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Whole Genome Sequencing in Real-Time Investigation and Management of a Pseudomonas aeruginosa Outbreak on a Neonatal Intensive Care Unit

Published online by Cambridge University Press:  08 June 2015

Rebecca J. Davis ,
Slade O. Jensen ,
Sebastiaan Van Hal ,
Björn Espedido ,
Adrienne Gordon ,
Rima Farhat  and
Raymond Chan
Rebecca J. Davis*
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney NSW Australia
Slade O. Jensen
Affiliation:
Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney NSW Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney NSW Australia
Sebastiaan Van Hal
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney NSW Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney NSW Australia
Björn Espedido
Affiliation:
Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Sydney NSW Australia Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney NSW Australia
Adrienne Gordon
Affiliation:
Department of Perinatal Medicine, Royal Prince Alfred Hospital, Sydney NSW Australia University of Sydney, NSW Australia
Rima Farhat
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney NSW Australia
Raymond Chan
Affiliation:
Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Sydney NSW Australia
*
Address correspondence to Rebecca J. Davis, BMBS, Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Missenden Rd, Camperdown, 2050 NSW Australia ([email protected]).
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Abstract

OBJECTIVE

To use whole genome sequencing to describe the likely origin of an outbreak of Pseudomonas aeruginosa in a neonatal unit.

DESIGN

Outbreak investigation.

SETTING

The neonatal intensive care unit service of a major obstetric tertiary referral center.

PATIENTS

Infants admitted to the neonatal unit who developed P. aeruginosa colonization or infection.

METHODS

We undertook whole genome sequencing of P. aeruginosa strains isolated from colonized infants and from the neonatal unit environment.

RESULTS

Eighteen infants were colonized with P. aeruginosa. Isolates from 12 infants and 7 environmental samples were sequenced. All but one of the clinical isolates clustered in ST253 and no differences were detected between unmapped reads. The environmental isolates revealed a variety of sequence types, indicating a large diverse bioburden within the unit, which was subsequently confirmed via enterobacterial repetitive intergenic consensus–polymerase chain reaction typing of post-outbreak isolates. One environmental isolate, obtained from a sink in the unit, clustered within ST253 and differed from the outbreak strain by 9 single-nucleotide polymorphisms only. This information allowed us to focus infection control activities on this sink.

CONCLUSIONS

Whole genome sequencing can provide detailed information in a clinically relevant time frame to aid management of outbreaks in critical patient management areas. The superior discriminatory power of this method makes it a powerful tool in infection control.

Infect. Control Hosp. Epidemiol. 2015;36(9):1058–1064

Type
Original Articles
Information
Infection Control & Hospital Epidemiology , Volume 36 , Issue 9 , September 2015 , pp. 1058 - 1064
Copyright
© 2015 by The Society for Healthcare Epidemiology of America. All rights reserved 

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