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2022-05-18Zeitschriftenartikel
Using unique ORFan genes as strain-specific identifiers for Escherichia coli
dc.contributor.authorFerrandis-Vila, Marta
dc.contributor.authorTiwari, Sumeet K.
dc.contributor.authorMamerow, Svenja
dc.contributor.authorSemmler, Torsten
dc.contributor.authorHECTOR Consortium
dc.contributor.authorMenge, Christian
dc.contributor.authorBerens, Christian
dc.date.accessioned2024-09-18T14:29:55Z
dc.date.available2024-09-18T14:29:55Z
dc.date.issued2022-05-18none
dc.identifier.other10.1186/s12866‑022‑02508‑y
dc.identifier.urihttp://edoc.rki.de/176904/12205
dc.description.abstractBackground Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers. Results Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible. Conclusions The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.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.subjectORFan geneeng
dc.subjectStrain identificationeng
dc.subjectmultiplex PCReng
dc.subjectqPCReng
dc.subjectE. colieng
dc.subjecthost-specificityeng
dc.subjectanimal experimenteng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleUsing unique ORFan genes as strain-specific identifiers for Escherichia colinone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/12205-6
dc.type.versionpublishedVersionnone
local.edoc.container-titleBMC Microbiologynone
local.edoc.container-issn1471-2180none
local.edoc.pages14none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://bmcmicrobiol.biomedcentral.com/none
local.edoc.container-publisher-nameSpringer Naturenone
local.edoc.container-volume22none
local.edoc.container-reportyear2022none
dc.description.versionPeer Reviewednone

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