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Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry

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Abstract

Staphylococcal species, notably, coagulase-negative staphylococci (CoNS), are frequently misidentified using phenotypic methods. The partial nucleotide sequences of the tuf and gap genes were determined in 47 reference strains to assess their suitability, practicability, and discriminatory power as target molecules for staphylococcal identification. The partial tuf gene sequence was selected and further assessed with a collection of 186 strains, including 35 species and subspecies. Then, to evaluate the efficacy of this genotyping method versus the technology of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS), the 186 strains were identified using MALDI-TOF-MS (Axima® Shimadzu) coupled to the SARAMIS® database (AnagnosTec). The French National Reference Center for Staphylococci identification method was used as a reference. One hundred and eighty-four strains (98.9%) were correctly identified by tuf gene sequencing. Only one strain was misidentified and one was unidentified. MALDI-TOF-MS identified correctly 138 isolates (74.2%). Four strains were misidentified, 39 were unidentified, five were identified at the group (hominis/warneri) level, and one strain was identified at the genus level. These results confirm the value of MALDI-TOF-MS identification for common species in clinical laboratory practice and the value of the partial tuf gene sequence for the identification of all staphylococcal species as required in a reference laboratory.

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Acknowledgments

We thank Christine Gardon, Christine Courtier, Céline Spinelli, and Caroline Bouveyron for their technical assistance, Christian Curel, Michel Roch, and Nader Baïda (I2A company) for generously providing us with the Shimadzu Axima® mass spectrometer, the SARAMIS® identification database, and the SirWeb MALDI-TOF software.

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Authors and Affiliations

  1. Laboratoire de Bactériologie, Centre de Biologie et Pathologie Est, Hospices Civils de Lyon, Bron, France

    M. Bergeron, O. Dauwalder, A.-M. Freydiere, M. Bes, H. Meugnier, Y. Benito, J. Etienne, G. Lina, F. Vandenesch & S. Boisset

  2. Centre National de Référence des Staphylocoques, Université Lyon 1, Lyon, France

    O. Dauwalder, M. Bes, H. Meugnier, Y. Benito, J. Etienne, G. Lina, F. Vandenesch & S. Boisset

  3. INSERM U851, IFR128, Lyon, France

    O. Dauwalder, M. Bes, H. Meugnier, Y. Benito, J. Etienne, G. Lina, F. Vandenesch & S. Boisset

  4. Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université de Lyon, 69622, Villeurbanne, France

    M. Gouy

  5. Laboratoire de Bacteriologie, Centre National de Référence des Staphylocoques, 59 Boulevard Pinel, 69677, Bron Cedex, France

    S. Boisset

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  1. M. Bergeron
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  2. O. Dauwalder
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  3. M. Gouy
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  4. A.-M. Freydiere
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  5. M. Bes
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  8. J. Etienne
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  9. G. Lina
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  10. F. Vandenesch
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  11. S. Boisset
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Correspondence to S. Boisset.

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François Vandenesch and Sandrine Boisset share senior authorship.

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Bergeron, M., Dauwalder, O., Gouy, M. et al. Species identification of staphylococci by amplification and sequencing of the tuf gene compared to the gap gene and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Eur J Clin Microbiol Infect Dis 30, 343–354 (2011). https://doi.org/10.1007/s10096-010-1091-z

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