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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 Magbanua (jpvm2{at}cam.ac.uk)
  1. Department of Haematology, University of Cambridge, United Kingdom
    1. Beng Tin Goh (beng.goh{at}bartsandthelondon.nhs.uk)
    1. Ambrose King Centre, Royal London Hospital, United Kingdom
      1. Claude-Edouard Michel (cm262{at}cam.ac.uk)
      1. Department of Haematology, University of Cambridge, United Kingdom
        1. Aura Aguirre-Andreasen (aura.beltran{at}lshtm.ac.uk)
        1. Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
          1. Sarah Alexander (sarah.alexander{at}hpa.org.uk)
          1. Sexually Transmitted Bacterial Reference Laboratory, Health Protection Agency, United Kingdom
            1. Ines Ushiro-Lumb (ines.ushiro-lumb{at}bartsandthelondon.nhs.uk)
            1. Virology Department, Royal London Hospital, United Kingdom
              1. Catherine Ison (catherine.ison{at}hpa.org.uk)
              1. Sexually Transmitted Bacterial Reference Laboratory, Health Protection Agency, United Kingdom
                1. Helen Lee (hl207{at}cam.ac.uk)
                1. Department of Haematology, University of Cambridge, United Kingdom

                  Abstract

                  Objective: To characterise a Chlamydia trachomatis (CT) variant strain from a patient with nongonococcal urethritis (NGU) whose first-void urine (FVU) displayed discrepant CT 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 CT 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 CT 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 CT variant was identified. Clinicians should be alerted to the possibility of undetected CT 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 CT detection.

                  • C trachomatis
                  • nucleic acid amplification test
                  • treatment failure
                  • variant

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