Table 4.

Primers’ and probes’ sequences used for adK, tcdA and tcdB C. difficile genes quantification. All probes were labeled with FAM and double quenching ZEN/IBFQ.

Gene	Oligonucleotide	Sequence (5’−3’)	Length (bp)	Ta (ºC)	Amplicon size (positions in reference genome)
adK	Forward primer	AGAAGAATATGTAAGTCTTGTGGAG	25	61.7	132 bp (118,849–118,981)
	Reverse primer	CTTAGATACAGTTTCTTCATTATCATCAG	29	61.6
	Labeled probe	ACATCACATACACCTTCTACTTTAGGAGGA	30	66.5
tcdA	Forward primer	ACTTASAAGTAGGTTTTATGCCAG	24	62.1–62.5	80 bp (744,059–744,139)
	Reverse primer	ATAGTAAGCTGAYRCATAAGCTC	23	59.3–63.6
	Labeled probe	TGGRCCACTTAAACTTATTGTRGAGCGA	28	66.3–69.9
tcdB	Forward primer	TCTTAGTAATTTAAGTGTAGCAATGAAAGT	30	63.2	162 bp (737,185–737347)
	Reverse primer	ATAGGTAATCCTTCAGATAATGTAGG	26	62.8
	Labeled probe	TTGATACTAATTCAACAACTTTGGCTGCATCTGT	34	68.8