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Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation.

Journal article
Authors M Mulet
M Gomila
A Ramírez
Sofia Cardew
Edward R.B. Moore
J Lalucat
E García-Valdés
Published in European journal of clinical microbiology & infectious diseases
Volume 36
Issue 2
Pages 351-9
ISSN 1435-4373
Publication year 2017
Published at Institute of Biomedicine, Department of Infectious Medicine
Pages 351-9
Language en
Links dx.doi.org/10.1007/s10096-016-2808-...
www.ncbi.nlm.nih.gov/entrez/query.f...
Subject categories Microbiology

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.

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