Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)

T Garrigos; C Neuwirth; A Chapuis; J Bador; L Amoureux; Collaborators

doi:10.1016/j.cmi.2020.03.031

Development of a database for the rapid and accurate routine identification of Achromobacter species by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)

Clin Microbiol Infect. 2021 Jan;27(1):126.e1-126.e5. doi: 10.1016/j.cmi.2020.03.031. Epub 2020 Apr 10.

Authors

T Garrigos¹, C Neuwirth², A Chapuis¹, J Bador², L Amoureux³; Collaborators

Collaborators

Collaborators:
E Andre⁴, E Barbier⁵, J Caillon⁶, E Cardot-Martin⁷, V Cattoir⁸, A Doléans-Jordheim⁹, F Echahidi¹⁰, A Ferroni¹¹, H Guet-Revillet¹², G Héry-Arnaud¹³, J Lipuma¹⁴, N Nørskov-Lauritsen¹⁵, C Peeters¹⁶, D Pierard¹⁰, C Segonds¹², E Thomas⁶, P Plésiat¹⁷, P Vandamme¹⁶, A Verroken¹⁸, H Vu-Thien¹⁹

Affiliations

¹ Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France.
² Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France.
³ Department of Bacteriology, University Hospital of Dijon, BP 37013, 21070, Dijon Cedex, France; UMR/CNRS 6249 Chrono-environnement, University of Bourgogne- Franche-Comté, Besançon, France. Electronic address: lucie.amoureux@chu-dijon.fr.
⁴ Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
⁵ INRA, UMR 1347 Agroécologie, Dijon Cedex, France; Université de Bourgogne Franche Comté, Dijon Cedex, France.
⁶ Centre Hospitalier Universitaire Nantes, service de Bactériologie-Hygiene, Nantes, France.
⁷ Department of Microbiology, Foch Hospital, Suresnes, France.
⁸ Service de Bactériologie-Hygiène hospitalière, Centre Hospitalier Universitaire de Rennes, Rennes, France.
⁹ Institut des agents infectieux, Hospices Civils de Lyon, Lyon, France.
¹⁰ Department of Microbiology, National Reference Center for Burkholderia Cepacia Complex, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium.
¹¹ Assistance Publique-Hôpitaux de Paris, Laboratoire de Microbiologie, Hôpital Necker-Enfants Malades, Paris, France; Université Paris Descartes, Faculté de médecine, Paris, France.
¹² Service de Bactériologie-Hygiène, Centre Hospitalier Universitaire de Toulouse, Toulouse, France.
¹³ Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, Brest, France.
¹⁴ Department of Pediatrics, University of Michigan, Ann Arbor, MI 48109 USA.
¹⁵ Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
¹⁶ Laboratory of Microbiology, National Reference Center for Burkholderia Cepacia Complex, Ghent University, Ghent, Belgium.
¹⁷ Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, France.
¹⁸ Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium.
¹⁹ Institute for Integrative Biology of the Cell, CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, France.

PMID: 32283265
DOI: 10.1016/j.cmi.2020.03.031

Abstract

Objectives: Achromobacter spp. are emerging pathogens in respiratory samples from cystic fibrosis patients. The current reference methods (nrdA-sequencing or multilocus sequence typing) can identify 18 species which are often misidentified by conventional techniques as A. xylosoxidans. A few studies have suggested that matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) provides accurate identification of the genus but not of species. The aims of this study were (a) to generate a database for MALDI-TOF/MS Bruker including the 18 species, (b) to evaluate the suitability of the database for routine laboratory identification, and (c) to compare its performance with that of the currently available Bruker default database.

Methods: A total of 205 isolates belonging to the 18 species identified by nrdA sequencing were used to build a local database. Main spectra profiles (MSPs) were created according to Bruker's recommendations for each isolate with the Biotyper software. Performance of the default Bruker database and ours for routine use were compared by testing 167 strains (including 38 isolates used from MSP creation) belonging to the 18 species identified by nrdA sequencing directly from colonies cultivated on various media.

Results: Our new database accurately identified 99.4% (166/167) of the isolates from the 18 species (score ≥2.0) versus only 50.9% (85/167) with the Bruker database. In the Bruker database 17.3% of the isolates (29/167) were incorrectly identified as another species despite a score of ≥2.0.

Conclusions: The use of MALDI-TOF/MS in combination with a database developed with samples from 18 Achromobacter species provides rapid and accurate identification. This tool could be used to help future clinical studies.

Keywords: Achromobacter; MALDI-TOF; mass spectrometry; nrdA; species identification.

MeSH terms

Achromobacter / classification
Achromobacter / genetics
Achromobacter / isolation & purification*
Databases, Factual*
Diagnostic Tests, Routine
Gram-Negative Bacterial Infections / diagnosis*
Gram-Negative Bacterial Infections / microbiology
Humans
Ribonucleoside Diphosphate Reductase / genetics
Software
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*

Substances

Ribonucleoside Diphosphate Reductase