title: Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment.
abstract: Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and a serious threat to Public Health because of overuse and misuse of antibiotics that have selected highly resistant strains against which very few therapeutic options exist. Herein is illustrated the intraclonal evolution of the genome of sequential isolates collected in a single CF patient from the early phase of pulmonary colonization to the fatal outcome. We also examined at the whole genome scale a pair of genotypically-related strains made of a drug susceptible, environmental isolate recovered from an ICU sink and of its multidrug resistant counterpart found to infect an ICU patient. Multiple genetic changes accumulated in the CF isolates over the disease time course including SNPs, deletion events and reduction of whole genome size. The strain isolated from the ICU patient displayed an increase in the genome size of 4.8% with major genetic rearrangements as compared to the initial environmental strain. The annotated genomes are given in free access in an interactive web application WallGene  designed to facilitate large-scale comparative analysis and thus allowing investigators to explore homologies and syntenies between P. aeruginosa strains, here PAO1 and the five clinical strains described.
authors.affiliation: Genostar, 60 rue Lavoisier, Montbonnot 38330, France. miganeh@genostar.com.
authors.forename: Céline
authors.initials: C
authors.lastname: Lucchetti-Miganeh
authors.affiliation: UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France. redel@imm.cnrs.fr.
authors.forename: David
authors.initials: D
authors.lastname: Redelberger
authors.affiliation: UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France. gchambonnier@imm.cnrs.fr.
authors.forename: Gaël
authors.initials: G
authors.lastname: Chambonnier
authors.affiliation: Genostar, 60 rue Lavoisier, Montbonnot 38330, France. rechenmann@genostar.com.
authors.forename: François
authors.initials: F
authors.lastname: Rechenmann
authors.affiliation: INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France. sylvie.elsen@cea.fr.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Elsen
authors.affiliation: UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France. bordi@imm.cnrs.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Bordi
authors.affiliation: Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France. katy.jeannot@univ-fcomte.fr.
authors.forename: Katy
authors.initials: K
authors.lastname: Jeannot
authors.affiliation: INSERM, UMR-S 1036, Biology of Cancer and Infection, Grenoble 38054, France. ina.attree-delic@cea.fr.
authors.forename: Ina
authors.initials: I
authors.lastname: Attrée
authors.affiliation: Laboratoire de Bactériologie, Faculté de Médecine-Pharmacie, Université de Franche-Comté, Besançon 25030, France. patrick.plesiat@univ-fcomte.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Plésiat
authors.affiliation: UMR7255-Laboratoire d'Ingénierie des Systèmes Macromoléculaires, CNRS-Aix Marseille University, Marseille 13402, France. bentzman@imm.cnrs.fr.
authors.forename: Sophie
authors.initials: S
authors.lastname: de Bentzmann