Table 8.

Detailed information about the primers and probes used in this study for the detection of Chlamydiaceae in raptors and corvids, including their final concentration in the PCR reagent mix. eGFP = enhanced green fluorescent protein (used as internal amplification control), ompA = outer membrane protein A; qPCR = real-time PCR.

Method	Target	Final Concentration	Primer & Probe	Sequence (5′–3′)	Amplicon Size (Base Pairs)	Annealing Temperature (°C)	References
Chlamydiaceae 23S rRNA qPCR	23S rRNA	500 nM	Ch23S-F Ch23S-R	CTGAAACCAGTAGCTTATAAGCGGT ACCTCGCCGTTTAACTTAACTCC	111	60	Ehricht et al. (2006) [64]
		200 nM	Ch23S-P	FAM-CTCATCATGCAAAAGGCACGCCG-TAMRA
Internal amplification control	eGFP	200 nM	eGFP-1-F	GACCACTACCAGCAGAACAC	177		Hoffmann et al. (2006) [65] PCR modified by Blumer et al. (2011) [66]
			eGFP-10-R	CTTGTACAGCTCGTCCATGC
			eGFP-HEX	HEX-AGCACCCAGTCCGCCCTGAGCA-BHQ1
C. psittaci ompA qPCR	ompA	900 nM	CppsOMP1-F	CACTATGTGGGAAGGTGCTTCA	76	60	Pantchev et al. (2009) [67]
			CppsOMP1-R	CTGCGCGGATGCTAATGG
		200 nM	CppsOMP1-S	FAM-CGCTACTTGGTGTGAC-TAMRA
Internal amplification control	eGFP	900 nM	eGFP-1-F	GACCACTACCAGCAGAACAC	132		Hoffmann et al. (2005) [68]
			eGFP-2-R	GAACTCCAGCAGGACCATG
		200 nM	eGFP-HEX	HEX-AGCACCCAGTCCGCCCTGAGCA-BHQ1
16S rRNA PCR (partial)	16S rRNA	300 nM	16S IGF (short) 16S IGR (short)	GATGAGGCATGCAAGTCGAACG CCAGTGTTGGCGGTCAATCTCTC	278	65	Blumer et al. (2007) [70], Modified from Everett et al. (1999) [75]
16S rRNA PCR (near-full length)	16S rRNA	300 nM	16S-IGF 16S-B1	CGGCGTGGATGAGGCAT TACGGYTACCTTGTTACGACTT	1481	57.5	Everett et al. (1999) [69] Hosokawa et al. (2006) [72]
C. buteonis oxaA qPCR	oxaA	600 nM	RSHA-F	ATTTCCAACACGCACTGCAT	80	60	Laroucau et al. (2019) [3]
			RSHA-R	TGGGACTAGGTGTTCTCCCT
		200 nM	RSHA-P	FAM-GGACAACATGCCTAGATGAAGA-TAMRA
Internal amplification control	eGFP	400 nM	eGFP-1-F	GACCACTACCAGCAGAACAC	132		Hoffmann et al. (2005) [68]
			eGFP-2-R	GAACTCCAGCAGGACCATG
		200 nM	eGFP-HEX	HEX-AGCACCCAGTCCGCCCTGAGCA-BHQ1
ompA typing PCR	ompA	200 nM	ompA F (CTU)	ATGAAAAAACTCTTGAAATCGG	1212	49	Sachse et al. (2008) [73]
			ompA rev	TCCTTAGAATCTGAATTGAGC