TABLE 1.

Primer and probe sequences for identification of various Shigella flexneri serotypes^a

Target	Accession no.	Sequence	Concn (nM)	Amplicon length (bp)	Reactive S. flexneri serotype(s)
Panel I
gtrII	AY900451	CAAACGACTCAGGAAATATGC	150	104	2a, 2b
		AATTCATAAATGCAACCATCCT	150
		FAM-CTCCATGAGCGCAGACACTTTTG	75
gtrV	CP000266	TTATTAATGTCATCGTCCATCC	400	112	5a, 5b
		CCACTCCCAGATTACGG	400
		Quasar670-GCAGGGTTGAACTTGAAAGAATACGAT	200
gtrX	L05001	AGCACCACATCAAAAATCTTC	500	106	1d, 2b, 3a, 5b, X
		CATACAATGATAAATACCAGTGAGCATT	500
		HEX-TATATTTAATTTGCATGCCCGGGC	250
wzx6	EU294165	GAGCGATCATTTCAACTTCA	500	122	6
		TACAACATGATTCGCGTTAATGT*	500
		Quasar 705-CGGTAATTCTAACTATATTGGGCTTG*	250
oac	X59553	GCATAAGAGCAACTGCTTTG	400	73	1b, 3a, 3b, 4b, 5a, 5b, 7b
		CGCGTAGTGGTGACTG	400
		Texas Red-ACGGCAAGGCTTGTGGCA	200
Panel II
gtrI	AF139596	AAATATGCCTCCATACAATTG	500	133	1a, 1b, 1d, 7a, 7b
		AGCATATGTATTAAACAATCAGCA	500
		FAM-GCTGTTAGCAACATCCGGTTCAAC	250
gtrIc	FJ905303	ACCTTAGGTTCAAATGGGTTAC	400	132	7a, 7b
		GAAATAGCCGTCTCTCGAATA	400
		Quasar 670-TGTTTTCACATTTAGTATTCCAAC*	200
gtrIV	AF288197	TCTCACATGATGGCACATTA	400	143	4a, 4b
		CCTAAGATCAAATGTGTGTGTGA	400
		HEX-TTTATACCCTGAAGGAAAATTTCAG*	200
ipaH	M76445	CCTTTTCCGCGTTCCTTGA	125	64	All Shigella species and serotypes
		CGGAATCCGGAGGTATTGC	125
		Quasar 705-CGCCTTTCCGATACCGTCTCTGCA	62.5

^aAssays were adapted from Gentle et al. (20), with some modifications marked with asterisks. gtr genes encode serotype-specific glucosyltransferases; oac encodes an O-acetyltransferase that mediates the addition of an acetyl group to a specific sugar in the backbone structure; wzx6 is the O-antigen synthesis gene specific to S. flexneri serotype 6.