title: Chromosomal Integration of the Klebsiella pneumoniae Carbapenemase Gene,blaKPC, in Klebsiella Species Is Elusive but Not Rare.
abstract: Carbapenemase genes inEnterobacteriaceaeare mostly described as being plasmid associated. However, the genetic context of carbapenemase genes is not always confirmed in epidemiological surveys, and the frequency of their chromosomal integration therefore is unknown. A previously sequenced collection ofblaKPC-positiveEnterobacteriaceaefrom a single U.S. institution (2007 to 2012;n= 281 isolates from 182 patients) was analyzed to identify chromosomal insertions of Tn4401, the transposon most frequently harboringblaKPCUsing a combination of short- and long-read sequencing, we confirmed five independent chromosomal integration events from 6/182 (3%) patients, corresponding to 15/281 (5%) isolates. Three patients had isolates identified by perirectal screening, and three had infections which were all successfully treated. When a single copy ofblaKPCwas in the chromosome, one or both of the phenotypic carbapenemase tests were negative. All chromosomally integratedblaKPCgenes were fromKlebsiellaspp., predominantlyK. pneumoniaeclonal group 258 (CG258), even though these represented only a small proportion of the isolates. Integration occurred via IS15-ΔI-mediated transposition of a larger, composite region encompassing Tn4401at one locus of chromosomal integration, seen in the same strain (K. pneumoniaeST340) in two patients. In summary, we identified five independent chromosomal integrations ofblaKPCin a large outbreak, demonstrating that this is not a rare event.blaKPCwas more frequently integrated into the chromosome of epidemic CG258K. pneumoniaelineages (ST11, ST258, and ST340) and was more difficult to detect by routine phenotypic methods in this context. The presence of chromosomally integratedblaKPCwithin successful, globally disseminatedK. pneumoniaestrains therefore is likely underestimated.
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA ajm5b@virginia.edu.|Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Mathers
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Nicole
authors.identifier: 0000-0002-4508-7969
authors.initials: N
authors.lastname: Stoesser
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Weidong
authors.initials: W
authors.lastname: Chai
authors.affiliation: Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Joanne
authors.initials: J
authors.lastname: Carroll
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Katie
authors.initials: K
authors.lastname: Barry
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Anita
authors.initials: A
authors.lastname: Cherunvanky
authors.affiliation: Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Sebra
authors.affiliation: Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Kasarskis
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Tim E
authors.initials: TE
authors.lastname: Peto
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.|Office of Hospital Epidemiology, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Costi D
authors.initials: CD
authors.lastname: Sifri
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Sheppard
mesh_terms: D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000737:chemistry* / Q000378:metabolism; D002999:Clone Cells; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D006801:Humans; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D007710:Klebsiella Infections / Q000453:epidemiology / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000201:enzymology / Q000235:genetics*; D016254:Mutagenesis, Insertional; D059645:Mutation Rate; D017422:Sequence Analysis, DNA; D014768:Virginia / Q000453:epidemiology; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D007527:Isoenzymes; D001618:beta-Lactamases; C547585:beta-lactamase KPC-2, Klebsiella pneumoniae
keywords: KPC; Klebsiella; Klebsiella pneumoniae carbapenemase; antibiotic resistance; carbapenemase; chromosomal; plasmid analysis; plasmids; transposons; whole-genome sequencing