Table 4.
In-silico matching of the assessed probes with target sequences in the 0-mismatch range (0 MM), the 1-base-mismatch range (1 MM), and the 2-bases-mismatch range (2 MM) (–, not matches indicated)
| Probea | Target organism | 0 MM | 1 MM | 2 MM |
|---|---|---|---|---|
| ACS 16S 729 | Acinetobacter spp. | 61.7% 3114/5046 |
57.6% 276/479 |
9.7% 45/463 |
| Entero all (variant 1: "A" at the wobble position) | Enterobacterales | 58.1% 1906/3282 |
47.0% 7110/15123 |
51.0% 521/1022 |
| Entero all (variant 2: "T" at the wobble position) | Enterobacterales | 46.5% 6526/14023 |
55.7% 2220/3987 |
54.0% 594/1101 |
| ENF 16S 191 | Enterococcus faecalis | 47.5% 322/678 |
18.8% 3/16 |
0% 0/1 |
| ENU 23S 140 Beimfohr | Enterococcus faecium | 97.3% 36/37 |
- | 25.0% 1/4 |
| EGA 16S 141 | Enterococcus gallinarum | 66.7% 2/3 |
- | - |
| ENC 16S 221 | Enterococcus spp. | 52.4% 1403/2677 |
11.7% 27/230 |
0.3% 4/1260 |
| ENC 176 23S kurz | Enterococcus spp. | 86.2% 125/145 |
0% 0/59 |
0% 0/999 |
| ESC 16S 468 | Escherichia coli | 28.3% 1983/7009 |
29.5% 165/559 |
7.9% 3/38 |
| Klpn23S | Klebsiella pneumoniae | 82.1% 55/67 |
0% 0/7 |
0% 0/2403 |
| Psae Ulm 16S 182 | Pseudomonas aeruginosa | 17.0% 747/4406 |
0.7% 8/1088 |
0.1% 6/4926 |
| Sal 23S 331 | Salmonella spp. | 95.1% 273/287 |
75.0% 3/4 |
0% 0/2236 |
| Sal Yer 23S 1705 Komp | none, prevention of cross-reaction with organisms other than Salmonella spp. | 100% 2198/2198 |
87.5% 239/273 |
29.9% 120/401 |
| SalYer 23S 1705 | Salmonella spp. | 94.9% 281/296 |
12.5% 34/271 |
0% 0/2246 |
| Komp Sal 23S 331 | none, prevention of cross-reaction with organisms other than Salmonella spp. | 100% 2181/2181 |
94.8% 165/174 |
99.0% 308/311 |
| Stalle 16S | Staphylococcus spp. | 38.7% 2154/5571 |
0.9% 51/5484 |
0.02% 17/99651 |
| Stau16S Kempf | Staphylococcus aureus | 68.1% 451/662 |
25.0% 14/56 |
0% 0/1052 |
| Stemal Hogardt | Stenotrophomonas maltophilila | 26.9% 77/286 |
14.3% 315/2207 |
6.7% 81/1211 |
| Saga (variant 1: "A" at the wobble position) | Streptococcus agalactiae | 94.1% 32/34 |
65.0% 134/206 |
- |
| Saga (variant 2: "C" at the wobble position) | Streptococcus agalactiae | 65.2% 135/207 |
93.9% 31/33 |
- |
| Spneu | Streptococcus pneumoniae | 97.4% 683/701 |
1.6% 20/1220 |
0.3% 7/2050 |
| Spn Komp | none, prevention of cross-reaction with bacteria other than Streptococcus pneumoniae | 98.6% 1197/1214 |
74.8% 2051/2741 |
99.9% 2141/2144 |
| Strep Franks = Str 16S 492 Jansen | Streptococcus spp. | 43.6% 3725/8553 |
3.1% 39/1239 |
0.03% 10/39762 |
| Bact 16 S 389 | Bacteroides spp. | 2.2% 463/21395 |
0.3% 27/9376 |
0.2% 17/9436 |
| Bact Komp | none, prevention of cross-reaction with Porphyromonas spp. | 99.3% 3110/3132 |
98.4% 29461/29941 |
99.9% 16677/16691 |
| Bact Komp 2 | none, prevention of cross-reaction with Prevotella spp. | 100% 10857/10858 |
97.9% 21873/22351 |
99.5% 4896/4921 |
| Mic | Micrococcus spp. | 78.4% 355/453 |
34.0% 34/100 |
4.5% 24/528 |
| Spy1 | Streptococcus pyogenes | 72.2% 143/198 |
100% 1/1 |
0% 0/2 |
aProbe names as stated in the supplementary material 1.