TABLE 1.

Primers used for the detection of E. coli ST131 clades

Assay and primer	Nucleotide sequence (5′-3′)	Primer concn (μM)	Target	PCR product size (bp)	Reference or source
ST131 clade assay
CladeAspe4-YF5	TGACGGGACGTGAGCAAATTA	0.15	Clade A specific (region 4)	707	This study (Table S1)
CladeAspe4-YR5	AGTCAGACCTAGCCACCCTT	0.15
ST131_R19-YF1	AGCAACGATATTTGCCCATT	0.15	ST131 specific (region 19)	580	11; this study
ST131_R19-YR1	GGCGATAACAGTACGCCATT	0.15
prfC-1615spe0-YF1	CAACGTTGAAGCAGTGTATGAG	0.08	prfC SNPs specific for the clade B	442	This study (Table S2)
prfC-d2034-YR1	TGACAATCGACGGCTTTAGA	0.08
C1-578spe-YF1	GGCCCCACAAATTGCTT	0.1	Clade C1	337	This study (Table S2)
C1-898-YR1	CGCACCTCCGATACCAAA	0.1
M27PP1C-YF1	TGAATCAAAGGTCCGAGCTG	0.08	M27PP1 region specific for the C1-M27 subclade	232	8; LC209430a
M27PP1C-YR1	TATGGCTGGCAGATGCTTTA	0.08
nrdI-534spe2-YF1	ACGGATTCAGGTAGACGATT	0.25	nrdI SNP specific for the C2 clade	164	This study (Table S2)
nrdI-678R	CCTCACCAAAGTTGCGATTAC	0.25
C-SNP1-700spe-YF1	CGCTGGCCAGTTATCTGAAAT	0.2	mgtA SNPs specific for the C clade	103	This study (Table S2)
C-SNP1-762spe-YR2	CCTTTCACCAACTGGGTTACT	0.2
C1-M27 subclade assay
ST131_R19-YF1	AGCAACGATATTTGCCCATT	0.15	ST131 specific (region 19)	580	11; this study
ST131_R19-YR1	GGCGATAACAGTACGCCATT	0.15
M27aer-spe-YF1	GCCGATGGGCTTTCCT	0.15	aer SNP specific for the C1-M27 subclade	140	This study (Table S2)
M27aer-YR2	GTCACCGCGTCTTCCAGT	0.15

^aGenBank/ENA/DDBJ accession number.