Table 2.

Primers for amplification of Escherichia coli genes related to phylogenetic grouping and virulence genes

Functional Category	Gene	Oligonucleotide sequence (5′–3′)	Annealing temperature (°C)	Product size (bp)	Reference
		Phylogenetic grouping
	chuA	f GACGAACCAACGGTCAGGAT r TGCCGCCAGTACCAAAGACA	55	279	Clermont et al. 2000 [7]
	YjaA	f TGAAGTGTCAGGAGACGCTG r ATGGAGAATGCGTTCCTCAAC	55	211
	TspE4.C2	f GAGTAATGTCGGGGCATTCA r CGCGCCAACAAAGTATTACG	55	152
		Virulence factors
Adhesins	papG	f GCATTTCTACGGTAACC r TCGTCAAATTTCTCAGTCAGA	50	295	Norinder et al. 2012 [40]
	Sfa	f CTCCGGAGAACTGGGTGCATCTTAC r CGGAGGAGTAATTACAAACCTGGCA	54	408	Le Bouguenec et al 1992 [41]
	Afa	f GCTGGGCAGCAAACTGATAACTCTC r CATCAAGCTGTTTGTTCGTCCGCCG	60	793	Le Bouguenec et al. 1992 [41]
	fimH	f TGCAGAACGGATAAGCCGTGG r GCAGTCACCTGCCCTCCGGTA	55	506	Johnson & Stell 2000 [22]
Toxins	hlyA	f AACAAGGATAAGCACTGTTCTGGCT r ACCATATAAGCGGTCATTCCCGTCA	55	1177	Yamamoto et al 1995 [42]
	cnf1	f AAGATGGAGTTTCCTATGCAGGAG r CATTCAGAGTCCTGCCCTCATTATT	52	498	Kuhar et al 1998 [43]
Iron uptake	aer	f TACCGGATTGTCATATGCAGACCGT r AATATCTTCCTCCAGTCCGGAGAAG	56	602	Yamammoto et al 1995 [44]
Protectins/serum resistance	traT	f GGTGTGGTGCGATGAGCACAG r CACGGTTCAGCCATCCCTGAG	57	288	Johnson and Stell 2000 [22]
Pathogen associated island	PAI	f GGACATCCTGTTACAGCGCGCA r TCGCCACCAATCACAGCCGAAC	57	922	Johnson and Stell 2000 [22]