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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.