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

Table 1 Comparison of the phenotypic and genotypic serotyping

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

ISSN: 1757-4749