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Table 2 Comparison of misclassified isolates with Random Forest to traditional laboratory testing

From: Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

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
  1. 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.