BEIPH Final Report. EQA Programme 2011 Chlamydia trachomatis (CTDNA11A) William G Mackay on behalf of QCMD and its Scientific Council April 2011

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1 BEIPH Final Report EQA Programme 2011 Chlamydia trachomatis (CTDNA11A) William G Mackay on behalf of QCMD and its Scientific Council April 2011 Not to be reproduced or quoted without permission of QCMD. Any queries about this report should be addressed to the QCMD Neutral Office. The Altum Building, Todd Campus, West of Scotland Science Park, Glasgow, G20 0XA, Scotland Tel: +44 (0) , Fax: +44 (0) , info@qcmd.org, Web:

2 Contents 1. Programme aims Programme details Panel composition Programme results Qualitative performance on the core proficiency samples Qualitative analysis of the EQA data for all panel samples Qualitative performance scores for all panel samples... 6 References... 7 Acknowledgements... 7 Appendix A of 8

3 1. Programme aims The primary aims of this External Quality Assessment Programme were to: 1) Determine the qualitative performance of participants testing for Chlamydia trachomatis (C. trachomatis) using molecular technologies. 2) Determine the incidence of false positive results. 3) Determine the performance of participants testing for Swedish variant C. trachomatis. 4) Determine reproducibility on duplicate samples. 5) Compare performance with previous distributions. Participants are encouraged to read the QCMD Participants' Manual, which can be downloaded from the QCMD website. Any queries about this report should be addressed to the QCMD Neutral Office 2. Programme details Table 1: Programme details CTDNA11A Date of panel distribution 07/03/2011 Number of respondents 49 (96%) Number of participants 51 Number of datasets submitted 50 Number of countries 1 Number of qualitative datasets submitted 50 (100%) Number of qualitative and quantitative datasets submitted 0 (0%) Two participants did not return results. Additional information on selected panel samples In urine Extended dilution series: Panel samples CTA11-05, -03, and -01. These samples contained a cultured strain of C. trachomatis that is also encountered as a pathogen. The amount of C. trachomatis DNA present in clinical specimens can vary widely. Panel sample CTA11-05, was present in clinically-relevant concentrations. Panel sample CTA11-01 was included to assess analytical sensitivity. Sample containing the Swedish variant of C. trachomatis: CTA This sample was included to assess the ability of laboratories to detect the Swedish variant of C. trachomatis. This strain of the pathogen is lacking 377 base pairs of the cryptic plasmid, which is commonly used as a target for molecular assays. In swab Extended dilution series: Panel samples CTA11-07, -06, -08, and -10. These samples contained a cultured strain of C. trachomatis that is also encountered as a pathogen. Panel samples CTA11-07, -06 and -08 were present in clinically-relevant concentrations. Panel sample CTA11-10 was included to assess analytical sensitivity. 3 of 8

4 Percentage of datasets 2011 Chlamydia trachomatis 3. Panel composition This EQA panel for the detection of C. trachomatis consisted of eight samples containing various concentrations of C. trachomatis in either urine or simulated swab and two samples negative for C. trachomatis, one in urine and one in simulated swab. C. trachomatis was cultured from a Dutch clinical isolate (LGV L2) obtained in The design and implementation of the QCMD EQA programmes is achieved in collaboration with scientific experts or expert groups in conjunction with the QCMD Executive and Scientific Council. The panel materials were prepared by a third party contracted to do so by QCMD. The production, storage and distribution of the EQA panels were undertaken using defined procedures to ensure homogeneity and stability. All panel materials were subjected to testing by laboratories recognised as expert in the detection of these targets. Table 2: Panel composition Sample Sample content Sample * matrix Sample conc. Copies/vial Sample status Sample type CTA11-05 Chlamydia trachomatis Urine 5x10 3 Frequently detected Core CTA11-03 Chlamydia trachomatis Urine 4x10 2 Detected CTA11-01 Chlamydia trachomatis Urine 5x10 1 Infrequently detected CTA11-04 C. trachomatis (Swedish Variant) Urine 1x10 6 Frequently detected Core CTA11-02 Ct. negative urine Urine Negative Core CTA11-07 Chlamydia trachomatis Swab 6x10 4 Frequently detected Core CTA11-06 Chlamydia trachomatis Swab 3x10 3 Frequently detected Core CTA11-08 Chlamydia trachomatis Swab 3x10 3 Frequently detected Core CTA11-10 Chlamydia trachomatis Swab 5x10 2 Detected CTA11-09 Ct. negative swab Swab Negative Core Key to Table 2 Sample: QCMD panel sample codes for the samples distributed to participants. Sample content: bacterial content of the panel samples. Sample matrix: material used as a matrix in preparation of the panel samples. Sample conc.: sample concentrations estimated by the production laboratory. The values quoted are a mean of two replicates generated using the Abbott RealTime CT/NG test on the Abbott m2000 platform. These values are for QCMD internal purposes only. They should not be used by participants for method comparison or as a target for individual laboratory assessment. Sample status: the sample status assigned to each panel sample consisting of 'Frequently detected', 'Detected', 'Infrequently detected' or 'Negative'. Please see Appendix A for more information. Sample type: panel samples classified as core proficiency samples. *Urine: Chlamydia trachomatis-negative urine collected from healthy adult volunteers. Swab: 1/10 dilution of TE buffer. Panel members designated core proficiency samples on the basis of scientific information, clinical relevance and clinical experience (published literature and professional clinical guidelines) and, where available and appropriate, established target performance limits taken from previous QCMD EQA distributions. Laboratories are expected to correctly analyse and report the core proficiency samples in order to show acceptable proficiency. 4. Programme results 4.1. Qualitative performance on the core proficiency samples Figure 1 shows the performance of BEIPH participants on the core proficiency samples. In this round of the EQA 80.0% of datasets returned to QCMD by BEIPH participants reported all core proficiency samples correctly. Figure 1: Performance on the core proficiency samples for all participants 90.0% 80.0% 70.0% 60.0% 50.0% 40.0% 30.0% 20.0% 10.0% 0.0% 80.0% 14.0% 4.0% 0.0% 2.0% 0.0% 0.0% 0.0% 7/7 6/7 5/7 4/7 3/7 2/7 1/7 0/7 Number of core samples correct 4 of 8

5 4.2. Qualitative analysis of the EQA data for all panel samples The number (percentage) of correct qualitative results are presented in Table 3. Qualitative data were returned by participants as 'positive', 'negative' or 'not determined'. Not determined results were counted as incorrect for all panel samples (positive or negative). QCMD organises datasets according to commercial and in-house technology groups, which are Conventional PCR, Real time PCR, NASBA, SDA, TMA and bdna. Where datasets were reported as other for a technology or kit method this was reviewed by the QCMD Neutral Office and assigned to an appropriate group where possible. Table 3: Number of correct qualitative results per panel member and technology type Sample Sample Sample conc. content Copies/vial PCR Total Conventional Real time SDA f datasets Commercial a Commercial c In-house d n=50 n=6 n=35 n=3 n=6 n % n % n % n % n % CTA11-05 Chlamydia trachomatis 5x CTA11-03 Chlamydia trachomatis 4x CTA11-01 Chlamydia trachomatis 5x CTA11-04 C. trachomatis (Swedish Variant) 1x CTA11-02 Ct. negative urine CTA11-07 Chlamydia trachomatis 6x CTA11-06 Chlamydia trachomatis 3x CTA11-08 Chlamydia trachomatis 3x CTA11-10 Chlamydia trachomatis 5x CTA11-09 Ct. negative swab Key to Table 3 Sample: QCMD panel sample codes for the samples distributed to participants. Sample content: bacterial content of the panel samples. Sample conc.: Sample concentrations estimated by the production laboratory. The values quoted are a mean of two replicates generated using the Abbott RealTime CT/NG test on the Abbott m2000 platform. These values are for QCMD internal purposes only. They should not be used by participants for method comparison or as a target for individual laboratory assessment. Total datasets: number and percentage of datasets reporting the correct qualitative result for each panel sample. A breakdown of the results for all datasets is also provided based on technology type. a: Roche Amplicor CT/NG (n=4), Roche COBAS Amplicor CT/NG (n=2). c: Abbott RealTime CT (n=2), Abbott RealTime CT/NG (n=10), Diagenode C. trachomatis real time PCR detection (n=1), Nanogen Chlamydia tr. Q-PCR Alert Kit (n=1), QIAGEN artus C. trachomatis PCR Kit (TM) (n=1), QIAGEN artus C. trachomatis Plus PCR Kit (RG) (n=3), QIAGEN artus C. trachomatis Plus PCR Kit (Rotor-Gene) (n=1), Roche COBAS 4800 CT/NG Test (n=2), Roche COBAS TaqMan CT Test v2.0 (n=14). d: Details not presented. f: BD Diagnostics BD ProbeTec ET System (n=6). 5 of 8

6 4.3. Qualitative performance scores for all panel samples Table 4: Qualitative performance scores per technology type Commercial Total PCR All technologies Conventional Real time c SDA f Sample Sample status Commercial a In-house d n=50 n=6 n=35 n=3 n= CTA11-05 Frequently detected CTA11-03 Detected CTA11-01 Infrequently detected CTA11-04 Frequently detected CTA11-02 Negative CTA11-07 Frequently detected CTA11-06 Frequently detected CTA11-08 Frequently detected CTA11-10 Detected CTA11-09 Negative Key to Table 4 Sample: QCMD panel sample codes for the samples distributed to participants. Sample status: the sample status assigned to each panel sample. Please see Appendix A for more information. Total. All technologies: number of datasets awarded each score (0 to 3). A breakdown of the results for all datasets is also provided based on technology type. These data are presented graphically in Figure 2. a: Roche Amplicor CT/NG (n=4), Roche COBAS Amplicor CT/NG (n=2). c: Abbott RealTime CT (n=2), Abbott RealTime CT/NG (n=10), Diagenode C. trachomatis real time PCR detection (n=1), Nanogen Chlamydia tr. Q-PCR Alert Kit (n=1), QIAGEN artus C. trachomatis PCR Kit (TM) (n=1), QIAGEN artus C. trachomatis Plus PCR Kit (RG) (n=3), QIAGEN artus C. trachomatis Plus PCR Kit (Rotor-Gene) (n=1), Roche COBAS 4800 CT/NG Test (n=2), Roche COBAS TaqMan CT Test v2.0 (n=14). d: Details not presented. f: BD Diagnostics BD ProbeTec ET System (n=6). Figure 2: Percentage of qualitative performance scores per technology type % a c d f a c d f a c d f a c d f a c d f a c d f a c d f a c d f a c d f a c d f CTA11-05 CTA11-03 CTA11-01 CTA11-04 CTA11-02 CTA11-07 CTA11-06 CTA11-08 CTA11-10 CTA11-09 Technology group per panel sample a: Conventional commercial PCR, c: Real time commercial PCR, d: Real time in-house PCR, f: SDA. 6 of 8

7 References Ripa T, Nilsson PA. A Chlamydia trachomatis strain with a 377-bp deletion in the cryptic plasmid causing false-negative nucleic acid amplification tests. Sexually Transmitted Diseases, 2007; 34(5): Acknowledgements Data analysis and report generation were performed by Calum Scott and William MacKay of the QCMD Neutral Office. QCMD The QCMD EQA programme samples, associated reports and data generated during this programme are intended for External Quality Assessment (EQA) and Proficiency Testing (PT) purposes only. QCMD operates according to a strict Code of Practice which is in line with ISO/IEC and associated standards. Data reported in QCMD programmes is representative of a laboratory s standard diagnostic testing protocols irrespective of the technology they use. The data provided in the reports are based on technical information provided by the individual laboratories as part of the assessment process, as such it does not constitute a formal technology method comparison. All text and images produced by QCMD are the property of QCMD unless otherwise stated. The reproduction and use of these materials is not permitted without the express written consent of QCMD. The use of the information provided in QCMD reports for commercial purposes is strictly prohibited. 7 of 8

8 Appendix A Assigning the sample status Sample status is assigned by peer-group consensus, based on the qualitative results returned by all participants in the full EQA programme. It is not a measure of the 'strength' of a positive sample nor is it technology-dependent, and is used solely for the scoring of the EQA data. The rationale for the sample status is: Frequently detected: More than 95% of datasets recorded the correct positive result. Detected: Between 65% and 95% of datasets recorded the correct positive result. Infrequently detected: Less than 65% of datasets recorded the correct positive result. Negative: A panel sample that does not contain the target and produces an unequivocal negative result. Scoring system for qualitative EQA data The scores awarded for qualitative EQA data were based on the sample status. The scoring system is represented in the following table, where 0 is 'highly satisfactory' and 3 is 'highly unsatisfactory'. Colour has been included as an extra visual aid. Scoring system based on the assigned sample status Sample status Participant's result Negative Not determined Positive Frequently detected Detected Infrequently detected Negative Further information about the QCMD method of analysing EQA data can be found in the following peer-reviewed publication: Staines HJ, Garcia-Fernandez L, Pogothata R, Wallace PS, MacKay WG, Van Loon AM. Monitoring performance of nucleic acid-based diagnostic measurement system users by EQA. Accred Qual Assur. 2009; 14: of 8

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