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Chlamydia trachomatis variant not detected by plasmid based nucleic acid amplification tests: molecular characterisation and failure of single dose azithromycin
  1. Jose Paolo V Magbanua1,
  2. Beng Tin Goh2,
  3. Claude-Edouard Michel1,
  4. Aura Aguirre-Andreasen3,
  5. Sarah Alexander4,
  6. Ines Ushiro-Lumb5,
  7. Catherine Ison4,
  8. Helen Lee1
  1. 1Department of Haematology, University of Cambridge, Cambridge CB2 2PT, UK
  2. 2Ambrose King Centre, Royal London Hospital, Whitechapel, London E1 1BB, UK
  3. 3Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
  4. 4Sexually Transmitted Bacteria Reference Laboratory, Health Protection Agency Centre for Infections, London NW9 5HT, UK
  5. 5Virology Department, Royal London Hospital, Whitechapel, London E1 2ES, UK
  1. Correspondence to:
 Helen Lee
 Department of Haematology, University of Cambridge, EABC Site, Long Road, Cambridge CB2 2PT, UK; hl207{at}


Objective: To characterise a Chlamydia trachomatis variant strain from a patient with non-gonococcal urethritis (NGU) whose first void urine (FVU) displayed discrepant Ctrachomatis test results and describe the clinical response to treatment.

Methods: The FVU specimen was assayed with an immune based Chlamydia Rapid Test (CRT) and various nucleic acid amplification tests (NAATs) to establish C trachomatis infection. Sequencing of the major outer membrane protein gene (omp1 also known as ompA) was undertaken to identify the serovar of the variant strain. Polymerase chain reaction (PCR) analysis was also conducted to determine whether the strain harboured deletions in the cryptic plasmid or was plasmid free.

Results: The FVU specimen was strongly reactive in CRT but negative with the plasmid based Amplicor PCR (Roche) and ProbeTec ET (Becton-Dickinson) assays. However, NAATs for 16S RNA (Aptima Combo 2, GenProbe), omp1 (RealArt CT PCR, Artus and in-house NAATs) or the outer membrane complex B protein gene (omcB) established C trachomatis infection. Sequencing of omp1 showed that the variant belonged to serovar I. PCR analysis indicated that the variant was plasmid free. The patient did not respond to single dose azithromycin treatment but subsequently responded to a course of doxycycline.

Conclusions: A pathogenic plasmid free C trachomatis variant was identified. Clinicians should be alerted to the possibility of undetected C trachomatis infection caused by such variants and the potential of azithromycin failure in patients with recurrent chlamydial NGU. The occurrence of this variant is rare and should not form the basis for judgment of the performance or usefulness of plasmid based NAATs for C trachomatis detection.

  • CRT, Chlamydia Rapid Test
  • DPBS, Dulbecco’s phosphate buffered saline
  • FVU, first void urine
  • hpf, high power field
  • GNID, Gram negative intracellular diplococci
  • NAATs, nucleic acid amplification tests
  • NGU, non-gonococcal urethritis
  • omp, outer membrane protein
  • PCR, polymerase chain reaction
  • PMNL, polymorphonuclear leucocytes
  • STI, sexually transmitted infections
  • C trachomatis
  • nucleic acid amplification test
  • treatment failure

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  • Funding: The study was funded by a grant from the Wellcome Trust, which had no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the article for publication. The corresponding author has full access to the data of the study and had final responsibility for the decision to submit for publication.

  • Competing interests: The authors from the University of Cambridge are equity holders of a spin-off company, Diagnostics for the Real World (DRW) Ltd, that was founded to take advantage of rapid test technologies developed at the University of Cambridge. Both the University of Cambridge and the Wellcome Trust are also equity holders of DRW. Other authors declare no competing interests.

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