Chlamydia NAATs: update in the clinical and laboratory setting

1. Chlamydia NAATs: update in the clinical and laboratory setting Gill Underhill St Mary’s Hospital Portsmouth

2. Chlamydia trachomatis Obligate intracellular gram negative organism Two forms: Infectious EB – elementary body – spore like Replicating RB – reticulate body – metabolically active From www.chlamydiae.com

3. Chlamydia trachomatis • Commonest bacterial STD • Spread by direct contact • Incubation period 7 – 14 days • Disease due to direct damage to cells and immunopathology causing fibrosis and scarring • Infection does not protect against re-infection

4. Chlamydia Infection in Men • Asymptomatic infection ~ 50% • Non specific urethritis • Strong associations with: Acute epididymitis Prostatitis Male infertility

5. Chlamydia Infection in Women • Asymptomatic infection ~ 70 % • Mucopurulent cervicitis • Urethral infection • Pelvic inflammatory disease in up to 40% - ascending infection involving uterus, fallopian tubes, and other pelvic structures • Complications include chronic pelvic pain, ectopic pregnancy and < 20% have infertility • Fitz-Hugh-Curtis syndrome – peri-hepatitis • Peri-splenitis, peri-nephritis, peri-appendicitis

6. Other Diseases • Proctitis – especially homosexual men • Reactive arthritis – acute onset. Involves mostly knees, ankles, toes • Reiter’s syndrome – mainly men - iritis, uveitis, conjunctivitis, and urethritis • Neonates infected during birth ~ 20% conjunctivitis and/or pneumonia

7. Treatment of Chlamydia • Tetracycline for 7 days • Erythromycin for 7 days in pregnancy • Azithromycin – single dose for patient compliance problems but more expensive • Neonates – erythromycin for 10 days

8. Diagnostic Options for Chlamydial Infections • Cell Culture • Direct Fluorescence Assay • Enzyme Immunoassay • Hybridisation Assay • Nucleic Acid Amplification Tests

9. Cell Culture • Original gold standard • High specificity ~100%, sensitivity 65-80%. • Continuous cell lines - McCoy • Incubate 48 - 72 hours - slow turnaround • Stain intracytoplasmic inclusions with fluorescein labelled monoclonal antibody • Labour intensive and expensive • Viable organisms – transport /storage critical • Not suitable for large workload – manual method

10. Direct Immunofluorescence • Smear of swab stained with fluorescein conjugated specific monoclonal antibody • Rapid turnaround (2 hours) • Specificity high ~ 95% • Sensitivity 70 – 80% • Relatively inexpensive • Viable organisms not required • Not suitable for large workloads – manual method

11. Enzyme Immunoassay • Standard antigen capture EIA • Sensitivity 60 – 80% • Lower specificity ~ 90% - false positives • Blocking assay improves specificity • Fast turnaround time 3 – 5 hours • Suitable for large workload and inexpensive • Viable organisms not required • Most popular test until recently

12. Nucleic Acid Amplification Tests • Amplify nucleic acid sequence specific for organism • High Sensitivity ~ 95% – can detect single copy DNA/RNA • High specificity 99 – 100% • Viable organisms not required • Rapid turnaround time (3 – 5 hours) • Suitable for urines

13. Nucleic Acid Amplification Tests • Technically demanding • Special areas required • Contamination problems • Specimen transport and storage critical • Expensive • No confirmatory test • PCR, SDA, TMA, (LCR)

14. Polymerase Chain Reaction Roche Amplicor first commercially available PCR. Target is chlamydia plasmid. Primers are biotin labelled to produce biotin labelled amplicons

15. Denaturation Denatured Amplicon Strands A-Tube Biotin Magnetic Microparticles D-cup Capture Probe Wash Wheel Cobas Amplicor Denaturation & Hybridization

16. Avidin-horseradish Peroxidase Conjugate forming complex with Biotin Tetramethylbenzidine (TMB) Substrate Hydrogen Peroxide Capture Probe Magnetic Microparticles Cobas Amplicor Conjugate & Substrate Addition

17. Cobas Amplicor PCR • Sensitivity 82 – 98%, specificity >99% • Test up to 66 patient specimens in one day on one COBAS Analyzer • Swabs in Amplicor specimen transport medium store at RT for up to 10 days. • Urine – store up to 24h at RT and up to 7 days at 2 - 8 oC • Internal amplification control • Multiplex available to detect CT and GC

18. Cobas Amplicor Tecan Miniprep Cobas

19. Transcription-Mediated Amplification (TMA) • RNA transcription amplification system using two enzymes, reverse transcriptase and T7 RNA polymerase • Isothermal, amplification of rRNA target • Produces over ten billion-fold amplification • Single-tube format • Gen-Probe Aptima Combo 2 assay

20. Gen-Probe APTIMA Combo 2 Test Detects Chlamydia and Neisseria gonorrhoea Uses three technologies: • Target capture specimen processing • Transcription-Mediated Amplification • Dual Kinetic Assay (DKA) detection

21. Target Capture Technology • Designed to: • Reduce false negatives by removing inhibitors • Simplify sample processing • Different specimens • Allows testing of urine and swabs in same run

22. Transcription-Mediated Amplification

23. Detection by Dual Kinetic Assay (DKA) Technology • Modification of Hybridization Protection Assay (HPA) Technology • Two different acridinium ester labels on different DNA probes • Allows simultaneous detection of two different nucleic acid targets

24. Hybridization Protection Assay Hybridization rRNA AE 60°C + 1 hour Hybridize AE AE DNA Probe AE AE Hybrids

25. Hybridization Protection Assay Selection/Detection luminometer

26. Gen-Probe Aptima-Combo 2 Assay • Sensitivity 94 – 100%, specificity 98 – 100% • One sample, One test = Two results • CT/GC targets co-amplified and individually detected in a single tube • Suitable for large workloads • Transport medium allows storage up to 30C: 30 days for urine; 60 days for swabs

27. Automation with the DTS 1600 Instrument

28. Tigris • In development • Full automation: sample processing, amplification, detection • Continuous specimen loading capability • Simultaneous analysis of up to four different assays

29. ProbeTec Strand Displacement Amplification (SDA) Target gene – chlamydia plasmid • Target generation phase dsDNA heat denatured to give ssDNA 2. Amplification phase SDA isothermal. ssDNA amplified using DNA polymerase, restriction enzyme, primers with restriction enzyme recognition sites, bumpers 3. Detection phase – ET fluorescence energy transfer

30. ProbeTec SDA ssDNA with restriction site Amplification primer binds DNA polymerase extends primer dsDNA with restriction sites

31. ProbeTec SDA DNA polymerase binds, extends displacing previously made strand Restriction enzyme binds Nicks one strand dsDNA Hairpin secondary structure Quenching dye Fluorescent dye Restriction site repeatedly nicked and new strands made and displaced Each displaced strand enters cycle DNA strands bind to probe and detected by Energy Transfer

32. ProbeTec ET Assay

33. ProbeTec ET Assay • Sensitivity 80.5 – 95.7%, • Lower sensitivity for female urines • Specificity 93.8 – 99.8% • Internal amplification control • Rapid turnaround • Suitable for large workloads • Semi-automated • Viper

34. Near Patient Tests • EIA based available • Result in 30 minutes • Less sensitive and specific • Higher cost • NAAT based tests in development • More sensitive and specific but high costs

35. Chlamydia trachomatis Which Test for Screening?

36. Ideal Screening Test • High sensitivity and specificity • Suitable for non invasive samples – urine • Fast turnaround time • Low cost • Not affected by inhibitory substances • Transport and storage of samples not critical

37. Ideal Screening Test • Does not require expensive equipment, expertise or separate work areas • Suitable for large workloads • Able to automate • Easy to perform – “black box” • Point of care testing – increase compliance

38. Which Test? House of Commons Select Committee on Health  - Third Report 22 May 2003 We believe it is scandalous that a sub-optimal test, with an accuracy rate markedly below the best tests, is still widely in use in England for the detection of chlamydia. Indeed, we believe that health providers would be highly vulnerable to damages claims made by patients who had received a false negative diagnosis and had thus not had treatment for chlamydia infection.

39. Which Test? • Cell culture, DIF, EIA, hybridisation assays not sensitive enough. • NAATs higher sensitivity (urine?) • Which NAAT? – depend on local needs but how do they compare in performance? • DoH funded study in collaboration with MHRA (Medicines and Healthcare products Regulatory Agency) and MiDAS (Microbiological Diagnostics Assessment Service)to evaluate three NAATs

40. Evaluation of NAATs Aim to provide information on: • Comparative performance of three commercial NAATs using urine samples • Which ones best meet the needs of Trusts and the national screening programme • Results from repeat testing – testing algorithm • Development of reference testing algorithm and role of Lightcycler assays • Future evaluation design and logistics

41. NAAT Evaluation Three evaluation sites: TMA – Liverpool - Aptima Combo/DTS 1600 SDA – Portsmouth - Probetec ET with Viper? PCR - UCL/Liverpool - Cobas Amplicor/Miniprep • Urine samples submitted for routine testing • Sample anonymised and divided in 4 aliquots • Samples sent overnight to other labs for testing • Each site - 510 neg and 170 pos (M/F) • Total 1530 neg and 510 pos tested by 3 methods • Aim to detect difference in sensitivity of 5%

42. Portsmouth Routine samples SDA 170 positive/510 negative repeat STRBL Four aliquots SDA Portsmouth nextday TMA Liverpool PCR UCLH PCR Liverpool/UCLH 170 positive 510 negative TMA Liverpool 170 positive 510 negative

43. Developments • Full automation • Combined chlamydia/gonorrhoea test • New molecular tests e.g Abbott and molecular beacons to replace LCx • Combined cervical cytology and chlamydia sample • Point of care NAAT – portable “black box” • Screening of men?

44. Acknowledgements Roche Diagnostics Gen-Probe Becton Dickinson www.chlamydiae.com