer C, Bernard H, Prager R, Rabsch W, Hiller P, Malorny B, et al. An outbreak of Salmonella Newport associated with mung bean sprouts in Germany and the Netherlands, October to November 2011. Euro Surveill. 2014;19(1):20665.  https://doi.org/10.2807/1560-7917.ES2014.19.1.20665  PMID: 24434173 
  9. Elviss NC, Little CL, Hucklesby L, Sagoo S, Surman-Lee S, de Pinna E, et al. Microbiological study of fresh herbs from retail premises uncovers an international outbreak of salmonellosis. Int J Food Microbiol. 2009;134(1-2):83-8.  https://doi.org/10.1016/j.ijfoodmicro.2009.01.015  PMID: 19237218 
  10. Kamalika J, Ubeyratne H, Kleer J, Hildebrandt G, Fries R, Khattiya R, et al. Prevalence of Salmonella in marketed Penaeus monodon shrimps in North Western Province, Sri Lanka. Berl Munch Tierarztl Wochenschr. 2008;121(11-12):418-21. PMID: 19086691 
  11. Heinitz ML, Ruble RD, Wagner DE, Tatini SR. Incidence of Salmonella in fish and seafood. J Food Prot. 2000;63(5):579-92.  https://doi.org/10.4315/0362-028X-63.5.579  PMID: 10826714 
  12. Colombe S, Jernberg C, Löf E, Angervall AL, Mellström-Dahlgren H, Dotevall L, et al. Outbreak of unusual H2S-negative monophasic Salmonella Typhimurium strain likely associated with small tomatoes, Sweden, August to October 2019. Euro Surveill. 2019;24(47):1900643.  https://doi.org/10.2807/1560-7917.ES.2019.24.47.1900643  PMID: 31771698 
  13. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-20.  https://doi.org/10.1093/bioinformatics/btu170  PMID: 24695404 
  14. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Comput Biol. 2017;13(6):e1005595.  https://doi.org/10.1371/journal.pcbi.1005595  PMID: 28594827 
  15. Seeman T. mlst. Github. Available from: https://github.com/tseemann/mlst
  16. Jolley KA, Maiden MC. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11(1):595.  https://doi.org/10.1186/1471-2105-11-595  PMID: 21143983 
  17. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357-9.  https://doi.org/10.1038/nmeth.1923  PMID: 22388286 
  18. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008.  https://doi.org/10.1093/gigascience/giab008  PMID: 33590861 
  19. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92.  https://doi.org/10.1093/bib/bbs017  PMID: 22517427 
  20. Zhou Z, Alikhan NF, Mohamed K, Fan Y, Achtman M, Agama Study Group. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res. 2020;30(1):138-52.  https://doi.org/10.1101/gr.251678.119  PMID: 31809257 
  21. Alikhan NF, Zhou Z, Sergeant MJ, Achtman M. A genomic overview of the population structure of Salmonella. PLoS Genet. 2018;14(4):e1007261.  https://doi.org/10.1371/journal.pgen.1007261  PMID: 29621240 
  22. Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, et al. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 2015;53(5):1685-92.  https://doi.org/10.1128/JCM.00323-15  PMID: 25762776 
  23. Bharat A, Petkau A, Avery BP, Chen JC, Folster JP, Carson CA, et al. Correlation between phenotypic and in silico detection of antimicrobial resistance in Salmonella enterica in Canada using Staramr. Microorganisms. 2022;10(2):292.  https://doi.org/10.3390/microorganisms10020292  PMID: 35208747 
  24. Salipante SJ, Hall BG. Inadequacies of minimum spanning trees in molecular epidemiology. J Clin Microbiol. 2011;49(10):3568-75.  https://doi.org/10.1128/JCM.00919-11  PMID: 21849692 
  25. Gaertner JP, Mendoza JA, Forstner MR, Hahn D. Recovery of Salmonella from biofilms in a headwater spring ecosystem. J Water Health. 2011;9(3):458-66.  https://doi.org/10.2166/wh.2011.173  PMID: 21976193 
  26. McCarthy N, Giesecke J. Case-case comparisons to study causation of common infectious diseases. Int J Epidemiol. 1999;28(4):764-8.  https://doi.org/10.1093/ije/28.4.764  PMID: 10480708 
  27. Pogreba-Brown K, O’Connor P, Matthews J, Barrett E, Bell ML. Case-case analysis of Campylobacter and Salmonella - using surveillance data for outbreak investigations and monitoring routine risk factors. Epidemiol Infect. 2018;146(15):1916-21.  https://doi.org/10.1017/S0950268818002200  PMID: 30092849 
  28. Benedict KM, Collier SA, Marder EP, Hlavsa MC, Fullerton KE, Yoder JS. Case-case analyses of cryptosporidiosis and giardiasis using routine national surveillance data in the United States - 2005-2015. Epidemiol Infect. 2019;147:e178.  https://doi.org/10.1017/S0950268819000645  PMID: 31063098 
  29. Fonteneau L, Jourdan Da Silva N, Fabre L, Ashton P, Torpdahl M, Müller L, et al. Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015. Euro Surveill. 2017;22(7):30463.  https://doi.org/10.2807/1560-7917.ES.2017.22.7.30463  PMID: 28230522 

Data & Media loading...

Submit comment
Comment moderation successfully completed
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error