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Journal of Clinical Microbiology
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Epidemiology

Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa

Richard A. Stanton, Gillian McAllister, Jonathan B. Daniels, Erin Breaker, Nicholas Vlachos, Paige Gable, Heather Moulton-Meissner, Alison Laufer Halpin
John P. Dekker, Editor
Richard A. Stanton
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Gillian McAllister
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Jonathan B. Daniels
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Erin Breaker
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Nicholas Vlachos
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Paige Gable
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Heather Moulton-Meissner
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Alison Laufer Halpin
aDivision of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
bCommissioned Corps, U.S. Public Health Service, Rockville, Maryland, USA
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John P. Dekker
National Institute of Allergy and Infectious Diseases
Roles: Editor
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DOI: 10.1128/JCM.00214-20
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ABSTRACT

Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.

FOOTNOTES

    • Received 4 February 2020.
    • Returned for modification 2 March 2020.
    • Accepted 28 May 2020.
    • Accepted manuscript posted online 3 June 2020.
  • Supplemental material is available online only.

  • This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.
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Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa
Richard A. Stanton, Gillian McAllister, Jonathan B. Daniels, Erin Breaker, Nicholas Vlachos, Paige Gable, Heather Moulton-Meissner, Alison Laufer Halpin
Journal of Clinical Microbiology Aug 2020, 58 (9) e00214-20; DOI: 10.1128/JCM.00214-20

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Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa
Richard A. Stanton, Gillian McAllister, Jonathan B. Daniels, Erin Breaker, Nicholas Vlachos, Paige Gable, Heather Moulton-Meissner, Alison Laufer Halpin
Journal of Clinical Microbiology Aug 2020, 58 (9) e00214-20; DOI: 10.1128/JCM.00214-20
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KEYWORDS

HAI
Pseudomonas aeruginosa
antibiotic resistance
cgMLST

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