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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

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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.

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Funding

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).

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Authors and Affiliations

  1. Institut des Agents infectieux, Centre de Biologie et Pathologies Nord, Hôpital de la Croix Rousse, Lyon, France

    T. Durand, O. Dauwalder, O. Dumitrescu, F. Laurent & V. Rodríguez-Nava

  2. UMR CNRS 5557, Ecologie Microbienne – Groupe de Recherche “Pathogènes Opportunistes et Environnement” – ISPB-Faculté de Pharmacie, Université Lyon 1, Lyon, France

    F. Vautrin, E. Bergeron & V. Rodríguez-Nava

  3. bioMérieux France, Microbiology R&D, La Balme-les-Grottes, France

    V. Girard, S. Polsinelli, V. Monnin & G. Durand

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  1. T. Durand
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Correspondence to V. Rodríguez-Nava.

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Durand, T., Vautrin, F., Bergeron, E. et al. 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. Eur J Clin Microbiol Infect Dis 39, 559–567 (2020). https://doi.org/10.1007/s10096-019-03758-x

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