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2020-03-09Zeitschriftenartikel
Genome-based Salmonella serotyping as the new gold standard
dc.contributor.authorBanerji, Sangeeta
dc.contributor.authorSimon, Sandra
dc.contributor.authorTille, Andreas
dc.contributor.authorFruth, Angelika
dc.contributor.authorFlieger, Antje
dc.date.accessioned2024-02-26T13:33:04Z
dc.date.available2024-02-26T13:33:04Z
dc.date.issued2020-03-09none
dc.identifier.other10.1038/s41598-020-61254-1
dc.identifier.urihttp://edoc.rki.de/176904/11519
dc.description.abstractSalmonella enterica is the second most reported bacterial cause of food-borne infections in Europe. Therefore molecular surveillance activities based on pathogen subtyping are an important measure of controlling Salmonellosis by public health agencies. In Germany, at the federal level, this work is carried out by the National Reference Center for Salmonella and other Bacterial Enteric Pathogens (NRC). With rise of next generation sequencing techniques, the NRC has introduced whole-genome-based typing methods for S. enterica in 2016. In this study we report on the feasibility of genome-based in silico serotyping in the German setting using raw sequence reads. We found that SeqSero and seven gene MLST showed 98% and 95% concordance, respectively, with classical serotyping for the here evaluated serotypes, including the most common German serotypes S. Enteritidis and S. Typhimurium as well as less frequently found serotypes. The level of concordance increased to >99% when the results of both in silico methods were combined. However, both tools exhibited misidentification of monophasic variants, in particular monophasic S. Typhimurium and therefore need to be fine-tuned for reliable detection of this epidemiologically important variant. We conclude that with adjustments Salmonella genome-based serotyping might become the new gold standard.eng
dc.language.isoengnone
dc.publisherRobert Koch-Institut
dc.rights(CC BY 3.0 DE) Namensnennung 3.0 Deutschlandger
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/de/
dc.subjectbacterial infectioneng
dc.subjectevolutionary biologyeng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleGenome-based Salmonella serotyping as the new gold standardnone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/11519-7
dc.type.versionupdatedVersionnone
local.edoc.container-titlescientific reportsnone
local.edoc.container-issn2045-2322none
local.edoc.pages10none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.nature.com/srep/none
local.edoc.container-publisher-nameSpringer Naturenone
local.edoc.container-volume10none
local.edoc.container-reportyear2020none

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