A citywide, clonal outbreak of Pseudomonas aeruginosa

BACKGROUND: Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in community-acquired infections with P. aeruginosa in Cape Town, South Africa.

METHODS: Cases were defined as P. aeruginosa isolated from any clinical sample, and "wild-type" as susceptibility to all antibiotics tested. Residential addresses of community-acquired wild-type cases were mapped. Whole genome sequencing and multi-locus sequence typing were used to determine clonality and identify virulence genes. A clinical study in a subset of patients with bloodstream infection compared demographic and clinical characteristics between sequence types.

RESULTS: The outbreak lasted 10 months from December, 2016 to September, 2017 with 3321 documented cases. At the peak, cases reached 2.3-fold baseline rates. Cases were distributed widely across the city. Multi-locus sequence type (ST) 303 was predominant during the outbreak. Fifty-one virulence genes were differentially present in ST303 compared with other sequence types, including genes involved in biofilm formation, iron uptake, and gut penetration.

CONCLUSION: The investigation confirmed a citywide outbreak of P. aeruginosa. We identified a predominant outbreak-associated clone, ST303, which harbored genes that could contribute to virulence and survival in adverse environmental conditions such as those associated with drought.