Table 4. Review of publications for evaluation of MALDI-TOF MS for the identification of Nocardia species.
| Commercial DB | "In-house" DB | |||||||
|---|---|---|---|---|---|---|---|---|
| System | Reference method | ID criteria to species/genus | Ni/Ns for DB validation | DB version | Correct ID to species/genus | Ni/Ns for DB development | Correct ID to species/genus | Reference |
| Bruker Autoflex Speed | MLSA | ≥ 2.0/< 2.0 and ≥ 1.7 | See notea | BioTyper ver. 3.1 | 0%/32.0%a | 5/5 | 95.0%/5.0%a | This study |
| Bruker microflex LT | 16S rRNA gene and conventional | ≥ 2.0/< 2.0 and ≥ 1.7 | 148/15 | BioTyper ver. 3.1 | 41.9%/15.5% | 232/53 | 89.9%/4.7% | [23] |
| Bruker (Model not specified) | 16S rRNA, hsp65 and secA1 genes | ≥ 1.9/< 1.9 and ≥ 1.7 | 87/25 | BioTyper ver. 3.1 | 52.8%/6.9% | 13/13 | 82.8%/11.5% | [22] |
| Bruker microflex LT | 16S rRNA gene and conventional | ≥ 2.0/< 2.0 and ≥ 1.7 | 64/22 | BioTyper ver. 3.1 | 15.6%/25.0% | 192/73 | 90.6%/9.4% | [18] |
| Bruker microflex LT | 16S rRNA and secA1 genes | ≥ 2.0/< 2.0 and ≥ 1.7 | 74/14 | BioTyper ver. 3.1 | 14.9%/52.7% | ND | ND | [19] |
| Andromas | 16S rRNA, hsp65 genes, conventional | See noteb | 51/12 | See noteb | 80.4%/17.6% | ND | ND | [21] |
| Bruker microflex LT | 16S rRNA gene and conventional | ≥ 2.0/< 2.0 and ≥ 1.7 | 43/9 | BioTyper ver. 3.0.2 | 23.3%/20.9% | 110/17 | 79.1%/9.3% | [20] |
Abbreviations: ID, identification; Ni/Ns, number of isolates/number of species; DB, database; MLSA, multilocus sequence analysis.
a In the present study, all 25 Nocardia clinical isolates collected were involved for validation of the commercial Bruker Biotyper database. While for the "in-house" database, five of the 25 Nocardia isolates were used for databased development, and the rest 20 isolates were used for "in-house" database validation. See details in Methods section.
b An Andromas database (database version not specified) was employed in the study by Farfour et al. Criteria for correct identification to species level: percentage of common peaks is ≥ 68% and more than 10% difference between the first two best-match species. Criteria for correct identification to genus level: percentage of common peaks is ≥ 68% yet less than 10% difference between the first two best-match species.