Region I Advisory Board MeetingWells Beach, ME

June 9, 2008

Use and Verification of STD Nucleic Acid Amplification Tests

for non-FDA Cleared Clinical Specimens

Presenter: Sally Liska, DrPHDirector, San Francisco PH Lab

sally_liska@sfdph.org

“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 Testingat 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 & OropharyngealSpecimens

• 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

TOTAL 22 178 200

Performance CharacteristicsPharyngeal Gonorrhea

Sensitivity Specificity

CULTURE 47.4 % 100 %

LCR 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

72.5%

28.2%

43.4%

70.0%

5.1% 6.6%6.4% 4.3% 4.7%7.1%

1.1%

11.7%

0%

20%

40%

60%

80%

Urethral GC Rectal GC PharyngealGC

Urethral CT Rectal CT* PharyngealCT**

% o

f v

isit

s

Median Percent Tested

Median Positivity

Symptomatic vs. Asymptomatic Infection

0.5%

7.8%

6.7%

7.7%

1.0%

4.8%

9.2%

8.5%

0.0%

2.0%

4.0%

6.0%

8.0%

10.0%

Pre

vale

nce o

f In

fecti

on

Asymptomatic Symptomatic

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

TestTest Sensitivity (%)Sensitivity (%) Specificity (%)Specificity (%)

CT:CT:

CultureCulture 44.444.4 100100

AC2AC2 100100 99.899.8

SDASDA 66.766.7 100100

GC:GC:

CultureCulture 40.440.4 100100

AC2AC2 84.384.3 99.499.4

SDASDA 71.971.9 99.599.5

Performance of NAAT’s on 1,110 Rectal Swab Specimens

TestTest Sensitivity (%)Sensitivity (%) Specificity (%)Specificity (%)

CT:CT:

CultureCulture 26.526.5 100100

AC2AC2 92.692.6 99.699.6

SDASDA 63.263.2 100100

GC:GC:

CultureCulture 43.243.2 100100

AC2AC2 93.293.2 99.799.7

SDASDA 78.478.4 99.999.9

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 ▪ Reportable range

▪ Specificity ▪ Reference range

▪ Precision ▪ Other characteristics

▪ Accuracy 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