. 2011 Feb 4;77(7):2458–2470. doi: 10.1128/AEM.02322-10

TABLE 2.

Primers and PCR conditions for gene targets of the STEC binary typing system

Genes^a							PCR conditions
Gene name	Locus	Virulence function	Associated with diarrhea	Associated with HUS and/or outbreaks	Variable among STEC isolates	Reference(s)	Primers (forward/reverse)	Annealing temp (°C)	Product size (bp)	Reference(s)
agn43	Chromosome	Biofilms	×			53	CTGGAAACCGGTCTGCCCTT/CCTGAACGCCCAGGGTGATA	55	433	53
agn43_EDL933	Chromosome	Biofilms	×			53	CGTATCGCTGTGCCCGATAAC/CCGTATACGAGTTGTCAGAATCA	55	707	46, 53
chuA	Chromosome	Iron uptake	×			44	GACGAACCAACGGTCAGGAT/TGCCGCCAGTACCAAAGACA	55	279	9
cif	Chromosome	Cell cycle control				37	AACAGATGGCAACAGACTGG/AGTCAATGCTTTATGCGTCAT	50	383	4
espC	Chromosome	Hemolysis	×		×	41	TAGTGCAGTGCAGAAAGCAGTT/AGTTTTCCTGTTGCTGTATGCC	55	301	53
iutA	Chromosome	Iron uptake			×	34	GGCTGGACATCATGGGAACTGG/CGTCGGGAACGGGTAGAATCG	60	301	43
paa	Chromosome	Colonization	×			1, 4	ATGAGGAACATAATGGCAGG/TCTGGTCAGGTCGTCAATAC	50	350	4
pic	Chromosome	Hemolysis	×			50	ACTGGATCTTAAGGCTCAGGAT/GACTTAATGTCACTGTTCAGCG	48	572	53
stx₁	Chromosome	Toxin	×			15	ATAAATCGCCATTCGTTGACTAC/AGAACGCCCACTGAGATCATC	65→60	180	47
stx₂	Chromosome	Toxin	×	×		15	GGCACTGTCTGAAACTGCTCC/TCGCCAGTTATCTGACATTCTG	65→60	255	47
stx_2c	Chromosome	Toxin	×	×		15	GCGGTTTTATTTGCATTAGT/AGTACTCTTTTCCGGCCACT	50	124	65
stx_2d	Chromosome	Toxin	×			15	GGTAAAATTGAGTTCTCTAAGTAT/CAGCAAATCCTGAACCTGACG	52	175	65
ECs3737	ETT2	TTSA			×	52	GGAAATCTGCATTAACTCTTCTGC/CGGGAATACCATCCAGTCG	50	530	51
eivF	ETT2	TTSA			×	52	ATTACTGCTCATTGACCGAAGC/GATTTCCAACACGGCTCTGG	60	457	51
etrA	ETT2	TTSA			×	52	CTTCTTCCTAACGAAACATCATTA/TGACATATCAACTTTCTCTTACGC	52	914	51
yqeH	ETT2	TTSA			×	52	CATGCAATAGTTGCTCAATGC/CCCATTCTCTTTTCGATTCG	55	553	51
fyuA	HPI	Iron uptake			×	29	TGATTAACCCCGCGACGGGAA/CGCAGTAGGCACGATGTTGTA	60	784	26
irp2	HPI	Iron uptake			×	29	AAGGATTCGCTGTTACCGGAC/TCGTCGGGCAGCGTTTCTTCT	60	280	29
eaeA	LEE	Attachment	×			25	GACCCGGCACAAGCATAAGC/CCACCTGCAGCAACAAGAGG	65→60	384	47
espA-γ1	LEE	Unknown	×			17	GCGAGTTCTTCGACATC/ACGAATACCAGTTACACTT	55	333	17
espI^b	LPA	Mucosal			×	59	ATGGACAGAGTGGAGACAG/GCCACCTTTATTCTCACCA	50	560	59
iha	LPA	Attachment			×	59	CAGTTCAGTTTCGCATTCACC/GTATGGCTCTGATGCGATG	50	1,305	59
lpfA_O26	LPF operon	Attachment			×	62	GTTCTGTTTGCCTTATCTGC/TAAGTCAGGTTGAAGTCGAC	55	509	62
lpfA_O113	LPF operon	Attachment			×	62	ATGAAGCGTAATATTATAG/TTATTTCTTATATTCGAC	50	573	12
nleC	OI-36	Unknown	×	×		10	ACAGTCCAACTTCAACTTTTCC/ATCGTACCCAGCCTTTCG	55	777	10
nleG2-3	OI-57	Unknown	×	×		10	GGATGGAACCATACCTGG/CGCAATCAATTGCTAATGC	55	551	10
nleG	OI-71	Unknown	×	×		10	ATGTTATCGCCCTCTTCTATAAAT/ACTTAATACTACACTAATAAGATCCA	55	902	10
efa1a	OI-112	Colonization	×	×	×	7, 31, 70	TATCAGGCCAATCAAAACAG/AGACACTGGTAAATTTCGC	48	974	24
nleB	OI-112	Colonization	×	×	×	7, 31, 70	GGAAGTTTGTTTACAGAGACG/AAAATGCCGCTTGATACC	55	297	10
pagC	OI-112	Immune evasion	×	×	×	7, 31, 70	ATGAGTGGTTCAAGACTGG/CCAACTCCAACAGTAAATCC	55	521	31
sen	OI-112	Enterotoxin	×	×	×	7, 31, 70	GGATGGAACCATACCTGG/CGCAATCAATTGCTAATGC	55	551	31
lpfA_O157/OI-141	OI-141	Attachment			×	62	CTGCGCATTGCCGTAAC/ATTTACAGGCGAGATCGTG	55	412	62
lpfA_O157/OI-154	OI-154	Attachment			×	62	GCAGGTCACCTACAGGCGGC/CTGCGAGTCGGCGTTAGCTG	55	525	62
saa	pO113	Hemolysis			×	8, 49	CGTGATGAACAGGCTATTGC/ATGGACATGCCTGTGGCAAC	60	119	8
subA	pO113	Toxin			×	8, 49	TATGGCTTCCCTCATTGC/TATAGCTGTTGCTTCTGACG	50	556	49
ehxA	pO157	Hemolysis	×		×	5, 6, 41, 57, 58	GCATCATCAAGCGTACGTTCC/AATGAGCCAAGCTGGTTAAGCT	65→60	534	47
espP	pO157	Mucosal damage	×		×	5, 6, 41, 57, 58	AAACAGCAGGCACTTGAACG/GGAGTCGTCAGTCAGTAGAT	50	1,830	5
etpD	pO157	Type II secretion			×	5, 6, 57, 58	CGTCAGGAGGATGTTCAG/CGACTGCACCTGTTCCTGATTA	48	1,062	58
katP	pO157	Catalase peroxidase			×	5, 6, 57, 58	TGCATCCGTTGATGATGTTT/TTTCAGGAACGGTGAGATCC	55	720	5
toxB	pO157	Toxin			×	5, 6, 57, 58	ATACCTACCTGCTCTGGATTGA/TTCTTACCTGATCTGATGCAGC	55	599	64
ureC	Urease cluster	Ureolysis			×	16, 45	TCTAACGCCACAACCTGTAC/GAGGAAGGCAGAATATTGGG	50	397	41

ETT2, E. coli type III secretion apparatus; HPI, high-pathogenicity island; LEE, locus of enterocyte effacement; LPA, locus of proteolysis activity; LPF, long polar fimbriae; OI, O island; TTSA, type III secretion apparatus.

Also known as nleA.