Table 1.

Primers, probes and commercial kits used in this study for detection, quantification and genotyping

Organism	Target	Primers and probes (5′ to 3′)		Product size	References
C. trachomatis	CT cryptic plasmid			206 bp	COBAS ® TaqMan ® CT test, v2.0, Roche
U. urealyticum	ureB gene	UUureF	GATCACATTTCCACTTATTTGAAACA	100 bp	Mallard et al. [18]
		UUureR	AAACGACGTCCATAAGCAACTTTA
		UUure2MGB	AAACGAAGACAAAGAAC
U. parvum	ureB gene	UPureF	GATCACATTTTCACTTGTTTG AAGTG	99 bp	Mallard et al. [18]
		UPureR	AACGTCGTCCATAAGCAACTTTG
		UPure1MGB	AGGAAATGAAGATAAAGAAC
M. gentalium	MgPa adhesin gene	MgPa-355 F	GAGAAATACCTTGATGGTCAGCAA	78 bp	Jensen et al. [19]
		MgPa-432R	GTTAATATCATATAAAGCTCTACCGTTGTTATC
		MgPa-380	FAM-ACTTTGCAATCAGAAGGT-MGB
HPV				140-150 bp	Genera Biosystems Ltd
HSV-2	Glycoprotein D gene	H5	TGTGCTATCCCCATCACGGT	239 bp	Powell et al. [24]
		H6	GGCTCGGTGCTCCAGGATAA
		HSVgs-1	CCGCTGGAACTACTATGACAGCTTCAGC
		HSVgs-2	CCGTCAGCGAGGATAACCTGGG
XMRV	Integrase gene	XMRV4552F	CGAGAGGCAGCCATGAAGG	122 bp	Schlaberg et al. [22]
		XMRV4653R	GAGATCTGTTTCGGTGTAATGGAAA
		XMRV4673R	CCCAGTTCCCGTAGTCTTTTGAG
		XMRV4572MGB	6FAMAGTTCTAGAAACCTCTACACTCMGBNFQ
BK virus	TAg	BK-Hirsch-1	AGCAGGCAAGGGTTCTATTACTAAAT	128 bp	Hirsch et al. [23]
		BK-Hirsch-2	GAAGCAACAGCAGATTCTCAACA
		Probe	HEXAAGACCCTAAAGACTTTCCCTCTGATCTACACCAGTTTBHQ1
T. vaginalis	A6p region	TVA5	GATCATGTTCTATCTTTTCA	102 bp	Riley et al. [20], Tabrizi et al. [21]
		TVA6	GATCACCACCTTAGTTTACA
		TV-F1AS	TTACACTCTGAGTTCTTTCTTCTA
		TV-F2AS	AGTCTTTTTTAGATTTTGAAACA
Human β-globin	β-globin gene	GH20	GAAGAGCCAAGGACAGGTAC	268 bp	Resnick et al. [16]
		PC04	CAACTTCATCCACGTTCACC