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

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.