Infection control and hospital epidemiology · 2015
Whole Genome Sequencing in Real-Time Investigation and Management of a Pseudomonas aeruginosa Outbreak on a Neonatal Intensive Care Unit.
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Davis Rebecca J, Jensen Slade O, Van Hal Sebastiaan, Espedido Björn, Gordon Adrienne, Farhat Rima, Chan Raymond
Аннотация
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.
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.