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Table 1 Comparison of the phenotypic and genotypic serotyping

From: Draft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence

Phenotypic results PCR results Genome sequencing results
Agglutination reactions Phenotypic serotype [[2]] Genes detected using PCR scheme [[3]]. PCR serotype [[3]] Serotype derived from genome sequence according to PCR scheme [[3]] Number of SNPs different in the core regions compared with reference strain Proportion of reference mapped to
Type I 1a gtrI 1a 1a 2549 0.88
Type I + Group 6 1b gtrI + oac 1b 1b 2552 0.87
MASF 1c 1c gtrI + gtrC 1c 1c 2661 0.88
Type II + Y 2a gtrII 2a 2a 731 0.91
Type II + X 2b gtrII + gtrX 2b 2b 2650 0.89
Type III + X 3a gtrIII + gtrX 3a 3a 6947 0.86
Type III + Y 3b gtrIII 3b 3b 6976 0.85
Type III + Y 3c gtrIII 3c Not included in the PCR scheme Not included in the PCR scheme 7030 0.85
Type IV + Y 4a gtrIV 4a 4a 2595 0.87
Type IV + Group 6 4b gtrIV + oac 4b 4b 2528 0.87
Type V + Y 5a gtrV + oac 5a Not included in the PCR scheme Not included in the PCR scheme 4388 0.89
Type V + X 5b gtrV + oac + gtrX 5b Not included in the PCR scheme Not included in the PCR scheme 4294 0.88
Type VI 6 wzx6 6 6 47787 0.74
MASF IV-1 E1037 E1037 gtrIV + lpt-O MASF IV-1 E1037 4a with Ipt-O (opt) gene 3333 0.88
X X gtrX X X 6937 0.84
Y Y No amplification Y Y 752 0.92