Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak.

Cameron, David R; Pitton, Melissa; Oberhaensli, Simone; Schlegel, Katja; Prod'hom, Guy; Blanc, Dominique S; Jakob, Stephan M; Que, Yok-Ai (2022). Parallel Evolution of Pseudomonas aeruginosa during a Prolonged ICU-Infection Outbreak. Microbiology spectrum, 10(6), e0274322. American Society for Microbiology 10.1128/spectrum.02743-22

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Most knowledge about Pseudomonas aeruginosa pathoadaptation is derived from studies on airway colonization in cystic fibrosis; little is known about adaptation in acute settings. P. aeruginosa frequently affects burned patients and the burn wound niche has distinct properties that likely influence pathoadaptation. This study aimed to genetically and phenotypically characterize P. aeruginosa isolates collected during an outbreak of infection in a burn intensive care unit (ICU). Sequencing reads from 58 isolates of ST1076 P. aeruginosa taken from 23 patients were independently mapped to a complete reference genome for the lineage (H25338); genetic differences were identified and were used to define the population structure. Comparative genomic analysis at single-nucleotide resolution identified pathoadaptive genes that evolved multiple, independent mutations. Three key phenotypic assays (growth performance, motility, carbapenem resistance) were performed to complement the genetic analysis for 47 unique isolates. Population structure for the ST1076 lineage revealed 11 evolutionary sublineages. Fifteen pathoadaptive genes evolved mutations in at least two sublineages. The most prominent functional classes affected were transcription/two-component regulatory systems, and chemotaxis/motility and attachment. The most frequently mutated gene was oprD, which codes for outer membrane porin involved in uptake of carbapenems. Reduced growth performance and motility were found to be adaptive phenotypic traits, as was high level of carbapenem resistance, which correlated with higher carbapenem consumption during the outbreak. Multiple prominent linages evolved each of the three traits in parallel providing evidence that they afford a fitness advantage for P. aeruginosa in the context of human burn infection. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative pathogen causing infections in acutely burned patients. The precise mechanisms required for the establishment of infection in the burn setting, and adaptive traits underpinning prolonged outbreaks are not known. We have assessed genotypic data from 58 independent P. aeruginosa isolates taken from a single lineage that was responsible for an outbreak of infection in a burn ICU that lasted for almost 2.5 years and affected 23 patients. We identified a core set of 15 genes that we predict to control pathoadaptive traits in the burn infection based on the frequency with which independent mutations evolved. We combined the genotypic data with phenotypic data (growth performance, motility, antibiotic resistance) and clinical data (antibiotic consumption) to identify adaptive phenotypes that emerged in parallel. High-level carbapenem resistance evolved rapidly, and frequently, in response to high clinical demand for this antibiotic class during the outbreak.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Department of Intensive Care, Emergency Medicine and Anaesthesiology (DINA) > Clinic of Intensive Care
07 Faculty of Human Sciences > Institute of Psychology > Personality Psychology, Differential Psychology and Diagnostics
08 Faculty of Science > Department of Biology > Bioinformatics and Computational Biology

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Cameron, David Robert, Pitton, Melissa Phung-Kieu, Oberhänsli, Simone, Schlegel, Katja, Jakob, Stephan, Que, Yok-Ai


600 Technology > 610 Medicine & health
100 Philosophy > 150 Psychology
300 Social sciences, sociology & anthropology > 370 Education




American Society for Microbiology




Pubmed Import

Date Deposited:

08 Nov 2022 09:53

Last Modified:

25 Dec 2022 00:16

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

adaptative evolution antibiotic resistance carbapenems oprD outer membrane porin D




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