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Concordance of SNP- and allele-based typing workflows in the context of a large-scale international Salmonella Enteritidis outbreak investigation.

Microbial genomics - 1 Mar 2020

Coipan Claudia E, Dallman Timothy J, Brown Derek, Hartman Hassan, van der Voort Menno, van den Berg Redmar R, Palm Daniel, Kotila Saara, van Wijk Tom, Franz Eelco

Abstract excerpt

A large European multi-country Salmonella enterica serovar Enteritidis outbreak associated with Polish eggs was characterized by whole-genome sequencing (WGS)-based analysis, with various European institutes using different analysis workflows to identify isolates potentially related to the outbreak. The objective of our study was to compare the output of six of these different typing workflows (distance matrices...

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PMID: 32101514
DOI: 10.1099/mgen.0.000318
PMCID: PMC7200063

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