Table 2.
Comparison of misclassified isolates with Random Forest to traditional laboratory testing
| Isolate | Phenotypea | Random Forest (RF)a | Votesb | Location in SNP tree | Serotype Shigella/E. coli (agglutination) | Properties against RF classification |
|---|---|---|---|---|---|---|
| IBESS811 | E | S | 0.99 |
Within S. sonnei |
S. sonnei phase 1/ O-negative | Motility |
| IBESS97 | E | S | 0.80 |
Within S. flexneri |
S. flexneri, inconclusive/ O135 | Inconclusive Shigella serotype |
| IBESS1163 | E | S | 0.76 |
Within S. flexneri |
S. flexneri, inconclusive/ O135 | Inconclusive Shigella serotype |
| IBESS911 | E | S | 0.68 |
Within S. flexneri |
S. flexneri, inconclusive/ O135 | Inconclusive Shigella serotype |
| IBESS996 | S | E | 0.53 | Within EIEC / S. flexneri | S. flexneri 3a/ O135 | None, hybrid isolated |
| IBESS988 | S | E | 0.56 | Within EIEC / S. flexneri | S. flexneri 3b/ O135 | None, hybrid isolated |
| IBESS419 | S | E | 0.57 |
Within S. flexneri |
Provisional/O-negative | None, hybrid isolate, provisional Shigellad |
| IBESS232 | S | E | 0.60 |
Within S. flexneri |
Provisional/O-negative | None, hybrid isolate, provisional Shigellad |
| IBESS470 | S | E | 0.82 | Within EIEC | Provisional/O-negative | None, hybrid isolate, provisional Shigellad |
| IBESS810 | S | E | 0.89 | Within EIEC | Auto agglutinablec | None, hybrid isolate, provisional Shigellad |
RF Random Forest. aE Escherchia, S Shigella. bfraction of votes for classification in Random Forest. cIn-silico serotype, using E. coli serotypeFinder 2.0 of the Center for Genomic Epidemiology [23]: provisional/O-negative. d Hybrid isolates Isolates that possess characteristics of both Shigella spp. and E. coli.