title: Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation.
abstract: Fifty-two Pseudomonas strains that were difficult to identify at the species level in the phenotypic routine characterizations employed by clinical microbiology laboratories were selected for genotypic-based analysis. Species level identifications were done initially by partial sequencing of the DNA dependent RNA polymerase sub-unit D gene (rpoD). Two other gene sequences, for the small sub-unit ribosonal RNA (16S rRNA) and for DNA gyrase sub-unit B (gyrB) were added in a multilocus sequence analysis (MLSA) study to confirm the species identifications. These sequences were analyzed with a collection of reference sequences from the type strains of 161 Pseudomonas species within an in-house multi-locus sequence analysis database. Whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analyses of these strains complemented the DNA sequenced-based phylogenetic analyses and were observed to be in accordance with the results of the sequence data. Twenty-three out of 52 strains were assigned to 12 recognized species not commonly detected in clinical specimens and 29 (56 %) were considered representatives of at least ten putative new species. Most strains were distributed within the P. fluorescens and P. aeruginosa lineages. The value of rpoD sequences in species-level identifications for Pseudomonas is emphasized. The correct species identifications of clinical strains is essential for establishing the intrinsic antibiotic resistance patterns and improved treatment plans.
authors.affiliation: Department of Biology, Microbiology, Edificio Guillem Colom, Universitat de les Illes Balears, Crtra.Valldemossa km 7.5, 07122, Palma de Mallorca, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Mulet
authors.affiliation: Department of Biology, Microbiology, Edificio Guillem Colom, Universitat de les Illes Balears, Crtra.Valldemossa km 7.5, 07122, Palma de Mallorca, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Gomila
authors.affiliation: Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Ramírez
authors.affiliation: Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.
authors.forename: S
authors.initials: S
authors.lastname: Cardew
authors.affiliation: Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden.
authors.forename: E R B
authors.initials: ER
authors.lastname: Moore
authors.affiliation: Department of Biology, Microbiology, Edificio Guillem Colom, Universitat de les Illes Balears, Crtra.Valldemossa km 7.5, 07122, Palma de Mallorca, Spain.|Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Lalucat
authors.affiliation: Department of Biology, Microbiology, Edificio Guillem Colom, Universitat de les Illes Balears, Crtra.Valldemossa km 7.5, 07122, Palma de Mallorca, Spain. elena.garciavaldes@uib.es.|Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain. elena.garciavaldes@uib.es.
authors.forename: E
authors.initials: E
authors.lastname: García-Valdés
mesh_terms: D016000:Cluster Analysis; D027081:DNA Gyrase / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D005838:Genotype; D006801:Humans; D058885:Multilocus Sequence Typing; D010641:Phenotype; D010802:Phylogeny; D011549:Pseudomonas / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D011552:Pseudomonas Infections / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases; D027081:DNA Gyrase