title: Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae.
abstract: Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae species may spread resistance to carbapenems, an antibiotic class of last resort, thereby rendering common health care-associated infections nearly impossible to treat. To determine the diversity of carbapenemase-encoding plasmids and assess their mobility among bacterial species, we performed comprehensive surveillance and genomic sequencing of carbapenem-resistant Enterobacteriaceae in the National Institutes of Health (NIH) Clinical Center patient population and hospital environment. We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem resistance genes on a wide array of plasmids. K. pneumoniae and E. cloacae isolated simultaneously from a single patient harbored two different carbapenemase-encoding plasmids, indicating that plasmid transfer between organisms was unlikely within this patient. We did, however, find evidence of horizontal transfer of carbapenemase-encoding plasmids between K. pneumoniae, E. cloacae, and C. freundii in the hospital environment. Our data, including full plasmid identification, challenge assumptions about horizontal gene transfer events within patients and identify possible connections between patients and the hospital environment. In addition, we identified a new carbapenemase-encoding plasmid of potentially high clinical impact carried by K. pneumoniae, E. coli, E. cloacae, and Pantoea species, in unrelated patients and in the hospital environment.
authors.affiliation: National Human Genome Research Institute, Bethesda, MD 20892, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Conlan
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Pamela J
authors.initials: PJ
authors.lastname: Thomas
authors.affiliation: National Human Genome Research Institute, Bethesda, MD 20892, USA.
authors.forename: Clayton
authors.initials: C
authors.lastname: Deming
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Morgan
authors.initials: M
authors.lastname: Park
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
authors.forename: Anna F
authors.initials: AF
authors.lastname: Lau
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Dekker
authors.affiliation: National Human Genome Research Institute, Bethesda, MD 20892, USA.
authors.forename: Evan S
authors.initials: ES
authors.lastname: Snitkin
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Tyson A
authors.initials: TA
authors.lastname: Clark
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Khai
authors.initials: K
authors.lastname: Luong
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Song
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Yu-Chih
authors.initials: YC
authors.lastname: Tsai
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Boitano
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Dayal
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Shelise Y
authors.initials: SY
authors.lastname: Brooks
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Schmidt
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Alice C
authors.initials: AC
authors.lastname: Young
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: James W
authors.initials: JW
authors.lastname: Thomas
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Gerard G
authors.initials: GG
authors.lastname: Bouffard
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Blakesley
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Bethesda, MD 20852, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.affiliation: Pacific Biosciences, Menlo Park, CA 94025, USA.
authors.forename: Jonas
authors.initials: J
authors.lastname: Korlach
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, MD 20892, USA.
authors.forename: David K
authors.initials: DK
authors.lastname: Henderson
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, MD 20892, USA. karen.frank@nih.gov tpalmore@mail.nih.gov jsegre@nhgri.nih.gov.
authors.forename: Karen M
authors.initials: KM
authors.lastname: Frank
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, MD 20892, USA. karen.frank@nih.gov tpalmore@mail.nih.gov jsegre@nhgri.nih.gov.
authors.forename: Tara N
authors.initials: TN
authors.lastname: Palmore
authors.affiliation: National Human Genome Research Institute, Bethesda, MD 20892, USA. karen.frank@nih.gov tpalmore@mail.nih.gov jsegre@nhgri.nih.gov.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Segre
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis*; D003428:Cross Infection; D004755:Enterobacteriaceae / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D006779:Hospitals, Public; D006801:Humans; D009316:National Institutes of Health (U.S.); D010957:Plasmids; D011159:Population Surveillance; D060888:Real-Time Polymerase Chain Reaction; D014481:United States; D001618:beta-Lactamases / Q000096:biosynthesis*
chemical_list: D001426:Bacterial Proteins; D001618:beta-Lactamases; C063912:carbapenemase