Genotypic and phenotypic evolution of a Pseudomonas aeruginosa ST395 strain during 11-year in hospital spread.

P. aeruginosa is an opportunistic pathogen responsible of hospital-acquired infections in immunocompromised patients. Although in-host evolution of P. aeruginosa is well documented, little is known about this pathogen evolution during its spread on a hospital scale. The high-risk multidrug resistant clone ST395 spread among more than 300 patients in the University Hospital of Besançon between 1997 and 2008. We used a WGS approach to identify the origin of the outbreak, the features that could have helped its implantation in our hospital and those associated with the end of the epidemics. The genomes of 54 representative isolates were fully sequenced. The phylogenetic tree indicated two distinct clusters corresponding to two parallel outbreaks. The ancestor of the ST395 clone possibly contaminated our hospital water network during its construction in 1979. This hypothesis is supported by the fact that the ST395 strain had a specific genomic island carrying 6 copper transporter genes implicated in copper resistance, correlated with the resistance to this metal which water supply network is made of. The late isolates displayed independent genomic signatures of chronic adaptation in patients (altered LPS and porin OprD, and extinction of MexAB-oprM efflux pump overproduction). Some of these mutations were associated with a decreased in vitro fitness. We hypothesize that the independent emergence of isolates adapted to chronic infection, and thus the accumulation of epidemiological dead-ends, participated to the end of the hospital outbreak of P. aeruginosa ST395.