Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a
SNP analysis
Salmonella
food surveillance
metagenomics
outbreak
strain-level
Journal
Microbial genomics
ISSN: 2057-5858
Titre abrégé: Microb Genom
Pays: England
ID NLM: 101671820
Informations de publication
Date de publication:
04 2021
04 2021
Historique:
entrez:
7
4
2021
pubmed:
8
4
2021
medline:
20
11
2021
Statut:
ppublish
Résumé
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a
Identifiants
pubmed: 33826490
doi: 10.1099/mgen.0.000547
pmc: PMC8208685
doi:
Types de publication
Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
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