title: Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC.
abstract: The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance of this mobility in short-term evolution, such as within nosocomial outbreaks, is unknown. Using a combination of short- and long-read whole-genome sequencing of 281 blaKPC-positive Enterobacteriaceae isolates from a single hospital over 5 years, we demonstrate rapid dissemination of this carbapenem resistance gene to multiple species, strains, and plasmids. Mobility of blaKPC occurs at multiple nested genetic levels, with transmission of blaKPC strains between individuals, frequent transfer of blaKPC plasmids between strains/species, and frequent transposition of blaKPC transposon Tn4401 between plasmids. We also identify a common insertion site for Tn4401 within various Tn2-like elements, suggesting that homologous recombination between Tn2-like elements has enhanced the spread of Tn4401 between different plasmid vectors. Furthermore, while short-read sequencing has known limitations for plasmid assembly, various studies have attempted to overcome this by the use of reference-based methods. We also demonstrate that, as a consequence of the genetic mobility observed in this study, plasmid structures can be extremely dynamic, and therefore these reference-based methods, as well as traditional partial typing methods, can produce very misleading conclusions. Overall, our findings demonstrate that nonclonal resistance gene dissemination can be extremely rapid, presenting significant challenges for public health surveillance and achieving effective control of antibiotic resistance.
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom anna.sheppard@ndm.ox.ac.uk ajm5b@virginia.edu.
authors.forename: Anna E
authors.initials: AE
authors.lastname: Sheppard
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Nicole
authors.identifier: 0000-0002-4508-7969
authors.initials: N
authors.lastname: Stoesser
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wilson
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, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Luke W
authors.initials: LW
authors.lastname: Anson
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Adam
authors.initials: A
authors.lastname: Giess
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Louise J
authors.initials: LJ
authors.lastname: Pankhurst
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Alison
authors.initials: A
authors.lastname: Vaughan
authors.affiliation: Food and Drug Administration, Laurel, Maryland, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Grim
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Heather L
authors.initials: HL
authors.lastname: Cox
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Yeh
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, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: A Sarah
authors.initials: AS
authors.lastname: Walker
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom.
authors.forename: Tim E
authors.initials: TE
authors.lastname: Peto
authors.affiliation: Modernizing Medical Microbiology Consortium, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom Public Health England, Microbiology Services, London, United Kingdom.
authors.forename: Derrick W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA Clinical Microbiology, Department of Pathology, University of Virginia Health System, Charlottesville, Virginia, USA anna.sheppard@ndm.ox.ac.uk ajm5b@virginia.edu.
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Mathers
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D015373:Bacterial Typing Techniques; D015780:Carbapenems / Q000494:pharmacology; D003227:Conjugation, Genetic; D004251:DNA Transposable Elements; D004755:Enterobacteriaceae / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D004756:Enterobacteriaceae Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D015870:Gene Expression; D022761:Gene Transfer, Horizontal; D059014:High-Throughput Nucleotide Sequencing; D059765:Homologous Recombination; D006801:Humans; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D062486:Public Health Surveillance; D062606:Tertiary Care Centers; D014768:Virginia / Q000453:epidemiology; D018440:beta-Lactam Resistance / Q000235:genetics*; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems; D004251:DNA Transposable Elements; D001618:beta-Lactamases