Laboratory Update Region I Wells Beach Maine June 13 2009 Richard Steece PhD DABMM DrRSteeceaolcom Chlamydia and Gonorrhea 102 Tests Old and New Test Performance Issues ID: 727663
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CDC National Infertility Prevention ProjectLaboratory UpdateRegion IWells Beach, MaineJune 1-3, 2009
Richard
Steece
, Ph.D., D(ABMM)
DrRSteece@aol.comSlide2
Chlamydia and Gonorrhea “102”Tests - Old and NewTest Performance IssuesSensitivity/SpecificityPositive Predictive Value (PPV)Negative Predictive Value (NPV)Frequently Asked Questions (FAQ)Slide3
Chlamydia Laboratory MethodsCulture (Cell Culture) Slide4
Advantages/DisadvantagesCell CultureADVANTAGESUsed 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 possibleDISADVANTAGESComparatively expensiveMany 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)Slide5
Chlamydia Laboratory MethodsNon-cultureANTIGEN DETECTION Direct Fluorescent Antibody (DFA) Enzyme Immunoassay (EIA)NUCLEIC ACID DETECTION METHODS Nucleic Acid Probe (GenProbe) Hybrid Capture (Digene)Slide6
Advantages/Disadvantages Non-cultureADVANTAGESUsed for many types of specimens, e.g. endocervical, urethral, rectal, ocular, etc. (DFA)Effective for large scale screening (EIA/NAP)Viable organism not requiredEvaluate quality of specimens (DFA)InexpensiveRapid turn around timeDISADVANTAGES
Not suitable for large volume testing (DFA)
Lack of sensitivity (compared to amplified tests)
Not FDA cleared for alternate specimens, e.g. urine, etc.Slide7
Chlamydia Laboratory Methods Non-cultureNucleic 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)Slide8
Advantages/DisadvantagesNAATsADVANTAGESMost sensitive and specific testsEffective for large scale screeningRapid turn around timeNAATs are FDA cleared for urine specimensMay be used with some alternate specimensDISADVANTAGESSome versions not suitable for large volume screeningHigh technical skill requiredSpecial facilities or clean area requiredExpensive Slide9
Chlamydia Rapid TestsPoint of Care Tests (POCTs)Wampole ClearviewQuidel Quickview - InvernessSlide10
Advantages/DisadvantagesPOCTsADVANTAGESRapid turn around timeAllows treatment of patient while in clinicDISADVANTAGESExpensiveNot suitable for large volume screeningPoor sensitivity with some POCTs Complexity non-waived Slide11
Gonorrhea Laboratory MethodsCultureThayer Martin, etc.Genetic transformation (Gonostat)Direct Microscopic ExamGram StainSlide12
Advantages/DisadvantagesBacterial CultureADVANTAGESAll types of specimens, e.g. endocervical, urethral, rectal, pharyngeal, ocular, etc.Meets medico-legal standards (specificity)Used for strain studies fingerprintingSusceptibility testing possibleDISADVANTAGESSome variables, e.g. various culture, media, etc.Delayed turn around timeLack of sensitivity (compared to amplified tests)Slide13
GonorrheaLaboratory MethodsNon-CultureNucleic acid detection methodNucleic Acid Probe (GenProbe)Hybrid Capture (Digene)Slide14
Advantages/DisadvantagesNAP and NAPSAADVANTAGESEffective for large scale screeningViable organism not requiredRapid turn around timeInexpensiveModerate technical skill requiredDISADVANTAGESLack of sensitivity (compared to amplified tests)Not FDA cleared for alternate specimens, e.g. urine, etc.Slide15
Gonorrhea Laboratory MethodsNucleic 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)Slide16
Advantages/DisadvantagesNucleic Acid Amplified Tests (NAATs)ADVANTAGESMost sensitive and specific testsEffective for large scale screeningRapid turn around timeNAATs are FDA cleared for urine specimensMay be used with some alternate specimens DISADVANTAGESSome versions not suitable for large volume screeningHigh technical skill requiredSpecial facilities or clean area requiredExpensiveSlide17
Test Performance IssuesSensitivity – 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.Slide18
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.Slide19
Performance estimates1 of different tests to detect chlamydia and gonorrhea Sensitivity, % Specificity,%CT Culture 40-70 >99GC Culture 45-65 >99DFA 50-70 95-99EIA 60-70 95-99NAP/NAPSA 60-75 97-99NAATs
95-98
>99
1
Performance estimates vary widely due to differences in statistical analysisSlide20Slide21
Example of NPV using PrevalenceSensitivity is 95%Specificity is 99%Prevalence is 20.0% NPV=(1-.20)(.99)/(1-.20)(.99)+(.20)(1-.95)x100NPV=.792/.792(.01)x100
NPV=.9875
x 100 =
NPV
of
99%Slide22
Example of NPV using PrevalenceSensitivity is 95%Specificity is 99%Prevalence is 20.0% NPV=(1-.20)(.99)/(1-.20)(.99)+(.20)(1-.95)x100NPV=.792/.792+(.01)x100
NPV=.9875
x 100 =
NPV
of
99%
Sensitivity is 85%
NPV=.9635 x 100 =
NPV of 96%Slide23
Graph Courtesy of Abbot LaboratoriesSlide24
Example of PPV using PrevalenceSensitivity 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%Slide25
Example of PPV using PrevalenceSensitivity 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%Slide26
Example of PPV using PrevalenceSensitivity 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%Slide27
Example of PPV using PrevalenceSensitivity 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%Slide28
Example of PPV using PrevalenceSensitivity 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%Slide29
Example of PPV using PrevalenceSensitivity 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%Slide30
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%)Slide31
Graph Courtesy of Abbot LaboratoriesSlide32
Example of PPV using PrevalenceSensitivity 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%Slide33
Example of PPV using PrevalenceSensitivity 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%Slide34
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.
Frequently Asked Questions (FAQ)Slide35
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.
Frequently Asked Questions (FAQ)Slide36
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
Frequently Asked Questions (FAQ)Slide37
Lots of tearsThe End - QuestionsSlide38
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.
Frequently Asked Questions (FAQ)