Table 1. Oligonucleotide primers used for the ArrayTube, quantitative real-time –PCR, and PCR for subsequent sequencing.

Gene	Primers	Primer sequence, 5′→ 3′	Gene location	Base pair	Reference
23S rRNA*	U23F-19	ATTGAMAGGCGAWGAAGGA			(17)
	23R-22	biotin-GCYTACTAAGATGTTTCAGTTC
Chlamydiaceae 16S rRNA†	16SrRNA-9	GCGAAGGCGCTTTTCTAATTTAT	734–756‡	76	(6)
	16SrRNA-10	CCAGGGTATCTAATCCTGTTTGCT	809–786‡
Chlamydia trachomatis ompA†	OmpA-9	TGCCGCTTTGAGTTCTGCTT	33–52§	75	(6)
	OmpA-10	GTCGATCATAAGGCTTGGTTCAG	108–86§
C. pneumoniae ompA†	Cpn ompAF1	ATAGACCTAACCCGGCCTACAATAAG	301–330	108	(6)
	Cpn ompAR1	GTGAACCACTCTGCATCGTGTAA	353–333	53
C. psittaci ompA†	CpsF	GCAACTCCTACGGAGTCTTAA	260–279	93	(6)
	CpsB	GGCATCTTGTAAATGTTTCCCTAT	331–354
C. pecorum ompA†	Cp-F	GTTTTCGACAGAGTCCTCAA	208–227	118	This study
	CpRT-R	ATTCTAATTTGCTCTTCTGG	325–305
C. abortus ompA†	CpaOMP1-F	GCAACTGACACTAAGTCGGCTACA	763–786	82	(15)
	CpaOMP1-R	ACAAGCATGTTCAATCGATAAGAGA	845–821
C. suis ompA†	Cs-F	GGAGATTATGTTTTCGATCGC	195–216	122	This study
	Cs-R	TAAGCTGCATTACTCGTTGTTTCA	338–292
β-actin†	β-actin-3	GGTGCATCTCTGCCTTACAGATC	412–434¶	73	(6)
	β-actin-4	ACAGCCTGGATAGCAACGTACAT	52–30#
C. trachomatis ompA**	ompAF-1	GTGCCGCCAGAAAAAGAT	−60–40§	1542	(6)
	ompAR-2	CCAGAAACACGGATAGTGTTATTA	55–31††
C. pneumoniae ompA**	CPF1	TTACAAGCCTTGCCTGTAGGGA	70–91‡‡	1098	(8)
	CPB4	AGAATCTGGACTGACCAGATACGTGAG	1169–1142‡‡
C. psittaci ompA**	Cps-1	GTATTAAAAGTTGATGTGAATAA	217–239§§	1022	(8)
	Cps-B4	TTGATTAAGCGTGCTTCACCAGTGATT	1169–1143§§
C. suis ompA**	Cs-F	GGAGATTATGTTTTCGATCGC	195–216	959	This study
	Cs-R	TAGAATCTGAATTGAGCGTTTACGTGA	1154–1128
C. pecorum ompA**	Cp-F	GTTTTCGACAGAGTCCTCAA	208–227	966	This study
	Cp-R	GAATCTGAACTGACCAGATACGTGAG	1173–1148
16Sr RNA**	16SrRNA-F	CAGTCGAGAATCTTTCGCAAT	362–382c	904	(6)
	16SrRNA-R	TACTGCCCATTGTAGCACGTGTGT	1265–1232c

*Primers used in ArrayTube (Alere Technologies, Jena, Germany).
†Primer pairs used for real-time PCR of ompA DNA and of cDNA from RNA for 16SrRNA for detecting Chlamydiaceae.
‡Primer location based on reference strain L₂/434 16SrRNA sequence.
§Primer location based on reference strain L₂/434 ompA sequence.
¶Primer location based on position within intron 3 of the human β-actin sequence.
#Primer location based on position within exon 3 of the human β-actin sequence.
**Primer pairs used for PCR.
‡‡Primer location based on intergenic region of reference strain L₂/434 downstream of ompA sequence.
‡‡Primer location based on C. pneumoniae strain TW183 ompA.
§§Primer location based on C. psittaci avian type C strain ompA.