TABLE 3.
Detection and identification of P. stewartii and other Pantoea species by PCR and MALDI-TOF MS analysis
| Species, strain (other datuma) | cPCR resultb with primers: |
qPCR resultc withd: |
Log score in MALDI-TOF MS for speciesd | ||||||
|---|---|---|---|---|---|---|---|---|---|
| 338/339 | 340/341 | 356/341 | 342/343 | 383/385 | TM and primer set 340/354 | SG and primer set 356/357 | SG and primer set 364/365 | ||
| P. stewartii | |||||||||
| CFBP 3614T (i+) | + | + | + | + | + | 20.6 | 21.1 | 20.9 | 2.0 |
| DC116 (i−) | + | + | + | + | + | 20.1 | 19.8 | 17.3 | 2.1 |
| DC117 (Ps) | + | + | + | + | + | 20.2 | 19.2 | 18.9 | 2.2 |
| DC119 (Ps) | + | + | + | + | + | 20.1 | 19.1 | 19.2 | 2.1 |
| DC122 (i−) | + | + | + | + | + | 20.0 | 19.6 | 20.1 | 2.1 |
| DC133 (i−) | + | + | + | + | + | 20.3 | 20.0 | 20.6 | 2.2 |
| DC145 (Ps) | + | + | + | + | + | 20.2 | 18.3 | 18.1 | 2.2 |
| DC146 | + | + | + | + | + | 20.7 | 20.3 | 20.4 | 2.2 |
| DC147 | + | + | + | + | + | 20.8 | 19.8 | 19.0 | 2.2 |
| DC162 | + | + | + | + | + | 20.0 | 19.2 | 17.8 | 2.2 |
| DC172T (Ps, i−) | + | + | + | + | + | 20.5 | 18.7 | 19.1 | 2.0 |
| DC283 (Ps, i−) | + | + | + | + | + | 21.6 | 20.3 | 20.2 | 2.1 |
| DC405 | + | + | + | + | + | 21.3 | 18.7 | 19.7 | 2.3 |
| DC406 | + | + | + | + | + | 21.1 | 19.0 | 19.8 | 2.2 |
| DC407 (Ps) | + | + | + | + | + | 20.9 | 19.9 | 17.7 | 2.4 |
| DC408 | + | + | + | + | + | 20.7 | 17.9 | 18.8 | 2.2 |
| EstA1 (i−) | + | + | + | + | + | 18.3 | 20.4 | 17.7 | 2.2 |
| SS102 (Ps) | + | + | + | + | + | 19.9 | 20.1 | 17.3 | 2.2 |
| SS104 (Ps) | + | + | + | + | + | 19.8 | 18.7 | 20.0 | 2.0 |
| SW2 (Ps) | + | + | + | + | + | 20.6 | 19.5 | 19.2 | 2.1 |
| P. agglomerans | |||||||||
| 48b/90 (i−) | − | − | − | − | − | 32.1 | 35.1 | 31e | 2.4 |
| AL807540 | ND | ND | − | ND | − | >40 | 36.6 | 35.6 | 2.2 |
| AL910982 | ND | ND | − | ND | − | 32.6 | 37.6 | 33e | 2.0 |
| C9-1 | − | − | − | − | − | 35.0 | >40 | >40 | 2.2 |
| DC556 | − | − | − | − | − | 37.9 | 38.3 | >40 | 2.3 |
| DSM 3493T | − | − | − | − | − | 36.0 | 39.3 | ND | 2.3 |
| Eh252 | − | − | − | − | − | 38.6 | 38.2 | 33.7 | 2.2 |
| Eh2b/89 | − | − | − | − | − | 36.9 | 34.1 | 36.4 | 2.1 |
| Eh583 | − | − | − | − | − | 37.8 | >40 | >40 | 2.4 |
| Ehb4188 | − | − | − | − | − | 36.8 | 36.0 | >40 | 2.4 |
| Ehg102 | − | − | − | − | − | 37.6 | 35.6 | >40 | 2.3 |
| Ehg3-108 | − | − | − | − | − | >40 | 38.1 | 36.3 | 2.4 |
| EhgPD713 | − | − | − | − | − | >40 | 37.6 | 37.8 | 2.3 |
| EhNZ | − | − | − | − | − | 33.1 | 38.3 | >40 | 2.4 |
| EhY112 (i−) | − | − | − | − | − | 34.8 | >40 | >40 | 2.3 |
| KasEh1 | − | − | − | − | − | >40 | ND | ND | 2.3 |
| EhMB96 (i−) | − | − | − | − | − | 36.0 | >40 | 35.8 | 2.3 |
| Pa81883 | − | − | − | − | − | 35.7 | 36.8 | >40 | 2.3 |
| Pa82245 | − | − | − | − | − | 34.9 | 34.6 | >40 | 2.3 |
| Pa83873 | − | − | − | − | − | 33.3 | 36.0 | >40 | 2.3 |
| P. ananatis | |||||||||
| CU2093 | − | − | − | − | − | >40 | >40 | 36.9 | No ID |
| DC129 (i+) | − | SB | − | − | − | >40 | >40 | >40 | 2.1 |
| DC532 | − | SB | − | − | − | 38.2 | >40 | >40 | 2.1 |
| P. dispersa | |||||||||
| DSM 30073T (i−) | − | − | − | − | − | 31.9 | 39.5 | 37.9 | 2.0 |
| NCPPB 2285 | + | + | − | (+) | − | 36.6 | >40 | >40 | 2.3 |
| Others | |||||||||
| DC429 (i−) | − | − | − | − | − | >40 | 37.0 | >40 | No ID |
| DC437 (i−) | − | − | − | − | − | 38.2 | 35.3 | 36.1 | No ID |
| DC443 (G+) | − | − | − | − | − | >40 | 33.9 | 34.7 | No ID |
| DC444 (G+) | − | − | − | − | − | 35.5 | 32.6 | 35.6 | No ID |
| S. marcescens | |||||||||
| Sm B2 | − | − | − | − | − | >40 | >40 | 35.8 | 2.2 |
| Sm B14 | − | − | − | − | − | 36.1 | >40 | 35.2 | 2.2 |
a
i+ or i−, result of indole assay; Ps, previously identified as P. stewartii; G+, Gram positive (KOH test).
b
+, positive PCR result; −, negative PCR result; SB, shadow band in wrong position; (+), weak product formation.
c
TM, TaqMan primer 353; SG, SYBR green.
d
ND, not done; ID, identification.
e
Atypical baseline increase.