Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens.
epidemiology
genomics
microbiology
molecular subtyping
nomenclature
outbreak detection
salmonella
Journal
Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
ISSN: 1560-7917
Titre abrégé: Euro Surveill
Pays: Sweden
ID NLM: 100887452
Informations de publication
Date de publication:
05 2020
05 2020
Historique:
entrez:
28
5
2020
pubmed:
28
5
2020
medline:
23
12
2020
Statut:
ppublish
Résumé
BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection.AimWe aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels.MethodsThe system was applied to
Identifiants
pubmed: 32458794
doi: 10.2807/1560-7917.ES.2020.25.20.1900519
pmc: PMC7262494
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
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