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Genomic epidemiology of an endoscope-associated outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae

Marsh, JW and Krauland, MG and Nelson, JS and Schlackman, JL and Brooks, AM and Pasculle, AW and Shutt, KA and Doi, Y and Querry, AM and Muto, CA and Harrison, LH (2015) Genomic epidemiology of an endoscope-associated outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae. PLoS ONE, 10 (12).

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Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL)-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsedfield gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak.


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Marsh, JWjwmarsh@pitt.eduJWMARSH
Krauland, MGmgk8@pitt.eduMGK8
Nelson, JS
Schlackman, JLjlg135@pitt.eduJLG135
Brooks, AM
Pasculle, AWawp1@pitt.eduAWP1
Shutt, KAshuttk@pitt.eduSHUTTK
Doi, Yyod4@pitt.eduYOD4
Querry, AM
Muto, CAcamuto@pitt.eduCAMUTO
Harrison, LHlharriso@edc.pitt.eduLHARRISO
ContributionContributors NameEmailPitt UsernameORCID
Date: 1 December 2015
Date Type: Publication
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Journal or Publication Title: PLoS ONE
Volume: 10
Number: 12
DOI or Unique Handle: 10.1371/journal.pone.0144310
Institution: University of Pittsburgh
Schools and Programs: Graduate School of Public Health > Epidemiology
Graduate School of Public Health > Infectious Diseases and Microbiology
School of Medicine > Infectious Diseases and Microbiology
Refereed: Yes
Date Deposited: 23 Aug 2016 14:54
Last Modified: 30 Mar 2021 14:56


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