Table 2. Primers and probes and their final concentration (nM) in the PCR reagent mix for different quantitative PCR (qPCR) and conventional PCR (PCR) tests used in this study.

Method	Target	Primer & Probe	Sequence (5’-3’)	Final conc. of primers and Probes in the PCR reagent mix	Amplicon size (base pairs)	Annealing temperature (°C)	references
Chlamydiaceae 23S rRNA qPCR	23S rRNA	Ch23S-F	CTGAAACCAGTAGCTTATAAGCGGT	500 nM	111	60	Ehricht et al. [32]
		Ch23S-R	ACCTCGCCGTTTAACTTAACTCC
		Ch23S-p	FAM-CTCATCATGCAAAAGGCACGCCG-TAMRA	200 nM
	eGFP	eGFP-1-F	GACCACTACCAGCAGAACAC	200 nM	177		Hoffmann et al. [33]
		eGFP-10-R	CTTGTACAGCTCGTCCATGC
		eGFP-HEX	HEX-AGCACCCAGTCCGCCCTGAGCA-BHQ1
DNA microarray assay PCR	23S rRNA	U23F-19	ATTGAMAGGCGAWGAAGGA	500 nM	171	50	Ehricht et al., Borel et al. [32, 34]
		23R-22	biotin-GCYTACTAAGATGTTTCAGTTC
	eGFP	eGFP-11-F	CAGCCACAACGTCTATATCATG	50 nM	276		Hoffmann et al. [33]
		eGFP-10-R-Bio	Bio-CTTGTACAGCTCGTCCATGC
16S rRNA PCR	16S rRNA	16S IGF (short)	GATGAGGCATGCAAGTCGAACG	300 nM	278	58	Pospischil et al. [35]
		16S IGR (short)	CCAGTGTTGGCGGTCAATCTCTC
C. psittaci ompA qPCR	ompA	CppsOMP1-F	CACTATGTGGGAAGGTGCTTCA	900 nM	76	60	Pantchev et al. [36]
		CppsOMP1-R	CTGCGCGGATGCTAATGG
		CppsOMP1-S	FAM-CGCTACTTGGTGTGAC-TAMRA	200 nM
	eGFP	eGFP-1-F	GACCACTACCAGCAGAACAC	900 nM	132		Hoffmann et al. [33] PCR modified by Blumer et al [37]
		eGFP-2-R	GAACTCCAGCAGGACCATG
		eGFP-Hex	HEX-AGCACCCAGTCCGCCCTGAGCA-BHQ1	200 nM
MLST PCR	enoA	YPenoA3	CCTATGATGAATCTCATTAATGG	200 nM	450–500	53	Pannekoek et al. [31]
		YPenoA4	CCCAACCATCAAAATCTTCTTCCG
	fumC	YPfumC1	GGGCTCCTGAGGTTATGCC		500–600	53
		YPfumC2	CGCAAATAATGAATCACCTTATC
	gatA	YPgatA3	GCCTTAGAGTTAAGAAATGCCG		500–600	60
		YPgatA4	CCCCCTGTATCGGAACCTAACGC
	gidA	YPgidA1	GCTTATTAGAGAGCTGTCCTGGC		500–670	53
		YPgidA2	CGCGTTTTCTAACCCACGG
	hemN	YPhemN1	GGATCCATTTCGGAGGAGGC		500–630	53
		YPhemN2	CCTGAAAGGATTTTCTCATGG
	hflX	YPhflX3	GAGATTTTTGCTAATCGAGCG		500–610	53
		YPhflX4	GTAAAACATCTTCATGTAACGC
	oppA	YPoppA3	ATGCGCAAGATATCAATGGG		500–610	60
		YPoppA4	GGCAAGGTTTGGTGTAACTCGC
ompA PCR	ompA	ompA F (CTU)	ATGAAAAAACTCTTGAAATCGG	200 nM	1200	49	Sachse et al. [30]
		ompA rev	TCCTTAGAATCTGAATTGAGC