Identification of Lactobacilli from Deep Carious Lesions by Means of Species-Specific PCR and MALDI-TOF Mass Spectrometry

Background: The aim of the present study was to compare MALDI-TOF results for the identification of 87 lactobacilli, isolated from soft or hard carious dentin from 70 first molars of 7- to 8-year-old children with those obtained by species-specific PCR. Methods: The 87 isolates were analyzed by MALDI-TOF MS (Microflex LT, MALDI Biotyper 3.0, Bruker Daltonik, Bremen, Germany), using a reference data base of 4110 strains including > 90 lactobacillus species. For the identification with species-specific PCR, oligonucleotide primers (16S rRNA) specific for L. casei, L. paracasei, L. rhamnosus, L. gasseri, L. plantarum, and L. acidophilus were used; type strains served as controls. The PCR-products were separated electrophoretically on a 1.5% agarose gel and identified by their position on the gel. Results: For 93% of the strains both methods produced concordant results; 40 strains were identified as L. rhamnosus, 16 as L. paraeasei subsp. paraeasei,15 as L. paracasei subsp. tolerans, 4 as L. paraeasei, 3 as L. gasseri, 2 as L. plantarum, and 1 as L. casei. In 4.5% of the cases the results were discordant. Of the 3 strains, not identified by species-specific PCR, 1 strain was identified by MALDI-TOF MS as L. spec. and 1 as L. parabuchneri. One strain could not be identified by either method. Conclusions: Both methods are highly sensitive. Limitations can be the precision of the primers (PCR) or the scarcity of strains from a certain habitat in the data base. Additional information is necessary for the strains without or with discordant identification.