Prevalence, virulence potential, and pulsed-field gel electrophoresis profiling of Shiga toxin-producing Escherichia coli strains from cattle

Dong, Hee-Jin; Lee, Soomin; Kim, Woohyun; An, Jae-Uk; Kim, Junhyung; Kim, Danil; Cho, Seongbeom

doi:10.1186/s13099-017-0169-x

Gut Pathogens

Table 1 Primer sequences and the PCR conditions used in this study

From: Prevalence, virulence potential, and pulsed-field gel electrophoresis profiling of Shiga toxin-producing Escherichia coli strains from cattle

Target gene	Nucleotide sequences (5′–3′)	PCR conditions				Amplicon size (bp)	References
Target gene	Nucleotide sequences (5′–3′)	Denaturation	Annealing	Extension	Cycle	Amplicon size (bp)	References
stx 1	CAGTTAATGTGGTGGCGAAGG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	348	[58]
stx 1	CACCAGACAATGTAACCGCTG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	348	[58]
stx 2	ATCCTATTCCCGGGAGTTTACG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	584	[58]
stx 2	GCGTCATCGTATACACAGGAGC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	584	[58]
stx 1c	TTTTCACATGTTACCTTTCCT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	498	[42]
stx 1c	CATAGAAGGAAACTCATTAGG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	498	[42]
stx 1d	CTTTTCAGTTAATGCGATTGCT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	192	[42]
stx 1d	AACCCCATGATATCGACTGC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	192	[42]
stx 2a	GCGATACTGRGBACTGTGGCC	94 °C, 50 s	65 °C, 40 s	72 °C, 30 s	25	349	[59]
stx 2a	CCGKCAACCTTCACTGTAAATGTG	94 °C, 50 s	65 °C, 40 s	72 °C, 30 s	25	349	[59]
stx 2c	GCGGTTTTATTTGCATTAGT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	124	[42]
stx 2c	AGTACTCTTTTCCGGCCACT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	124	[42]
stx 2d	GGTAAAATTGAGTTCTCTAAGTAT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	175	[42]
stx 2d	CAGCAAATCCTGAACCTGACG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	175	[42]
stx 2e	ATGAAGAAGATGTTTATAGCG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	267	[42]
stx 2e	TCAGTTAAACTTCACCTGGGC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	267	[42]
stx 2f	AGATTGGGCGTCATTCACTGGTTG	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	428	[42]
stx 2f	TACTTTAATGGCCGCCCTGTCTCC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	428	[42]
stx 2g	GTTATATTTCTGTGGATATC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	573	[42]
stx 2g	GAATAACCGCTACAGTA	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	573	[42]
eae	ATTACTGAGATTAAGGCTGAT	94 °C, 20 s	58 °C, 20 s	72 °C, 90 s	35	682	[4]
eae	ATTTATTTGCAGCCCCCCAT	94 °C, 20 s	58 °C, 20 s	72 °C, 90 s	35	682	[4]
tir	CATTACCTTCACAAACCGAC	94 °C, 40 s	57 °C, 60 s	72 °C, 75 s	30	1550	[60]
tir	CCCCGTTAATCCTCCCAT	94 °C, 40 s	57 °C, 60 s	72 °C, 75 s	30	1550	[60]
esp B	GCCGTTTTTGAGAGCCAGAAT	94 °C, 40 s	63 °C, 45 s	72 °C, 60 s	30	633	[60]
esp B	ATCATCCTGCGCTCTGCGAAC	94 °C, 40 s	63 °C, 45 s	72 °C, 60 s	30	633	[60]
etp D	CGTCAGGAGGATGTTCAG	94 °C, 30 s	54 °C, 60 s	72 °C, 90 s	30	1062	[61]
etp D	CGACTGCACCTGTTCCTGATTA	94 °C, 30 s	54 °C, 60 s	72 °C, 90 s	30	1062	[61]
ehx A	GTTTATTCTGGGGCAGGCTC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	166	[58]
ehx A	CTTCACGTCACCATACATAT	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	25	166	[58]
Kat P	CTTCCTGTTCTGATTCTTCTGG	94 °C, 30 s	58 °C, 60 s	72 °C, 150 s	30	2125	[27]
Kat P	AACTTATTTCTCGCATCATCC	94 °C, 30 s	58 °C, 60 s	72 °C, 150 s	30	2125	[27]
esp P	AAACAGCAGGCACTTGAACG	94 °C, 30 s	58 °C, 60 s	72 °C, 150 s	30	1830	[25]
esp P	GGAGTCGTCAGTCAGTAGAT	94 °C, 30 s	58 °C, 60 s	72 °C, 150 s	30	1830	[25]
iha	CTGGCGGAGGCTCTGAGATCA	94 °C, 60 s	57 °C, 60 s	72 °C, 120 s	30	827	[62]
iha	TCCTTAAGCTCCCGCGGCTGA	94 °C, 60 s	57 °C, 60 s	72 °C, 120 s	30	827	[62]
sub A	CGGCTTATCATCCTGTCAGC	94 °C, 45 s	57 °C, 60 s	74 °C, 60 s	30	233	[63]
sub A	TATAGCTGTTGCTTCTGACG	94 °C, 45 s	57 °C, 60 s	74 °C, 60 s	30	233	[63]
stc E	GGCTCCGGAGGTGGGGGAAT	94 °C, 30 s	60 °C, 60 s	72 °C, 15 s	30	399	[53]
stc E	GAAGCCGGTGGAGGAACGGC	94 °C, 30 s	60 °C, 60 s	72 °C, 15 s	30	399	[53]
saa	CGTGATGAACAGGCTATTGC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	119	[56]
saa	ATGGACATGCCTGTGGCAAC	94 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	119	[56]
tetA	GCTACATCCTGCTTGCCTTC	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	210	[64]
tetA	CATAGATCGCCGTGAAGAG	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	210	[64]
tetB	TTGGTTAGGGGCAAGTTTTG	95 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	659	[64]
tetB	GTAATGGGCCAATAACACCG	95 °C, 60 s	56 °C, 60 s	72 °C, 60 s	30	659	[64]
tetC	CTTGAGAGCCTTCAACCCAG	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	418	[64]
tetC	ATGGTCGTCATCTACCTGCC	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	418	[64]
tetD	AAACCATTACGGCATTCTGC	95 °C, 60 s	60 °C, 60 s	72 °C, 60 s	30	787	[64]
tetD	GACCGGATACACCATCCATC	95 °C, 60 s	60 °C, 60 s	72 °C, 60 s	30	787	[64]
tetE	AAACCACATCCTCCATACGC	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	278	[64]
tetE	AAATAGGCCACAACCGTCAG	95 °C, 60 s	58 °C, 60 s	72 °C, 60 s	30	278	[64]
tetG	GCTCGGTGGTATCTCTGCTC	95 °C, 60 s	60 °C, 60 s	72 °C, 60 s	30	468	[64]
tetG	AGCAACAGAATCGGGAACAC	95 °C, 60 s	60 °C, 60 s	72 °C, 60 s	30	468	[64]
ampC	CCCCGCTTATAGAGCAACAA	94 °C, 60 s	61 °C, 120 s	72 °C, 180 s	35	634	[65]
ampC	TCAATGGTCGACTTCACACC	94 °C, 60 s	61 °C, 120 s	72 °C, 180 s	35	634	[65]
catA1	AGTTGCTCAATGTACCTATAACC	95 °C, 60 s	57 °C, 70 s	72 °C, 120 s	32	547	[64]
catA1	TTGTAATTCATTAAGCATTCTGCC	95 °C, 60 s	57 °C, 70 s	72 °C, 120 s	32	547	[64]
cmlA	CCGCCACGGTGTTGTTGTTATC	95 °C, 60 s	57 °C, 70 s	72 °C, 120 s	32	698	[64]
cmlA	CACCTTGCCTGCCCATCATTAG	95 °C, 60 s	57 °C, 70 s	72 °C, 120 s	32	698	[64]
qnr	TATCTCCCTGTCGTTCCAG	94 °C, 30 s	52 °C, 30 s	72 °C, 30 s	30	399	[66]
qnr	AGAACTCGCCGATCAATG	94 °C, 30 s	52 °C, 30 s	72 °C, 30 s	30	399	[66]
bla _CMY	TGGCCAGAACTGACAGGCAAA	94 °C, 60 s	49 °C, 90 s	72 °C, 60 s	35	462	[67]
bla _CMY	TTTCTCCTGAACGTGGCTGGC	94 °C, 60 s	49 °C, 90 s	72 °C, 60 s	35	462	[67]
bla _OXA	TATCTACAGCAGCGCCAGTG	94 °C, 60 s	62 °C, 120 s	72 °C, 60 s	31	199	[65]
bla _OXA	CGCATCAAATGCCATAAGTG	94 °C, 60 s	62 °C, 120 s	72 °C, 60 s	31	199	[65]
bla _TEM	TACGATACGGGAGGGCTTAC	94 °C, 60 s	62 °C, 60 s	72 °C, 60 s	30	717	[68]
bla _TEM	TTCCTGTTTTTGCTCACCCA	94 °C, 60 s	62 °C, 60 s	72 °C, 60 s	30	717	[68]

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ISSN: 1757-4749

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