Novel multiplex real-time PCR assays reveal a high prevalence of diarrhoeagenic Escherichia coli pathotypes in healthy and diarrhoeal children in the south of Vietnam

Table 5 Sequences of primers and probes to detect DEC in this study

Diarrhoeagenic *E. coli* target	Primer/probe name	Sequence * (5′-3′)	Amplicon size (bp)
ETEC	elt_ETEC_F	CTCGGTCAGATATGYGATTCTT	100
	elt_ETEC_R	AACATTTCAGGTCGAAGTCC
	elt_ETEC_ probe	FAM-TGTGTCCTTCATCCTTTC AATGGCTT-BHQ1
	est_ETEC_F	GCTAAACCAGYAGRGTCTTCAA	137
	est_ETEC_R	GCAGGATTACAACACAATTCAC
	est_ETEC_ probe	LCCyan500-AGTRGTCCTGAAA GCATGAATAGTAGCA-BHQ1
EAEC	aggR_F	CCATTTATCGCAATCAGATTAA	92 [46]
	aggR_R	CAAGCATCTACTTTTGATATTCC
	aggR_probe	FAM-CAGCGATACATTAAGA CGCCTAAAGGA-BHQ1
EIEC/Shigella	ipaH_F	AGGTCGCTGCATGGCTGGAA	99 [47]
	ipaH_R	CACGGTCCTCACAGCTCTCA
	ipaH_probe	LCCyan500-AACTCAGTGCCTCT GCGGAGCTTCGACA-BHQ1
EPEC/EHEC	eae_F	CATTGATCAGGATTTTTCTGGTGA TA	102 [48]
	eae_R	CTCATGCGGAAATAGCCGTTA
	eae_probe	FAM-ATAGTCTCGCCAGTA TTCGCCACCAATACC-BHQ1
EPEC	bfpA_EPEC_	GTCTRTCTTTGATTGAATCKGC	108
	bfpA_EPEC_R	CATTCTGYGMCTTATTGGAATC
	bfpA_EPEC_probe	LCCyan500-ACCGTTACYGCM GGTGTGATGTTT-BHQ1
STEC	stx1_EHEC_F	GCATCTGATGAGTTTCCTTCTA	113
	stx1_EHEC_R	GTTCTGCGCATCAGAATTG
	stx1_EHEC_probe	FAM-AAGAGKCCGTGGGA TTACGCACAAT-BHQ1
	stx2_EHEC_F	ACRACGGACAGCAGYTATWC	111
	stx2_EHEC_R	GAACTCCATTAAMKCCAGATA
	stx2_EHEC_probe	LC Red 610-ATGCAAATCAGTCGTCA CTCACTGGT-BHQ1
EHE CO157	rfbE_O157_F	CAAGTCCACAAGGAAAGTAAAG	111
	rfbE_O157_R	GAGTTTATCTGCAAGGTGATTC
	rfbE_O157_probe	LCCyan500-AACTCAGTGCCTCT GCGGAGCTTCGACA-BHQ1
Internal control	uidA_F	GTGTGATATCTACCCGCTTCGC	82 [49]
	uidA_R	AGAACGGTTTGTGGTTAATCAGGA
	uidA_probe	CY5-TCGGCATCCGGTCAGTGGCAGT-BHQ2

*R (A/G), Y(C/T), S (G/C), W (A/T), M (A/C), K (G/T) according to International Union of Pure and Applied Chemistry (IUPAC)
Probe detection format (Roche Light Cycler II 480) as followed FAM: 498–580; LCCyan500: 440–488; CY5: 618–660; LC Red 610: 533–610; BlackBerry® Quencher: BHQ1, BHQ2

ISSN: 1471-2180