ArticleMicrobiology spectrum2022
Comparing Multiple Locus Variable-Number Tandem Repeat Analyses with Whole-Genome Sequencing as Typing Method for Salmonella Enteritidis Surveillance in The Netherlands, January 2019 to March 2020.
Article in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- The role of contaminated eggshells used in poultry feed in a diffuse nationwide outbreak ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2026Article
- Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin-Producing Escherichia coli, France, 2018-2022.Emerging infectious diseases · 2025Article
- Genomic epidemiology ofMicrobial genomics · 2025Article
- Key role of whole genome sequencing in resolving an international outbreak of monophasic Salmonella Typhimurium linked to chocolate products.BMC infectious diseases · 2025Article
- Large outbreak of typhoid fever on a river cruise ship used as accommodation for asylum seekers, the Netherlands, 2022.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- Whole-genome sequencing ofMicrobial genomics · 2023Article
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Abstract
In the Netherlands, whole-genome sequencing (WGS) was implemented as routine typing tool for Salmonella Enteritidis isolates in 2019. Multiple locus variable-number tandem repeat analyses (MLVA) was performed in parallel. The objective was to determine the concordance of MLVA and WGS as typing methods for S. Enteritidis isolates. We included S. Enteritidis isolates from patients that were subtyped using MLVA and WGS-based core-genome Multilocus Sequence Typing (cgMLST) as part of the national laboratory surveillance of Salmonella during January 2019 to March 2020. The concordance of clustering based on MLVA and cgMLST, with a distance of ≤5 alleles, was assessed using the Fowlkes-Mallows (FM) index, and their discriminatory power using Simpson's diversity index. Of 439 isolates in total, 404 (92%) were typed as 32 clusters based on MLVA, with a median size of 4 isolates (range:2 to 141 isolates). Based on cgMLST, 313 (71%) isolates were typed as 48 clusters, with a median size of 3 isolates (range:2 to 39 isolates). The FM index was 0.34 on a scale from 0 to 1, where a higher value indicates greater similarity between the typing methods. The Simpson's diversity index of MLVA and cgMLST was 0.860 and 0.974, respectively. The median cgMLST distance between isolates with the same MLVA type was 27 alleles (interquartile range [IQR]:17 to 34 alleles), and 2 alleles within cgMLST clusters (IQR:1-5 alleles). This study shows the higher discriminatory power of WGS over MLVA and a poor concordance between both typing methods regarding clustering of S. Enteritidis isolates.
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