title: Pangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.
abstract: BACKGROUND
  Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.
  
  
  RESULTS
  The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.
  
  
  CONCLUSIONS
  We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.
authors.affiliation: Bioinformatics Analysis Group-GABi, Centro de Investigación y Desarrollo en Biotecnología-CIDBIO, 111221, Bogotá DC, Colombia. jmosquera@cidbio.org.|Grupo GEBIOMIC, FCEN, Universidad de Antioquia, Medellín, Colombia. jmosquera@cidbio.org.
authors.forename: Jeanneth
authors.initials: J
authors.lastname: Mosquera-Rendón
authors.affiliation: Grupo Bacterias y Cáncer, Universidad de Antioquia, Medellín, Colombia. ana.rada@colmayor.edu.co.|Grupo Biociencias, Institución Universitaria Colegio Mayor de Antioquia, Medellín, Colombia. ana.rada@colmayor.edu.co.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Rada-Bravo
authors.affiliation: Bioinformatics Analysis Group-GABi, Centro de Investigación y Desarrollo en Biotecnología-CIDBIO, 111221, Bogotá DC, Colombia. scardenas@cidbio.org.
authors.forename: Sonia
authors.initials: S
authors.lastname: Cárdenas-Brito
authors.affiliation: Grupo GEBIOMIC, FCEN, Universidad de Antioquia, Medellín, Colombia. mauricio.corredor@udea.edu.co.
authors.forename: Mauricio
authors.initials: M
authors.lastname: Corredor
authors.affiliation: Grupo Bacterias y Cáncer, Universidad de Antioquia, Medellín, Colombia. elianarestrepo.pineda@gmail.com.
authors.forename: Eliana
authors.initials: E
authors.lastname: Restrepo-Pineda
authors.affiliation: Bioinformatics Analysis Group-GABi, Centro de Investigación y Desarrollo en Biotecnología-CIDBIO, 111221, Bogotá DC, Colombia. abenitez@cidbio.org.|Centro de Investigación y Desarrollo en Biotecnología, Calle 64A # 52-53 Int8 Of203, 111221, Bogotá DC, Colombia. abenitez@cidbio.org.|Microbial Ecology, Nutrition & Health Research Unit, Agrochemistry and Food Technology Institute (IATA-CSIC), 46980, Paterna-Valencia, Spain. abenitez@cidbio.org.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Benítez-Páez
mesh_terms: D018441:Biofilms / Q000254:growth & development; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D010802:Phylogeny; D011552:Pseudomonas Infections / Q000235:genetics* / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000472:pathogenicity