Transcript Use and Verification of Nucleic Acid Amplification Tests

Region I Advisory Board Meeting
Wells Beach, ME
June 9, 2008
Use and Verification of STD
Nucleic Acid Amplification Tests
for non-FDA Cleared Clinical
Specimens
Presenter: Sally Liska, DrPH
Director, San Francisco PH Lab
[email protected]
“From Tommy Bahama [Levi Strauss]
to LL Bean”
Background: San Francisco Public
Health Laboratory
• Local PH Lab – support Communicable
Disease programs (STD, HIV, TB, etc.)
• Methods – microbiology, virology,
serology, molecular diagnostics
• Process > 100,000 specimens/yr from
DPH clinics, specialty clinics,
jails, NGO clinics, “events”,
etc.
Hx of CT/GC Lab Testing
at the SFDPH Lab
A. Culture for N. gonorrhoeae
B. Nucleic Acid Amplification (NAAT)
• Ligase Chain Reaction {LCR} – Abbott; 1995
• Strand Displacement Amplification {SDA} –
Becton Dickinson; 2001
• Transcription Mediated Amplification
{TMA} – Gen-Probe; 2004
• Polymerase Chain Reaction
{PCR}
Monthly STD stats – SFDPH Lab
STD NAAT Testing by Source; April, 2008
N = 5,000
Cervical/ Vaginal
12 %
Urethral/ Urine
45 %
Rectal
20 %
Oropharyngeal
22 %
Why Test Rectal & Oropharyngeal
Specimens
• Reduce acquisition and transmission of
STD agents (Chlamydia, Gonorrhea, HIV)
• Rectal infections can cause proctitis and
increase risk of HIV infection
• CDC recommendations for MSM –
 GC: annual screening of anatomical
sites w/ possible exposure
 CT: annual screening for urethral and
rectal infection
NAAT’s vs. Culture –
Pharyngeal Gonorrhea
LCR +
LCR -
TOTAL
Culture
Positive
8
1
9
Culture
Negative
14
177
191
22
178
200
TOTAL
Performance Characteristics
Pharyngeal Gonorrhea
CULTURE
LCR
Sensitivity Specificity
47.4 %
100 %
94.7 %
97.8 %
Page-Shafer et al in CID, 2002; 34:173-6
How Prevalent in Non-genital Sites?
Figure 1. City-specific median percent of visits where gonorrhea and
chlamydia tests were performed and positivity among MSM, 2002-2006
80%
72.5%
70.0%
Median Percent Tested
Median Positivity
% of visits
60%
43.4%
40%
28.2%
20%
11.7%
6.4%
4.3%
4.7%
5.1%
7.1%
6.6%
1.1%
0%
Urethral GC
Rectal GC
Pharyngeal
GC
Urethral CT
Rectal CT*
Pharyngeal
CT**
Symptomatic vs.
Asymptomatic Infection
10.0%
9.2%
8.5%
7.8%
Prevalence of Infection
8.0%
7.7%
6.7%
6.0%
4.8%
4.0%
2.0%
1.0%
0.5%
0.0%
C
r op
O
T
x
ryn
ha
C
m
ctu
e
TR
o
Or
C
G
Asymptomatic
x
ryn
a
ph
Symptomatic
GC
m
ctu
e
R
What if we didn’t sample these sites?
CT (n = 574) GC (n = 785)
Identified
47 %
36 %
Non-identified
53 %
64 %
From Kent et al; CID 2005:41
What About Women?
When to do rectal & pharyngeal screening in
women, what are the indicators?
1. HRSA recommends screening HIV +
women (by culture)
2. Medical indications – risk of reinfection if
not treated for (rectal) infection?
3. PH indications – prevalence for these
sites in women largely unknown
Use of NAAT’s for R & Ph
specimens
•
•
•
•
PRO’s
More sensitive than
culture
More universal than
CT culture
Faster turn around
time
Can be automated
CON’s
• May be more
expensive
• NAAT’s not approved
for these sites by FDA
Performance of NAATs on 1,110
Oropharyngeal Swab Specimens
Test
CT:
Culture
AC2
SDA
GC:
Culture
AC2
SDA
Sensitivity (%)
Specificity (%)
44.4
100
66.7
100
99.8
100
40.4
84.3
71.9
100
99.4
99.5
Performance of NAAT’s on
1,110 Rectal Swab Specimens
Test
CT:
Culture
AC2
SDA
GC:
Culture
AC2
SDA
Sensitivity (%)
Specificity (%)
26.5
92.6
63.2
100
99.6
100
43.2
93.2
78.4
100
99.7
99.9
CLIA ’88
• Federal regulation w/ oversight on clinical
labs – Dx, Rx & prevention of disease
• Section 493.1213 pertains to requirement
for Verification of Method Performance
for:
– In-house developed method
– Modification of a manufacturer’s procedure
– Method not cleared by the FDA
Verification
• A 1-time process completed before the test is
used for patient testing.
• Requires determination of the test performance
characteristics –
▪ Sensitivity
▪ Specificity
▪ Precision
▪ Accuracy
▪ Reportable range
▪ Reference range
▪ Other characteristics
required for test performance
From Cumitech 31; ASM press 1997
Verification Protocol
• Purpose of test – e.g. screening for R GC
• Write an SOP – pre to post-analytical
testing
• Procure specimens –
– 20 Positive
– 50 Negative
• Set acceptability criteria
• Statement of findings w/ regard to
implementation – document!
Options
•
•
•
•
Do a VERIFICATION of your NAAT
Regionalize testing service
Send specimens out to commercial lab
Reimbursement – MediCal will reimburse for testing multiple
sites
Acknowledgements
• SFDPH
Diane Campbell, Leah
Rauch & lab staff
Charlotte Kent, Dr. Jeff
Klausner & City Clinic
clinicians
• UCSF
Julius Schachter & Jeanne
Moncada
• CA STD Control
Drs. Gail Bolan & Chris Hall
• CDC – Dr. John Papp
• Manufacturers