Table 2. Oligonucleotide primers.

Primer	Sequence (5’- 3’)	Use
JRP5448	AAAAAAGCTTATAATTATCCTTATAAAACCATTTCGTGCGCCCAGATAGGGTG	cdtR-288a-IBS (+)
JRP5449	CAGATTGTACAAATGTGGTGATAACAGATAAGTCCATTTCTATAACTTACCTTTCTTTGT	cdtR-288a-EBS1d (-)
JRP5450	TGAACGCAAGTTTCTAATTTCGGTTTTTTATCGATAGAGGAAAGTGTCT	cdtR-288a-EBS2 (+)
JRP3867	CGAAATTAGAAACTTGCGTTCAGTAAAC	EBS universal (-)
JRP5632	AAAAGGATCCCTTCTATAATTAGAAGTTAAATAATTCTTC	Amplify cdtR gene and upstream region, introduces BamHI site (+)
JRP5633	AAAACTGCAGGAGACATCTCTTTTTTCTATTTATTATG	Amplify cdtR gene and upstream introduces PstI site (-)
DLP458	TAATAAAAATACTGCCCTCGACAAA	tcdA-specific for RT-ddPCR (+)
DLP459	ATAAATTGCATGTTGCTTCATAACT	tcdA-specific for RT-ddPCR (-)
JRP6107	GCTATTAGCGAGGATAACGATTTC	tcdB-specific for RT-ddPCR (+)
JRP6108	CTTTCCTAGTTCCATCATAAATCTACCA	tcdB-specific for RT-ddPCR (-)
JRP2443	CAAGAAATAACTCAGTAGATGATTTGCAA	tcdR-specific for RT-ddPCR (+)
JRP2444	TCTCCCTCTTCATAATGTAAAACTCTACTAAG	tcdR-specific for RT-ddPCR (-)
JRP6104	AGCACAAAGGATATTGCTCTACT	tcdC-specific for RT-ddPCR (+)
JRP6105	AAATGACCTCCTCATGGTCTTC	tcdC-specific for RT-ddPCR (-)
JRP3845	TGCAATACTACTTACAAGGCTCCTATAGA	cdtA-specific for RT-ddPCR (+)
JRP3846	TCTTTCCCATTCTTTAGCCTTTTC	cdtA-specific for RT-ddPCR (-)
JRP6238	GATGCATGCTTTATTCGTGTACATA	cdtR-specific for RT-ddPCR (+)
JRP6239	CGACATATATGGCCATTACTCATT	cdtR-specific for RT-ddPCR (-)
JRP2285	GGATGATATGATGAAGGTTAGAAACCT	rpoA-specific for RT-ddPCR (+)
JRP2286	CCCAATCCAAGTTCTTCTAGTTTTTG	rpoA-specific for RT-ddPCR (-)

(+) = forward primer, (-) = reverse primer