Table 1.

Primers used for MLST and MLVA methods for Chlamydia trachomatis^a

Region	Format	Direction	Primer	Sequence (5′ to 3′)	5′ position	Fragment length (bp)h
ompA (modified)	Outer	Forward	ompA OF	ATGAAAAAACTCTTGAAATCGGT	780060	575–584
	Outer	Reverse	ompA OR	TTAGAAGCGGAATTGTGCAT	778879
	Inner + Seq	Forward	ompA NF	CGCTTTGAGTTCTGCTTCCT	780025
	Inner + Seq	Reverse	OMP6ASb	TGAGCGTATTGGAAAGAAGC	779411
hctB (modified)	Outer	Forward	Hctb39Fc	CTCGAAGACAATCCAGTAGCAT	51219	624–733
	Outer	Reverse	Hctb794Rc	CACCAGAAGCAGCTACACGT	52014
	Inner + Seq	Forward	CT046 NF	AACTCCAGCTTTTACTGCTA	51959
	Inner + Seq	Reverse	CT046 NR3	CCCCAAATATGCAACAGGAT	51296
CT058 (modified)	Outer	Forward	CT222 Fc	CTTTTCTGAGGCTGAGTATGATTT	68713	600–601
	Outer	Reverse	CT1678 Rc	CCGATTCTTACTGGGAGGGT	67215
	Inner + Seq	Forward	CT058 NF	AGGTGGCTGCGTTAAGATAACT	68614
	Inner + Seq	Reverse	CT058 NR	AAATTGGCCTGAAGTAGAGACA	67992
CT058 (nested/original)	Outer	Forward	CT058 OF	TGTGGGACTTGCGTGATT	68763	1455–1456
	Outer	Reverse	CT058 OR	TAACCGTTCCATCCACATCT	67132
	Inner + Seq	Forward	CT222 Fc	CTTTTCTGAGGCTGAGTATGATTT	68713
	Inner + Seq	Reverse	CT1678 Rc	CCGATTCTTACTGGGAGGGT	67215
	Seq	Forward	CT811Fc,e	CGATAAGACAGATGCCGTTTTT	68122
	Seq	Reverse	CT1022Rc, e	TAAGCACAGCAGGGAATGCA	67871
	Seq	Forward	CT058 IFe	TGTCTCTACTTCAGGCCAATTT	68013
	Seq	Reverse	CT058 IRe	AATCCTCCTTGGCCTCTCTT	67903
CT144 (modified)	Outer	Forward	CT144:248Fc	ATGATTAACGTGATTTGGTTTCCTT	160641	443
	Outer	Reverse	CT144:1046Rc	GCGCACCAAAACATAGGTACT	161439
	Inner + Seq	Forward	CT144 NF	CGAAATCGGATATCTCTTTT	160920
	Inner + Seq	Reverse	CT144 NR	CCTAAACATACGGCTATTCC	161400
CT144 (nested/original)	Outer	Forward	CT144 OF	TCTATTGGGAATGAGCATCCT	160575	753
	Outer	Reverse	CT144 OR	TTCGCTCTCCCACAATCA	161495
	Inner + Seq	Forward	CT144:248Fc	ATGATTAACGTGATTTGGTTTCCTT	160641
	Inner + Seq	Reverse	CT144:1046Rc	GCGCACCAAAACATAGGTACT	161439
CT172 (modified)	Outer	Forward	Four610 Rc	CGTCATTGCTTGCTCGGCTT	195301	358–666
	Outer	Reverse	CT172 OR	GATCAAGCCATCTTAGACATGC	195798
	Inner + Seq	Forward	CT172 NF	AGGTCGCCCAAATTCCATGT	195376
	Inner + Seq	Reverse	CT172 NR	GCTCCGGCTATTTTGTTTAGGA	195778
pbpB (modified)	Outer	Forward	pbpB 1 Fc	TATATGAAAAGAAAACGACGCACC	780665	602
	Outer	Reverse	pbpB 2366 Rc	TGGTCAGAAAGATGCTGCACA	783030
	Inner + Seq	Forward	CT682 NF	TCATCACTTTGCGTATATGGCA	780750
	Inner + Seq	Reverse	CT682 NR	AAAAGCTTGCGTACTTGATCGA	781395
pbpB (nested/original)	Outer	Forward	pbpB1 OF	TTGTGTTTGGAATAGCTCGAA	780508	789 + 875
	Outer	Reverse	pbpB1 OR	AAGAACCTTCCATCTCCTGAAT	781550
	Outer	Forward	pbpB2 OF	GGAACGATCGAGCAGCTT	782060
	Outer	Reverse	pbpB2 OR	AGAAGCAATAGGAGAGCCGT	783136
	Inner + Seq	Forward	pbpB 1 Fc	TATATGAAAAGAAAACGACGCACC	780665
	Inner + Seq	Reverse	pbpB 823 Rc	CAGCATAGATCGCTTGCCTAT	781507
	Inner + Seq	Forward	pbpB 1455 Fc	GGTCTCGTTTTTGATGTTCTATTC	782111
	Inner + Seq	Reverse	pbpB 2366 Rc	TGGTCAGAAAGATGCTGCACA	783030
	Seq	Forward	pbpB2 IFf	CCCAACCCCTTATGTGGA	782545
	Seq	Reverse	pbpB2 IRf	TGGCGCCAACAAGCAAT	782700
CT1299 (modified)	Outer	Forward	CT1299 OF2	CAACAATCATCACGCCCTCT	291598	240–248g
	Outer	Reverse	CT1299 OR	AGCCGCTTTCTCGTTCTAAA	292017
	Inner + Seq	Forward	CT1299 OF	CGCTTAAGATTCTCGGAGGTA	291656
	Inner + Seq	Reverse	CT1299 reversed	AAGTCCACGTTGTCATTGTACG	291945
CT1335 (modified)	Outer	Forward	CT1335 OF2	AGTGGGTGTGAAGAACCGTA	737151	191-195g
	Outer	Reverse	CT1335 OR2	ACCAAACCCTTTTGCAGGAA	737463
	Inner + Seq	Forward	CT1335 OF	CGTCCTCTGGAAGGGAATAA	737202
	Inner + Seq	Reverse	CT1335 OR	TATGCCCCAAGGAAGAGTCA	737434

^aThe regions given in boldface were used in the modified methods. For the original MLST, different PCRs were used for the regions CT058 and CT144, which are given in italics. Nested PCRs were performed for each region. The primers used for the outer PCRs are indicated with Outer, those used for the inner PCRs are indicated with Inner, and those used for sequencing are indicated with Seq. The original MLST made use only of the inner PCRs in the targets CT058, CT144, and pbpB. Unless indicated otherwise, the primers were newly designed. Positions are given in base pairs relative to the sequence of reference strain D/UW-3/CX (GenBank accession no. AE001273).

^bPrimers were taken from Morré et al. (16).

^cPrimers were taken from Klint et al. (12).

^dPrimers were taken from Pedersen et al. (20).

^eFor original CT058, the primers CT811F and CT1022R were used for sequencing. In the nested version, these were replaced by CT058 IF and CT058 IR.

^fThe additional primers pbpB2 IF and pbpB2 IR were used only in the nested version.

^gThe fragment length indicated could not always be determined directly but could be calculated using reference sequences.

^hFragment length is the number of base pairs sequenced with the primers excluded.