Tracking the origins, spread and evolution of a MDR P. aeruginosa epidemic clone over ten years in a single hospital. Pseudomonas aeruginosa

Nosocomial transmission of Pseudomonas aeruginosa in healthcare facilities is a major concern for antimicrobial stewardship and patient health. In this retrospective investigation, we identified an outbreak of ST-621 P. aeruginosa (n=253 isolates) collected from 81 patients between May 2011 and December 2020. Outbreak cases were detected from 27 of 30+ wards and clinics, and from all floors of a single hospital. Explaining this endemicity, Bayesian evolution analysis predicted that the index case was introduced in the late 1990's, shortly after the hospital first opened. Since then, signatures of both patient-to-patient transmission and infections from contaminated environmental surfaces were observed. Further, phylogenetic analysis revealed the existence of two major clades, hereby named clade A and B. While clase A isoaltes were prevalent initially (2011-2013), clade B isolates dominated by 2014. This clonal replacement corresponded to a decreased prevalence of cefepime resistance (>50% of isolates in 2011 to 75% in 2015). At the molecular level, single nucleotide polymorphisms (SNPs) analysis revealed that the fixation of a stop-gain mutation in the OprD porin was at the origin of the clade B emergence. Finally, while the outbreak clones appeared to evolve at a steady rate of ~6 SNPs/year, a subset of patients were colonized (from 1 to up to 6 years) with a seemingly dormant clone accumulating mutations at a much-reduced rate (~2 SNPs/year). Analysis of within-host evolution showed that while variants in mucoidy, multidrug efflux, and cell wall synthesis were commonly acquired, specific pathways were distinct between patients. In conclusion, using whole genome sequencing data, we investigated the dynamics of a 10+ year outbreak within a single healthcare facility, from the emergence and fixation of beneficial mutations (3.g. carbapenem resistance) to independent adaptations occurring throughout the course of long-term P. aeruginosa chronic infection and colonization.