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Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation

European Journal of Clinical Microbiology & Infectious Diseases volume 36, pages 351–359 (2017)Cite this article

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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Acknowledgments

E. Moore acknowledges the support to the CCUG by the Department of Clinical Microbiology, Sahlgrenska University Hospital. A. Ramírez acknowledges the support of the Servicio de Microbiología, Hospital Universitario Son Espases.

Author information

Affiliations

  1. Department of Biology, Microbiology, Edificio Guillem Colom, Universitat de les Illes Balears, Crtra.Valldemossa km 7.5, 07122, Palma de Mallorca, Spain

    M. Mulet, M. Gomila, J. Lalucat & E. García-Valdés

  2. Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain

    A. Ramírez

  3. Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden

    S. Cardew & E. R. B. Moore

  4. Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Palma de Mallorca, Spain

    J. Lalucat & E. García-Valdés

Authors
  1. M. Mulet
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  2. M. Gomila
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  3. A. Ramírez
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  4. S. Cardew
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  5. E. R. B. Moore
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  6. J. Lalucat
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  7. E. García-Valdés
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Corresponding author

Correspondence to E. García-Valdés.

Ethics declarations

Isolates were obtained as part of the routine activity of the Servicio de Microbiologia of the Hospital Universitario Son Espases (Spain) and of the Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy of the University of Gothenburg (Sweden) and were analyzed anonymously in a retrospective manner. Ethical approval and informed consent were, thus, not required.

Conflict of interest

The authors declare that they have no conflict of interest.

Funding

This work was supported by project CGL2015-70925-P from the Spanish Economy and Competitiveness Ministry (with FEDER cofunding). M. Gomila was supported by a postdoctoral contract from the Conselleria d’Educació, Cultura i Universitats del Govern de les Illes Balears and the European Social Fund. M. Gomila was the recipient of a José Castillejo stipendium for exchange with the Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden.

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Fig. S1
figure 4

Dendrogram of relatedness between the 52 clinical isolates and the type strains Pseudomonas available in the Bruker taxonomy database. The dendrogram was generated by MALDI BioTyper software (vs. 1.0; Bruker Daltonics). Distance values were relative and normalized to a maximal value of 1000. (GIF 335 kb)

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Table S1

Bacterial strains included in the present study, their origins and the initial identifications as received. (DOCX 25 kb)

Table S2

GenBank accession numbers of sequences used in this study. Accession numbers indicated in bold are for sequences determined in this study. (DOCX 20 kb)

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Mulet, M., Gomila, M., Ramírez, A. et al. Uncommonly isolated clinical Pseudomonas: identification and phylogenetic assignation. Eur J Clin Microbiol Infect Dis 36, 351–359 (2017). https://doi.org/10.1007/s10096-016-2808-4

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  • DOI: https://doi.org/10.1007/s10096-016-2808-4

Keywords

  • Clinical Strain
  • Clinical Microbiology Laboratory
  • Sentry Antimicrobial Surveillance Program
  • Intrinsic Antibiotic Resistance
  • Biotyper Software