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2021-12-16Zeitschriftenartikel
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae
dc.contributor.authorViehweger, Adrian
dc.contributor.authorBlumenscheit, Christian
dc.contributor.authorLippmann, Norman
dc.contributor.authorWyres, Kelly L.
dc.contributor.authorBrandt, Christian
dc.contributor.authorHans, Jörg B.
dc.contributor.authorHölzer, Martin
dc.contributor.authorIrber, Luiz
dc.contributor.authorGatermann, Sören
dc.contributor.authorLübbert, Christoph
dc.contributor.authorPletz, Mathias W.
dc.contributor.authorHolt, Kathryn E.
dc.contributor.authorKönig, Brigitte
dc.date.accessioned2022-07-28T08:40:54Z
dc.date.available2022-07-28T08:40:54Z
dc.date.issued2021-12-16none
dc.identifier.other10.1099/mgen.0.000741
dc.identifier.urihttp://edoc.rki.de/176904/9990
dc.description.abstractGenomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done. We investigate two large hospital outbreaks of a carbapenemase-carrying Klebsiella pneumoniae strain in Germany and show the value of contextual data. By screening about 10 000 genomes, over 400 000 metagenomes and two culture collections using in silico and in vitro methods, we identify a total of 415 closely related genomes reported in 28 studies. We identify the relationship between the two outbreaks through time-dated phylogeny, including their respective origin. One of the outbreaks presents extensive hidden transmission, with descendant isolates only identified in other studies. We then leverage the genome collection from this meta-analysis to identify genes under positive selection. We thereby identify an inner membrane transporter (ynjC) with a putative role in colistin resistance. Contextual data from other sources can thus enhance local genomic surveillance at multiple levels and should be integrated by default when available.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.subjectgenomic surveillanceeng
dc.subjectmeta-analysiseng
dc.subjectantimicrobial resistanceeng
dc.subjectKPCeng
dc.subjectplasmidseng
dc.subjectcolistineng
dc.subject.ddc610 Medizin und Gesundheitnone
dc.titleContext-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniaenone
dc.typearticle
dc.identifier.urnurn:nbn:de:0257-176904/9990-4
dc.type.versionpublishedVersionnone
local.edoc.container-titleMicrobial Genomicsnone
local.edoc.container-issn2057-5858none
local.edoc.type-nameZeitschriftenartikel
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-urlhttps://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000741none
local.edoc.container-publisher-nameMicrobiology Societynone
local.edoc.container-volume7none
local.edoc.container-issue12none
local.edoc.container-year2021none
dc.description.versionPeer Reviewednone

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