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

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.

Identification of strains with phenotypes similar to those of Staphylococcus aureus isolated from table chicken eggs using MALDI-TOF MS and genotyping methods

“…Recently, an increasing number of published studies have used MALDI-TOF mass spectrometry to differentiate Staphylococcus strains, and the results obtained are comparable to the identification based on gene sequence analysis (1). In the present study we also made an attempt to identify the Staphylococcus strains using mass spectrometry.…”

Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry: a Fundamental Shift in the Routine Practice of Clinical Microbiology

“…In this study, 81.5% of identifications made by the MALDI-TOF MS were correct, compared to 98.9% of isolates identified correctly by tuf sequencing (91). Importantly, a database of 47 type strains was used to analyze sequence data, exceeding the number of entries present in the SAMARIS database at that time.…”

tuf Gene Sequence Analysis Has Greater Discriminatory Power than 16S rRNA Sequence Analysis in Identification of Clinical Isolates of Coagulase-Negative Staphylococci

“…However, because 16S rRNA analysis has low discriminatory power for the identifi- (4,12,20), other target genes, such as the tuf gene, have been studied for CNS identification and exhibit good resolution (2,6,14). In the genomic era, postsequencing analyses have become an important part of molecular diagnostics.…”