. 2023 Jan 20;13(2):299. doi: 10.3390/life13020299

Table 1.

Primers, amplicon size and annealing temperature used for the detection of resistance genes, integrons, virulence genes, phylogenetic groups, and genotyping of E. coli isolates.

Primer Name	Oligonucleotide Sequence (5′-3′)	Amplicon Size (bp)	Annealing Temp. °C	Specificity	Reference
E. coli Identification
UidA	F: ATCACCGTGGTGACGCATGTCGC	486	51	β-glucuronidase enzyme	[24]
UidA	R: CACCACGATGCCATGTTCATCTGC	486	51	β-glucuronidase enzyme	[24]
Resistance Genes
mcr1	F: CGGTCAGTCCGTTTGTTC	309	58	Colistin	[18]
mcr1	R: CTTGGTCGGTCTGTAGGG	309	58		[18]
mcr2	F:TGTTGCTTGTGCCGATTGGA	567	58		[29]
mcr2	R: AGATGGTATTGTTGGTTGCTG	567	58		[29]
mcr-3	F: TTGGCACTGTATTTTGCATTT	542	50		[30]
mcr-3	R: TTAACGAAATTGGCTGGAACA	542	50		[30]
mcr-4	F: ATTGGGATAGTCGCCTTTTT	487	56		[31]
mcr-4	R: TTACAGCCAGAATCATTATCA	487	56		[31]
bla _TEM	F: ATTCTTGAAGACGAAAGGGC	1150	60	Bêtalactamases	[32]
bla _TEM	R: ACGCTCAGTGGAACGAAAAC	1150	60	Bêtalactamases
tet(A)	F:AATTCTGAGCACTGTCGC	937	62	Tetracyclines
tet(A)	R: CTGCCTGGACAACATTGCTT	937	62
tet(B)	F: CTCAGTATTCCAAGCCTTTG	416	57
tet(B)	R: CTAAGCACTTGTCTCCTGTT	416	57
strA	F: ATTCTGACTGGTTGCCTGTC	1562	55	Streptomycin
strA	R: CGCAGATAGAAGGCAAGG	1562	55
strB	F: TTCTCATTGCGGACAACCT	1562	55
strB	R: TAGATCGCGTTGCTCCTCTT	1562	55
DfrAI	F: GTGAAACTATCACTAATGG	474	55	Trimethoprim
DfrAI	R: TTAACCCTTTTGCCAGATTT	474	55
DfrVII	F: TTGAAAATTTCATTGATT	474	55
DfrVII	R: TTAGCCTTTTTTCCAAATCT	474	55
sul1	F:TGGTGACGGTGTTCGGCATTC	789	63	Sulfamides
sul1	R: GCGAGGGTTTCCGAGAAGGTG	789	63
sul2	F: CGGCATCGTCAACATAACC	722	50
sul2	R: GTGTGCGGATGAAGTCAG	722	50
aadA	F: GCAGCGCAATGACATTCTTG	282	60	Streptomycin	[33]
aadA	R: ATCCTTCGGCGCGATTTTG	282	60	Streptomycin	[33]
floR	F: CACGTTGAGCCTCTATAT	868	55	Florfenicol	[32]
floR	R: ATGCAGAAGTAGAACGCG	868	55	Florfenicol
cmlA	F: TGTCATTTACGGCATACTCG	455	55	Chloramphenicol
cmlA	R: ATCAGGCATCCCATTCCCAT	455	55	Chloramphenicol
bla _SHV	F: CACTCAAGGATGTATTGTG	885	52	β-lactamases	[24]
bla _SHV	R: TTAGCGTTGCCAGTGCTCG	885	52
bla _CTX-M-g-1	F: GTTACAATGTGTGAGAAGCAG	1041	50
bla _CTX-M-g-1	R: CCGTTTCCGCTATTACAAAC	1041	50
bla _CTX-M-g-8	F: TGATGAGACATCGCGTTAAG	666	52
bla _CTX-M-g-8	R: TAACCGTCGGTGACGATTTT	666	52
bla _CTX-M-g-9	F: GTGACAAAGAGAGTGCAACGG	856	62
bla _CTX-M-g-9	R: ATGATTCTCGCCGCTGAAGCC	856	62
Virulence Genes
fimA	F: GTTGTTCTGTCGGCTCTGTC	447	55	Type 1 Fimbriae	[36]
fimA	R: ATGGTGTTGGTTCCGTTATTC	447	55	Type 1 Fimbriae
aer	F: TACCGGATTGTCATATGCAGACCGT	602	55	Aerobactin iron uptake system
aer	R: AATATCTTCCTCCAGTCCGGAGAAG	602	55	Aerobactin iron uptake system
stx1	F: CTGGATTTAATGTCGCATAGTG	150	55	Type 1 Shiga-toxin	[37]
stx1	R: AGAACGCCCACTGAGATCATC	150	55	Type 1 Shiga-toxin
stx2	F: GGCACTGTCTGAAACTGCTCC	255	55	Type 2 Shiga-toxin
stx2	R: TCGCCAGTTATCTGACATTCTG	255	55	Type 2 Shiga-toxin
hlyA	F: AACAAGGATAAGCACTGTTCTGGCT	1177	55	Alpha-hemolysin	[36]
hlyA	R: ACCATATAAGCGGTCATTCCCGTCA	1177	55	Alpha-hemolysin
cnf1	F: AAGATGGAGTTTCCTATGCAGGAG	498	55	Cytotoxic necrotizing factor 1
cnf1	R: CATTCAGAGTCCTGCCCTCATTATT	498	55	Cytotoxic necrotizing factor 1
papC	F:GACGGCTGTACTGCAGGGTGTGGCG	328	55	P Fimbriae
papC	R: ATATCCTTTCTGCAGGGATGCAATA	328	55	P Fimbriae
Phylogenetic Groups
chuA	F: GACGAACCAACGGTCAGGAT	279	55	Phylogenetic groups	[38,39]
chuA	R: TGCCGCCAGTACCAAAGACA	279	55
yjaA	F: TGAAGTGTCAGGAGACGCTG	211	55
yjaA	R: ATGGAGAATGCGTTCCTCAAC	211	55
tspE4.C2	F: GAGTAATGTCGGGGCATTCA	152	55
tspE4.C2	R: CGCGCCAACAAAGTATTACG	152	55
Genotyping
ERIC	F: ATGTAAGCTCCTGGGGATTCAC	*	52	Enterobacterial Repetitive Intergenic Consensus	[40]
ERIC	R: AAGTAAGTGACTGGGGTGAGCG	*	52	Enterobacterial Repetitive Intergenic Consensus	[40]

* Bands profile.