Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Adrian Viehweger, Christian Blumenscheit, Norman Lippmann, Kelly L. Wyres, Christian Brandt, Jörg B. Hans, Martin Hölzer, Luiz Irber, Sören Gatermann, Christoph Lübbert, Mathias W. Pletz, Kathryn E. Holt, Brigitte König

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8 Citations (Scopus)


Genomic 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.

Original languageEnglish
Article number000741
Number of pages12
JournalMicrobial Genomics
Issue number12
Publication statusPublished - Dec 2021


  • antimicrobial resistance
  • colistin
  • genomic surveillance
  • KPC
  • meta-analysis
  • plasmids

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