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Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures

  • T. Durand
  • F. Vautrin
  • E. Bergeron
  • V. Girard
  • S. Polsinelli
  • V. Monnin
  • G. Durand
  • O. Dauwalder
  • O. Dumitrescu
  • F. Laurent
  • V. Rodríguez-NavaEmail author
Original Article
  • 18 Downloads

Abstract

We assessed the performance of the VITEK® MS IVD V3.0 matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-ToF MS) V3.0 database for the identification of Nocardia spp. as compared with targeted DNA sequencing. A collection of 222 DNA sequence-defined Nocardia spp. strains encompassing 18 different species present or not in the database was tested. Bromocresol purple agar (BCP) and Columbia agar +5% sheep’s blood (COS) culture media were used together with two different preparation steps: direct smear and a “3 attempts” procedure that covered (1) spotting of an extract, (2) new spotting of the same extract, and (3) spotting of a new extract. The direct smear protocol yielded low correct identification rates (≤ 15% for both media) whereas protein extraction yielded correct identification results (> 67% regardless of the media used.). The use of 2 additional attempts using repeat or new extracts increased correct identification rates to 87% and 91% for BCP and COS, respectively. When using the 3 attempts procedure, the best identification results, independent of media types, were obtained for N. farcinica and N. cyriacigeorgica (100%). Identification attempts 2 and 3 allowed to increase the number of correct identifications (BCP, +20%; COS, +13%). The enhancement in performance during attempts 2 and 3 was remarkable for N. abscessus (81% for both media) and low prevalence species (BCP, 70%; COS, 85%). Up to 3.4% and 2.4% of the strains belonging to species present in the database were misidentified with BCP and COS media, respectively. In 1.9% of the cases for BCP and 1.4% for COS, these misidentifications concerned a species belonging to the same phylogenetic complex. Concerning strains that are not claimed in the V3.0 database, N. puris and N. goodfellowi generated “No identification” results and 100% of the strains belonging to N. arthritidis, N.cerradoensis, and N. altamirensis yielded a misidentification within the same phylogenetic complex. Vitek® MS IVD V3.0 is an accurate and useful tool for identification of Nocardia spp.

Keywords

Nocardia spp. MALDI-ToF BCP COS DNA sequencing 

Notes

Funding information

Florian VAUTRIN held a doctoral fellowship from the Region Auvergne-Rhône-Alpes. This study was funded by the VITEK® MS manufacturer (bioMérieux, R&D Microbiologie, La Balme-Les-Grottes, France).

Compliance with ethical standards

Disclaimer

The data analysis described here was performed without direct commercial influence by the device manufacturer.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • T. Durand
    • 1
  • F. Vautrin
    • 2
  • E. Bergeron
    • 2
  • V. Girard
    • 3
  • S. Polsinelli
    • 3
  • V. Monnin
    • 3
  • G. Durand
    • 3
  • O. Dauwalder
    • 1
  • O. Dumitrescu
    • 1
  • F. Laurent
    • 1
  • V. Rodríguez-Nava
    • 1
    • 2
    Email author
  1. 1.Institut des Agents infectieux, Centre de Biologie et Pathologies NordHôpital de la Croix RousseLyonFrance
  2. 2.UMR CNRS 5557, Ecologie Microbienne – Groupe de Recherche “Pathogènes Opportunistes et Environnement” – ISPB-Faculté de PharmacieUniversité Lyon 1LyonFrance
  3. 3.bioMérieux France, Microbiology R&DLa Balme-les-GrottesFrance

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