Table 1.
Identification methods reported in the literature for SBSEC isolates.
| Identification Method | S. alactolyticus | S. equinus | S. gallolyticus subsp. gallolyticus | S. gallolyticus subsp. macedonicus | S. gallolyticus subsp. pasteurianus | S. infantarius subsp. infantarius | S. lutetiensis (S. infantarius subsp. coli) | Reference | Comments |
|---|---|---|---|---|---|---|---|---|---|
| Phenotypic | Rarely used. Lack of revised nomenclature in culture collection deposits and imperfect updates of databases. | ||||||||
| Rapid ID 32 Strep (bioMérieux) | +/- | - | - | - | - | - | - | [17,33,39] | |
| Vitek 2 GP ID Card (bioMérieux) | +/- | +/- | +/- | - | +/- | +/- | +/- | [14,17,21,22,43,47] | |
| Genotypic a | Generally based on gene PCR and sequencing. Partial sequences of rpoB, sodA, groEL, and gyrB are more discriminative than 16S rRNA gene sequence, with groEL representing the best performer. Absence of curated sequencing databases and lack of revised nomenclature in culture collection strains. | ||||||||
| 16S rRNA | n.a. | + | + | + | + | +/- | +/- | [14,19,22,39,43,45,46,48,58] | |
| soda | + | + | + | + | + | + | + | [19,22,33,40,43,56,57] | |
| rpsB | n.a. | n.a. | + | n.a. | + | n.a. | n.a. | [21] | |
| gyrB | + | + | + | + | + | + | + | [40,51] | |
| 16S-23S ITS R | n.a. | + | + | + | + | + | + | [23,55] | |
| tanB | n.a. | n.a. | + | n.a. | n.a. | n.a. | n.a. | [52] | |
| SGPB0680 | n.a. | n.a. | n.a. | n.a. | + | n.a. | n.a. | [52] | |
| rpoB | + | + | + | + | + | + | + | [40] | |
| groES/EL b | + | + | + | + | + | + | + | [40,43,47] | |
| rnpB | n.a. | n.a. | + | n.a. | + | n.a. | n.a. | [44] | |
| recN c | n.a. | n.a. | + | n.a. | + | + | + | [51] | |
| MLST d | + | + | + | + | + | + | + | [5,42] | |
| Proteomic | Very fast and cheap, but highly dependent on the system, spectral databases and algorithms used | ||||||||
| MALDI TOF Bruker Biotyper | n.a. | - | - | - | +/- | - | + | [19,44,45,46,55,57,58] | |
| MALDI TOF Vitek MS | + | + | + | +/- | +/- | + | + | [44,45,46,55,56,58] |
From the literature a given method has been reported to: correctly identify SBSEC isolates to the species/subspecies level with high probability (“+”); be not able to correctly identify isolates to the species/subspecies level or correctly identify isolates with low probability (“-“); show discordant results (“+/-”); “n.a.” indicates that the SBSEC species/subspecies was not tested by the corresponding method. ITS R: interspacer region. a Genotypic methods are mainly based on gene PCR and sequencing. For 16S rRNA gene restriction fragment length polymorphism (RFLP) analysis has been also reported [48]. For gyrB gene real-time PCR without sequencing has been also described [51]. Refer to the text for details. b RFLP analysis of groESL gene has been also described [43,47]. c Real-time PCR for recN gene has been described [51]. d Multilocus Sequence Typing (MLST) based on PCR and sequencing of 7 housekeeping genes (dpr, gmk, rpoD, parC, pta, pyrC, recN) [42] or 10 housekeeping loci (ddlA, gki, glnA, mutS, mutS2, pheS, proS, pyrE, thrS, tpiA) [5].