title: Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization.
abstract: Carbapenem-resistant Klebsiella pneumoniae strains are formidable hospital pathogens that pose a serious threat to patients around the globe due to a rising incidence in health care facilities, high mortality rates associated with infection, and potential to spread antibiotic resistance to other bacterial species, such as Escherichia coli Over 6 months in 2011, 17 patients at the National Institutes of Health (NIH) Clinical Center became colonized with a highly virulent, transmissible carbapenem-resistant strain of K. pneumoniae Our real-time genomic sequencing tracked patient-to-patient routes of transmission and informed epidemiologists' actions to monitor and control this outbreak. Two of these patients remained colonized with carbapenemase-producing organisms for at least 2 to 4 years, providing the opportunity to undertake a focused genomic study of long-term colonization with antibiotic-resistant bacteria. Whole-genome sequencing studies shed light on the underlying complex microbial colonization, including mixed or evolving bacterial populations and gain or loss of plasmids. Isolates from NIH patient 15 showed complex plasmid rearrangements, leaving the chromosome and the blaKPC-carrying plasmid intact but rearranging the two other plasmids of this outbreak strain. NIH patient 16 has shown continuous colonization with blaKPC-positive organisms across multiple time points spanning 2011 to 2015. Genomic studies defined a complex pattern of succession and plasmid transmission across two different K. pneumoniae sequence types and an E. coli isolate. These findings demonstrate the utility of genomic methods for understanding strain succession, genome plasticity, and long-term carriage of antibiotic-resistant organisms.
  
  
  OBJECTIVE
  In 2011, the NIH Clinical Center had a nosocomial outbreak involving 19 patients who became colonized or infected with blaKPC-positive Klebsiella pneumoniae Patients who have intestinal colonization with blaKPC-positive K. pneumoniae are at risk for developing infections that are difficult or nearly impossible to treat with existing antibiotic options. Two of those patients remained colonized with blaKPC-positive Klebsiella pneumoniae for over a year, leading to the initiation of a detailed genomic analysis exploring mixed colonization, plasmid recombination, and plasmid diversification. Whole-genome sequence analysis identified a variety of changes, both subtle and large, in the blaKPC-positive organisms. Long-term colonization of patients with blaKPC-positive Klebsiella pneumoniae creates new opportunities for horizontal gene transfer of plasmids encoding antibiotic resistance genes and poses complications for the delivery of health care.
authors.affiliation: National Human Genome Research Institute, Bethesda, Maryland, USA.
authors.forename: Sean
authors.identifier: http://orcid.org/0000-0001-6848-3465
authors.initials: S
authors.lastname: Conlan
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA.
authors.forename: Morgan
authors.initials: M
authors.lastname: Park
authors.affiliation: National Human Genome Research Institute, Bethesda, Maryland, USA.
authors.forename: Clayton
authors.initials: C
authors.lastname: Deming
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA.
authors.forename: Pamela J
authors.initials: PJ
authors.lastname: Thomas
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA.
authors.forename: Alice C
authors.initials: AC
authors.lastname: Young
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA.
authors.forename: Holly
authors.initials: H
authors.lastname: Coleman
authors.affiliation: National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Sison
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, Maryland, USA.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Weingarten
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, Maryland, USA.
authors.forename: Anna F
authors.initials: AF
authors.lastname: Lau
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, Maryland, USA.
authors.forename: John P
authors.initials: JP
authors.lastname: Dekker
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, Maryland, USA.
authors.forename: Tara N
authors.initials: TN
authors.lastname: Palmore
authors.affiliation: National Institutes of Health Clinical Center, Bethesda, Maryland, USA.
authors.forename: Karen M
authors.initials: KM
authors.lastname: Frank
authors.affiliation: National Human Genome Research Institute, Bethesda, Maryland, USA jsegre@nhgri.nih.gov.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Segre
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics*; D003428:Cross Infection; D004269:DNA, Bacterial / Q000235:genetics; D004196:Disease Outbreaks; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D016521:Electrophoresis, Gel, Pulsed-Field; D004926:Escherichia coli; D005260:Female; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007710:Klebsiella Infections / Q000382:microbiology* / Q000635:transmission; D007711:Klebsiella pneumoniae / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development* / Q000302:isolation & purification; D008297:Male; D010957:Plasmids; D013997:Time Factors; D001618:beta-Lactamases / Q000096:biosynthesis / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D001618:beta-Lactamases; C063912:carbapenemase