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CDC National Infertility Prevention Project Laboratory Update Region I Wells Beach, Maine June 1-3, 2009 PowerPoint PPT Presentation


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CDC National Infertility Prevention Project Laboratory Update Region I Wells Beach, Maine June 1-3, 2009. Richard Steece , Ph.D., D(ABMM) [email protected] Chlamydia and Gonorrhea “102”. Tests - Old and New Test Performance Issues Sensitivity/Specificity Positive Predictive Value (PPV)

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CDC National Infertility Prevention Project Laboratory Update Region I Wells Beach, Maine June 1-3, 2009

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CDC National Infertility Prevention ProjectLaboratory UpdateRegion IWells Beach, MaineJune 1-3, 2009

Richard Steece, Ph.D., D(ABMM)

[email protected]


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Chlamydia and Gonorrhea “102”

Tests - Old and New

Test Performance Issues

Sensitivity/Specificity

Positive Predictive Value (PPV)

Negative Predictive Value (NPV)

Frequently Asked Questions (FAQ)


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Chlamydia Laboratory Methods

  • Culture (Cell Culture)


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ADVANTAGES

Used for many types of specimens, e.g. endocervical, urethral, rectal, ocular, etc.

Meets medico-legal standards (specificity)

Used for strain studies

(DNA fingerprinting)

Susceptibility testing possible

DISADVANTAGES

Comparatively expensive

Many variables involved, e.g. cell culture, medium, etc.

Technically more difficult than many non-culture tests

Delayed turn around time

Lack of sensitivity (compared to amplified tests)

Advantages/DisadvantagesCell Culture


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Chlamydia Laboratory MethodsNon-culture

ANTIGEN DETECTION

Direct Fluorescent Antibody (DFA)

Enzyme Immunoassay (EIA)

NUCLEIC ACID DETECTION METHODS

Nucleic Acid Probe (GenProbe)

Hybrid Capture (Digene)


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ADVANTAGES

Used for many types of specimens, e.g. endocervical, urethral, rectal, ocular, etc. (DFA)

Effective for large scale screening (EIA/NAP)

Viable organism not required

Evaluate quality of specimens (DFA)

Inexpensive

Rapid turn around time

DISADVANTAGES

Not suitable for large volume testing (DFA)

Lack of sensitivity (compared to amplified tests)

Not FDA cleared for alternate specimens, e.g. urine, etc.

Advantages/DisadvantagesNon-culture


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Chlamydia Laboratory Methods Non-culture

  • Nucleic Acid Amplification Tests (NAATs)

    • Roche AMPLICOR® CT/NG Test (PCR)

    • Roche COBAS AMPLICOR™ CT/NG Test (PCR)

    • GenProbe APTIMA COMBO 2® (TMA)

    • GenProbe APTIMA CT® (TMA)

    • BD ProbeTec™ ET (SDA)

    • BD ProbeTec™ Chlamydia trachomatis (CT) Qx Amplified DNA Assay (SDA)

    • Abbott RealTime CT/NG (PCR)


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ADVANTAGES

Most sensitive and specific tests

Effective for large scale screening

Rapid turn around time

NAATs are FDA cleared for urine specimens

May be used with some alternate specimens

DISADVANTAGES

Some versions not suitable for large volume screening

High technical skill required

Special facilities or clean area required

Expensive

Advantages/DisadvantagesNAATs


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Chlamydia Rapid TestsPoint of Care Tests (POCTs)

  • Wampole Clearview

  • Quidel Quickview - Inverness


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ADVANTAGES

Rapid turn around time

Allows treatment of patient while in clinic

DISADVANTAGES

Expensive

Not suitable for large volume screening

Poor sensitivity with some POCTs

Complexity non-waived

Advantages/DisadvantagesPOCTs


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GonorrheaLaboratory Methods

Culture

  • Thayer Martin, etc.

  • Genetic transformation (Gonostat)

    Direct Microscopic Exam

  • Gram Stain


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ADVANTAGES

All types of specimens, e.g. endocervical, urethral, rectal, pharyngeal, ocular, etc.

Meets medico-legal standards (specificity)

Used for strain studies fingerprinting

Susceptibility testing possible

DISADVANTAGES

Some variables, e.g. various culture, media, etc.

Delayed turn around time

Lack of sensitivity (compared to amplified tests)

Advantages/DisadvantagesBacterial Culture


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GonorrheaLaboratory Methods

Non-Culture

  • Nucleic acid detection method

    • Nucleic Acid Probe (GenProbe)

    • Hybrid Capture (Digene)


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ADVANTAGES

Effective for large scale screening

Viable organism not required

Rapid turn around time

Inexpensive

Moderate technical skill required

DISADVANTAGES

Lack of sensitivity (compared to amplified tests)

Not FDA cleared for alternate specimens, e.g. urine, etc.

Advantages/DisadvantagesNAP and NAPSA


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GonorrheaLaboratory Methods

  • Nucleic Acid Amplification Tests (NAATs)

    • Roche AMPLICOR® CT/NG Test (PCR)

    • Roche COBAS AMPLICOR™ CT/NG Test (PCR)

    • GenProbe APTIMA COMBO 2® (TMA)

    • GenProbe APTIMA GC® (TMA)

    • BD ProbeTec™ ET (SDA)

    • BD ProbeTec™ Neisseria gonorrhoeae (GC) Qx Amplified DNA Assay (SDA)

    • Abbott RealTime CT/NG (PCR)


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ADVANTAGES

Most sensitive and specific tests

Effective for large scale screening

Rapid turn around time

NAATs are FDA cleared for urine specimens

May be used with some alternate specimens

DISADVANTAGES

Some versions not suitable for large volume screening

High technical skill required

Special facilities or clean area required

Expensive

Advantages/DisadvantagesNucleic Acid Amplified Tests (NAATs)


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Test Performance Issues

Sensitivity – The ability of a test to detect patients who have the disease or condition for which they are being tested OR refers to the proportion of people with disease who have a positive test.

Specificity – The ability of a test to identify patients who do not have the disease or condition for which they are being tested OR refers to the proportion of people without disease who have negative test result.


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  • Positive Predictive Value (PPV)

    • The likelihood that an individual with a positive test has the disease.

  • Negative Predictive Value (NPV)

    • The likelihood that a person with a negative test does not have the disease.


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Performance estimates1 of different tests to detect chlamydia and gonorrhea

Sensitivity, % Specificity,%

CT Culture40-70>99

GC Culture45-65>99

DFA50-7095-99

EIA60-7095-99

NAP/NAPSA 60-7597-99

NAATs 95-98>99

1Performance estimates vary widely due to differences in statistical analysis


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Example of NPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 20.0%

  • NPV=(1-.20)(.99)/(1-.20)(.99)+(.20)(1-.95)x100

  • NPV=.792/.792(.01)x100

  • NPV=.9875 x 100 = NPV of 99%


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Example of NPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 20.0%

  • NPV=(1-.20)(.99)/(1-.20)(.99)+(.20)(1-.95)x100

  • NPV=.792/.792+(.01)x100

  • NPV=.9875 x 100 = NPV of 99%

  • Sensitivity is 85%

  • NPV=.9635 x 100 = NPV of 96%


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Graph Courtesy of Abbot Laboratories


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 20.0%

  • PPV=(.20)(.95)/(.20)(.95)+(1-.20)(1-.99)x100

  • PPV=.19/.19+(.008)x100

  • PPV=.9595 x 100 = PPV of 96%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 15.0%

  • PPV=(.15)(.95)/(.15)(.95)+(1-.15)(1-.99)x100

  • PPV=.1425/.1425+(.0085)x100

  • PPV=.9437 x 100 = PPV of 94%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 10.0%

  • PPV=(.10)(.95)/(.10)(.95)+(1-.10)(1-.99)x100

  • PPV=.095/.095+(.009)x100

  • PPV=.9134 x 100 = PPV of 91%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 5.0%

  • PPV=(.05)(.95)/(.05)(.95)+(1-.05)(1-.99)x100

  • PPV=.0475/.0475+(.0095)x100

  • PPV=.8333 x 100 = PPV of 83%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 2.0%

  • PPV=(.02)(.95)/(.02)(.95)+(1-.02)(1-.99)x100

  • PPV=.019/.019+(.0098)x100

  • PPV=.6597 x 100 = PPV of 66%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99%

  • Prevalence is 1.0%

  • PPV=(.01)(.95)/(.01)(.95)+(1-.01)(1-.99)x100

  • PPV=.0095/.0095+(.0099)x100

  • PPV=.4896 x 100 = PPV of 49%


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Example of PPV using Prevalence(Effect of repeating positive specimens)

  • 1-(1-Spec.)2 = 1-(1-.99)2 = 1-(.0001) = 99.99%

  • Sensitivity remains 95%

  • Revised Specificity is 99.99%

  • Prevalence is 1.0%

  • PPV=(.01)(.95)/(.01)(.95)+(1-.01)(1-.9999) x 100

  • PPV=.0095/.0095+(.000099) x 100

  • PPV=.9896 x 100 = PPV of 99%(49%)


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Graph Courtesy of Abbot Laboratories


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99.9%

  • Prevalence is 1.0%

  • PPV=(.01)(.95)/(.01)(.95)+(1-.01)(1-.999)x100

  • PPV=.0095/.0095+(.00099)x100

  • PPV=.9056 x 100 = PPV of 91%


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Example of PPV using Prevalence

  • Sensitivity is 95%

  • Specificity is 99.9%

  • Prevalence is 1.0%

  • PPV=(.01)(.95)/(.01)(.95)+(1-.01)(1-.999)x100

  • PPV=.0095/.0095+(.00099)x100

  • PPV=.9056 x 100 = PPV of 91%

  • Specificity is 99.99%, PPV of 99%


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Frequently Asked Questions (FAQ)

Question: How long after a patient has successfully completed appropriate antimicrobial therapy would you be able to detect antigen in their specimen (e.g. false positive) due to residual CT or GC DNA/RNA?

Answer: The current CDC Treatment (and Laboratory) Guidelines state that DNA or RNA may persist for up to 3 weeks after the successful completion of appropriate antimicrobial therapy. At the recent laboratory guidelines meeting, the expert panel recommended that this statement remain the same at this time. However, studies are being conducted to examine this with several "newer" NAATs and it is possible this recommendation may change in the future based on new data.


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Frequently Asked Questions (FAQ)

Question: How soon after a patient has unprotected sex would you be able to detect CT and/or GC with a nucleic acid amplification test (NAAT)?

Answer: Depending on the antigen load (i.e. amount of CT or GC in the ejaculate), a patient’s specimen could be positive very shortly after exposure (sex/rape/abuse), before actual infection, from minutes to hours after sex to upwards of several days.  If infection occurs there should be a latent or silent (undetectable) period for a short time.  Once again depending on antigen load, a positive (if the individual becomes infected) could be detected in some cases in as little as a week, looking at the life cycle of the organism.  However, the average time from actual infection to detectable shedding is more likely 2-4 weeks for CT, most likely a week sooner for GC. 


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Frequently Asked Questions (FAQ)

Question: Is test-of-cure recommended as a routine procedure after therapy for CT or GC infection with first-line CDC-recommended treatment regimens?

Answer: The guidelines do not recommend a test of cure for CT or GC, with a few exceptions


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The End - Questions

Lots of tears


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Frequently Asked Questions (FAQ)

Question: In the past our laboratory has given us the option of submitting urine or endocervical swabs on our patient/clients. Recently they have verified rectal swabs as an additional specimens. Is it possible to just send in rectal swabs instead of urine or endocervical?

Answer: Rectal swabs are not recommended for patients unless they have participated in anal sex.


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