Actinomyces Identification by Biochemical Tests and Partial 16S rRNA Sequencing

Objectives: Reliable characterization of Actinomyces species by phenotypic methods in clinical laboratories is notoriously problematic and time-consuming. The aim of this study was to compare the identification of Actinomyces species by biochemical tests and partial sequencing of the 16S rRNA gene. Methods: Forty-seven gram-positive, succinic acid-producing isolates from failed dental implant fixtures were identified by biochemical tests, including spot catalase and nitrate tests, enzyme reactions (urea, esculin, a-fucosidase, a-glucosidase, b-galactosidase, b-N-acetyl-glucosaminidase) using individual Rosco diagnostic tablets, and fermentation of carbohydrates (arabinose, glucose, maltose, mannitol, raffinose, rhamnose, sucrose, trehalose, and xylose). Partial sequencing of the isolates comprised of about 420 bp, and the sequences obtained were compared to those from the National Center of Biotechnology Information. Results: According to the biochemical results, the isolates were identified as A. gerencseriae (n=4), A. graevenitzii (n=1), A. israelii (n=7), A. naeslundii (n=4), A. odontolyticus (n=21), A. viscosus (n=6), and Actinomyces sp. (n=4). This phenotypic identification correlated with that obtained by partial 16S rRNA sequencing with similarity index ≥97% for 45/47 (96%) isolates at genus level and, at species level, for 30/47 (64%) isolates and for additional 7 isolates with somewhat lower similarity index. The best match of the phenotypic and sequence-based identification at species level was obtained for A. israelii and A. naeslundii isolates. Conclusions: A good agreement of identification at genus level was obtained using biochemical and partial 16S rRNA sequencing. However, when partial sequencing is used, additional phenotypic testing may help to confirm the identification at species level. 16S rRNA sequence data indicate the existence of new unnamed Actinomyces species in this dental implant material.