TABLE 1.
PCR primer sets used in this study
| Strain | Locusa | Sense primer | Antisense primer |
|---|---|---|---|
| C. muridarum | TC0319 | GCGGCAATCCCTCCTACC | TGACAACACGACAACATCCTG |
| Nigg | TC0357 | CATCTCCACAACTCACTCTG | AGGTTTGGGTCTTAATGAAATG |
| TC0419 | CTGTAGGAAGAGATGTTGAC | GGAGTTCGGATGTAATTCG | |
| 382.1b | GGCGTTATGTGTTTGACCTGTAG | GCGTCGTAAGAAAGGCTTGAAAG | |
| TC075 | TACGAACTATACGATGAATCC | TGTAGAATTGACGAGTAACG | |
| TC0181 (glgA) | TGTTTCAGGGTCCAAAATCG | CCTTCAAGACTATTCGGACTATG | |
| TC0831 (glpT) | TTGTAAGCGGTGTGATGTC | TTAGAATACCAGTGAGTCAGTAG | |
| TC0828 (mip) | CGGGTAAACCTAACGCTTCTATTG | AACTTCTCCTGTCTCGCATTCC | |
| TCA03 | ACTTACAACTTATTAACTCATCTG | TTGACCGCTATCTCTTAGG | |
| ORF 8b | GATGGGAAGGTCTAACTGATGAAG | GTTCGCAGGCTTGACTACG | |
| TCA04 | GCTATGGCTATTCTTCTGGTGTG | CCGCTCTCTAATCCTCCTATTCG | |
| TCA05 | CCCGAGCTAGACTTGAAAAT | CTCTTGTGGTAGAGTTCTAAGG | |
| TCA06 | CATCCCAAGCAGCAATTTACG | TGGCTCAGGAATCAAACATACG | |
| TCA07 | GGGAAAGTTTGTGGAATGTC | GCGAAGCAGTTCTACGAG | |
| TCA01 | GGCGTGTGTTTATTTCTGAG | TCTTCATCTCTTAATCCCATTTG | |
| TCA02 | CAAGCAACTATCTCTTTCCTC | CGGGCAATTTGTCTTAACC | |
| C. trachomatis | 16S rRNAc | CGTTAATACCCGCTGGATTTGAG | GCCCCGATCTTTGACAACTAAC |
| D/UW3-Cx | CT049 | GACAACCACTCCAGAATCAG | CCATCCGAAGAGCCTACC |
| CT084 | AAGTGTCCGCTCGCATTCC | TGTTCGTCCCAAGGTAAGATAGG | |
| CT142 | GCTTGGTGTATCAATCGTCTC | AATCTCCTCCATATCCATTATTCC | |
| CT382.1 | GGCGTTATGTGTTTAACTTGTAG | ACATCTATCAGCGTCGTAAG | |
| CT702 | AAGGTCTGTTGGGAAGGG | ATGATGATATTGTCTAAGTTGGC | |
| CT798 (glgA) | GCAGGGCTGTTGTTTGAGTAGT | AAGCGATGATGCCTTCCGTTT | |
| CT544 (uhpC) | GAGCGGCTTTACAGGATGGT | TCCTGAGCCACCTTCCCTAAA | |
| CT600 (pal) | GATAACCTCACGATTCTTGC | AGTGAATAAGCGGTCTGC | |
| pGP1 | GCCTCAGAGCTAAACATTCCT | TTGATAAACAAAATCACATCTGCG | |
| pGP2 | AAGGATGAATCGGTACATTTGTA | AAATTCAATGCGTTTTCTTCTAGA | |
| pGP3 | TCACCTTCTCGTACCAAAGC | TCTGGGAGCATGTTCTTAGTC | |
| pGP4 | CTGCTTCAACAAATAGAAAACTCT | AGACAAGATAAGCATAATCAAAGC | |
| pGP5 | TAGACCCGCAATCCAATTTATC | TTTGATGTGTATACTATGTCGTGT | |
| pGP6 | CGATGTGATAGGGAAAGTATGTG | TCTTTGTTTCTAGATGAAGGAAGA | |
| pGP7 | CTATCAGCTTAATGGAGGAGTTG | ACAGGAATCCCTATTTTAGAAACA | |
| pGP8 | CCATCTTCTTTGAAGCGTTGT | GTGCTCAGACTCCGACATAAT | |
| C. trachomatis | CTL0305 | ATGTTGTCGGAGAGTATAGAG | AACCACTTAGCATCTGTAGG |
| L2/434/Bu | CTL0339 | AAGTGTCCGCTCGCATTCC | TGTTCGTCCCAAGGTAAGATAGG |
| CTL071 | AAGGTCTGTTGGGAAGGG | ATGATGATATTGTCTAAGTTGGC | |
| CTL0803 (mip) | GTCGCTCTGCCTATCGTAG | GCATCCCTTTAATCACTTCAAC |
a
Chromosomal loci are identified by their annotated designations: C. muridarum Nigg, AE002160.2; C. trachomatis D/UW-3/Cx, AE001273.1; L2/434/Bu, AM884176.1. Plasmid ORFs are named as per the corresponding GenBank entry: pMoPn, AE002162; pCHL1 (C. trachomatis D/G0/86), J03321.
b
An unannotated ORF present in C. muridarum Nigg. Consequently, no formal locus designation was available.
c
The same 16S primer pair was used for all strains and contains a single mismatch with the C. muridarum gene that did not impair efficiency. Unless otherwise specified, the primer pair designed to amplify C. trachomatis D/UW-3/Cx was also used to assay L2/434/Bu, 25667R, E/Bour, and CT599 homologs.