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Volume 19, Number 12—December 2013
Research

Zoonotic Chlamydiaceae Species Associated with Trachoma, Nepal

Deborah DeanComments to Author , James Rothschild, Anke Ruettger, Ram Prasad Kandel, and Konrad Sachse
Author affiliations: Children's Hospital Oakland Research Institute, Oakland, California, USA (D. Dean, J. Rothschild); University of California, San Francisco, California, USA (D. Dean); University of California, Berkeley, California, USA (D. Dean); Friedrich-Loeffler-Institut, Jena, Germany (A. Ruettger, K. Sachse); Lumini Eye Hospital, Bhairahawa, Nepal (R.P. Kandel)

Main Article

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.

Main Article

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