Molecular characterization of cytolethal distending toxin gene-positive Escherichia coli from healthy cattle and swine in Nara, Japan

Hinenoya, Atsushi; Shima, Kensuke; Asakura, Masahiro; Nishimura, Kazuhiko; Tsukamoto, Teizo; Ooka, Tadasuke; Hayashi, Tetsuya; Ramamurthy, Thandavarayan; Faruque, Shah M; Yamasaki, Shinji

doi:10.1186/1471-2180-14-97

Table 4 PCR primers and conditions used in this study

From: Molecular characterization of cytolethal distending toxin gene-positive Escherichia coli from healthy cattle and swine in Nara, Japan

			PCR conditions			Amplicon
Primer	Sequence (5′-3′)	Target	Denaturing	Annealing	Extension	(bp)	Reference
Cdt-Bcomu	TAAATGGAATATACATGTCCG	cdt-IB?~?VB	94°C, 30 s	50°C, 30 s	72°C, 60 s	588	[10]
Cdt-Bcomd	TTTCCAGCTACTGCATAATC
Cdt-IIIAf	GTAGGCATTCTTATTCCA	cdt-IIIABC	94°C, 30 s	50°C, 30 s	72°C, 90 s	1,909	[10]
Cdt-IIICr	AGTTTTCTTATCTGTCGG
CdtIII/VB-F	CAGAAGGACTCAGATGTC
CdtIIIC-R	TGGTTGTTTGAGGTCAGT	cdt-IIIBC	94°C, 30 s	55°C, 30 s	72°C, 60 s	546	this study
CdtVC-R	GCTCTGTGGTACAACTTC	cdt-VBC	94°C, 30 s	55°C, 30 s	72°C, 60 s	537	this study
pVir-u	TCATGTGGAATAACTAGC	cdt-IIIABC	94°C, 30 s	52°C, 30 s	72°C, 120 s	2,818	this study
pVir-d	GTTCTGAACTTCACCAG
EaeA-f	AAACAGGTGAAACTGTTGCC	eaeA	94°C, 30 s	50°C, 30 s	72°C, 60 s	454	[10]
EaeA-r	CTCTGCAGATTAACCCTCTGC
BfpA-f	AATGGTGCTTGCGCTTGCTGC	bfpA	94°C, 60 s	56°C, 90 s	72°C, 90 s	324	[10]
BfpA-r	GCCGCTTTATCCAACCTGGTA
EAF-f	CAGGGTAAAAGAAGATGATAA	EAF	94°C, 60 s	60°C, 90 s	72°C, 90 s	397	[10]
EAF-r	TATGGGGACCATGTATTATCA
Est-f	ATTTTTMTTTCTGTATTRTCTT	est	94°C, 30 s	50°C, 30 s	72°C, 60 s	190	[10]
Est-r	CACCCGGTACARGCAGGATT
Elt-f	GGCGACAGATTATACCGTGC	elt	94°C, 30 s	54°C, 30 s	72°C, 60 s	450	[10]
Elt-r	CGGTCTCTATATTCCCTGTT
AstA-f	CACAGTATATCCGAAGGC	astA	94°C, 60 s	53°C, 60 s	72°C, 60 s	94	[10]
AstA-r	CGAGTGACGGCTTTGTAG
Eagg-f	CTGGCGAAAGACTGTATCAT	aggR	94°C, 60 s	53°C, 60 s	72°C, 60 s	630	[10]
Eagg-r	CAATGTATAGAAATCCGCTGTT
EVT1	CAACACTGGATGATCTCAG	stx1	94°C, 30 s	55°C, 30 s	72°C, 60 s	349	[10]
EVT2	CCCCCTCAACTGCTAATA
EVS1	ATCAGTCGTCACTCACTGGT	stx2	94°C, 30 s	55°C, 30 s	72°C, 60 s	110	[10]
EVC2	CTGCTGTCACAGTGACAAA
CNF1-f	GGGGGAAGTACAGAAGAATTA	cnf1	94°C, 60 s	55°C, 60 s	72°C, 60 s	1,112	[10]
CNF1-r	TTGCCGTCCACTCTCACCAGT
CNF2-f	TATCATACGGCAGGAGGAAGCACC	cnf2	94°C, 60 s	55°C, 60 s	72°C, 60 s	1,241	[10]
CNF2-r	GTCACAATAGACAATAATTTTCCG
InvE-f	AGTTCTCGGATGCTATGCTC	invE	94°C, 30 s	60°C, 30 s	72°C, 60 s	293	[10]
InvE-r	CAAGATTTAACCTTCGTCAACC
Saa-f	ACCTTCATGGCAACGAG	saa	94°C, 30 s	57°C, 30 s	72°C, 60 s	1,504	[23]
Saa-r	AATGGACATGCCTGTGG
Iha-f	GAAATCAGCATCCGAGG	iha	94°C, 30 s	55°C, 30 s	72°C, 60 s	410	[23]
Iha-r	ATACGCGTGGCTGCTG
Efa1-f	GTCAAAGGTGTTACAGAG	efa1	94°C, 30 s	55°C, 30 s	72°C, 60 s	640	[23]
Efa1-r	ATTCCATCCATCAGGCC
LpfAO113-f	ACTTGTGAAGTTACCTCC	lpfAO113	94°C, 30 s	55°C, 30 s	72°C, 60 s	360	[23]
LpfAO113-r	CGGTATAAGCAGAGTCG
EhaA-f	AGGCATGAGACACGATC	ehaA	94°C, 30 s	55°C, 30 s	72°C, 60 s	500	[23]
EhaA-r	AAGTCGTGCCATTGAGC
SubA-f	GTACGGACTAACAGGGAACTG	subA	94°C, 30 s	55°C, 30 s	72°C, 60 s	1,264	[22]
SubA-r	ATCGTCATATGCACCTCCG
SubB-f	GTAGATAAAGTGACAGAAGGG	subB	94°C, 30 s	55°C, 30 s	72°C, 60 s	715	[22]
SubB-r	GCAAAAGCCTTCGTGTAGTC
P2-A2	CACTGACAACGGCTGAAC	Upstream	94°C, 30 s	55°C, 30 s	72°C, 60 s	848	[18]
cdtA-F	AAATGGGGAGCAGGATAC	of cdt-VA
cdtC-F	GAACCCCAAATACAGACC	Downstream	94°C, 30 s	55°C, 30 s	72°C, 60 s	712	[18]
P2-C3	TGGTTGATGACGGTGTTA	of cdt-VC
eae-F	AGGATATTCTTTCTCTGAATA	eaeA	94°C, 30 s	55°C, 30 s	72°C, 60 s	1,300	[33]
eae-R	ATATYTATTTGCWGSVCCCCAT

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ISSN: 1471-2180

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