1. CT/NG Testing
Driven by CDC Guidelines

2. CT infections reported in the US continue to rise…
Chlamydia trachomatis (CT)
Infection Rates by Sex, 1990–2009
Chlamydia is the most frequently reported bacterial STD in the US
1.2 million cases of Chlamydia and 300,000 cases of gonorrhoeae were reported in 2009
Untreated Chlamydia infection can ascend to the upper genital tract resulting in:
Pelvic inflammatory disease (PID)
Infection and inflammation of the uterus, fallopian tubes, ovaries, or adjacent peritoneum
Neisseria gonorrhoeae
Chlamydia trachomatis (CT) infection remains the most frequently reported bacterial STD in the US and the incidence of infection continues to rise. The 1.2 million cases in 2009 represents the largest number of cases ever reported to the CDC for any condition. This is a 2.8% increase compared to 2008.
This increase most likely represents a continued increase in screening for this infection, expanded use of more sensitive tests, and more complete national reporting, but may also reflect a true increase in morbidity.
Untreated Chlamydia infection can ascend to the upper genital tract resulting in:
Pelvic Inflammatory Disease (PID)
Infection and inflammation of the uterus, fallopian tubes, ovaries, or adjacent peritoneum
All of which can lead to infertility.
 Click the mouse and the Neisseria gonorrhoeae (NG) infection rate graph will appear and illustrate that gonorrhoeae infection continues to drop. However, NG remains the second most commonly reported notifiable disease in the US. The 2009 rate represents a 10.5% decrease from 2008 data.
From CDC STD Surveillance 2009 –

3. The Burden for Adolescents and Young Adults
It is estimated that persons aged 15 – 24 yrs. represent 25% of sexually experienced population, but they acquire nearly
half of all new STD’s
15 – 19 yr. olds represent a 2.4 % increase for CT during 2008
20 – 24 yr. olds represent a 4.0% increase for CT during 2008
Under reporting is considered to be substantial
80%–90% of CT infections and 50% of NG infections in women are asymptomatic
The burden of this infection begins with adolescents and young adults. The CDC estimates that 19 million new STD infections occur each year, almost half of them among young people ages 15 to 24. STDs are widespread and add an estimated $14.7 billion to the nations healthcare costs each year, most people in the US remain unaware of the risk and consequences of all but the most prominent STD, HIV.
CT infections
Estimates suggest that even though young people aged 15 – 24 yrs. represent only 25 % of the sexually experienced population, they acquire half of all new STDs.
During 2008 – 2009 Chlamydia rates for persons aged 15 – 24 continue to increase.
Persons aged years are responsible for an annual increase of 2.4%
Persons aged 20 – 24 years are responsible for an annual increase of 4.0%
The Silent Epidemic
Under reporting of chlamydia infection is considered to be substantial because most people with chlamydia are not aware of their infections and do not seek testing. An estimated 2.8 million (1.2 million reported) CT infections and over 650,000 (300,000 reported) NG infections occur annually in the US.
Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010
From CDC STD Surveillance 2009 –

4. Routine Screening is Key to Reducing the Burden
CDC recommends the following:
Annual CT screening of sexually active women <25 yrs. and NG screening for those at risk
Screening of women >25 yrs. with risk factors; risk factors include new partners or multiple partners
All pregnant women should be screened for Chlamydia trachomatis during the first prenatal visit and those at risk for NG
Routine Screening is key to reducing the rates of Chlamydia and gonorrhea
To detect chlamydial infections, health-care providers frequently rely on screening tests. Annual screening of all sexually active women aged ≤25 years is recommended, as is screening of older women with risk factors (e.g., those who have a new sex partner or multiple sex partners)
Routine screening for N. gonorrhoeae in all sexually active women at risk for infection is recommended annually. Women aged <25 years are at highest risk for gonorrhea infection. Other risk factors that place women at increased risk include a previous gonorrhea infection, the presence of other STDs, new or multiple sex partners, inconsistent condom use, commercial sex work, and drug use.
All pregnant women should be routinely screened for Chlamydia trachomatis during the first prenatal visit. Women aged ≤25 years and those at increased risk for chlamydia (e.g., women who have a new or more than one sex partner) also should be retested during the third trimester to prevent maternal postnatal complications and chlamydial infection in the infant.
All pregnant women at risk for gonorrhea or living in an area in which the prevalence of Neisseria gonorrhoeae is high should be screened at the first prenatal visit for N. gonorrhoeae
Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010

5. Men aged 15 – 24 years Carry the burden of the highest chlamydia rates
Chlamydia rates for men
15 – 19 yr. old men represent a 5 % increase in CT
20 – 24 yr. old men represent the highest rate of CT infection with an increase of 6%
Screening of sexually active young men should be considered in clinical settings with a high prevalence of chlamydia; adolescent clinics, correctional facilities, and STD clinics
Women are usually the focus of Chlamydia infection due to the long term impact of the infection. However men aged 15 – 24 years of age carry the highest rates for chlamydia.
Infections in men are usually symptomatic resulting in lower rates of testing. However an increase in testing has been seen with non-invasive urine samples.
Evidence is insufficient to recommend routine screening for C. trachomatis in sexually active young men based on feasibility, efficacy, and cost-effectiveness. However, screening of sexually active young men should be considered in clinical settings associated with high prevalence of chlamydia (e.g., adolescent clinics, correctional facilities, and STD clinics).
MSM (Men who have Sex with Men)
A test for urethral infection with N. gonorrhoeae and C. trachomatis in men who have had insertive intercourse during the preceding year; testing of the urine using nucleic acid amplification testing (NAAT) is the preferred approach.
A test for rectal infection with N. gonorrhoeae and C. trachomatis in men who have had receptive anal intercourse during the preceding year (NAAT of a rectal swab is the preferred approach)
A test for pharyngeal infection with N. gonorrhoeae in men who have had receptive oral intercourse during the preceding year (NAAT is the preferred approach). Testing for C. trachomatis pharyngeal infection is not recommended.
The CDC also recommends annual screening for men engaged in receptive anal or oral intercourse (MSM)
Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010
From CDC STD Surveillance 2009 –

6. CDC Recommended specimen types New guidelines encourage movement toward self collected specimen types
Recommended Specimen Types for Women
Endocervical swabs specimens
Vaginal swabs; provider collected or self collected specimens
Urine specimens
Liquid based cytology specimens
Urine is the Preferred Specimen Type for Men
when a NAAT is used for Testing
Urine specimen
Urethral swab
There are a variety of specimens types available for CT and NG testing when using NAATs.
Endocervical is the specimen types used the most, however the public health sector is moving toward the use of self-collected vaginal swab specimens.
The Association for Public Health Laboratories (APHL) published the findings from an expert consultation meeting that took place during January 2009 reporting the following:
For female screening, vaginal swab specimens are the preferred specimen type. Self- collected vaginal swab specimens perform at least as well as with other approved specimens using NAATs, and women find this screening strategy highly acceptable.
Liquid based cytology specimens are a new addition to the guidelines. Many laboratories have “out of the vial strategies” and perform multiple tests out of one cytology specimen.
Urine is the preferred sample type for testing or screening men using NAATs. There is little need for urethral swab specimens and in some studies these samples are less sensitive than urine. Increased testing has been seen in men with the availability of urine testing.
Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010

7. Self collected specimens such as urine and vaginal swabs reduce barriers to testing
Urine is the preferred sample type for testing or screening men using NAATs. There is little need for urethral swab specimens and in some studies these samples are less sensitive than urine; urethral swab specimens and male urine were equivalent in specificity.
For female screening, vaginal swab specimens are the preferred specimen type. Vaginal swab specimens are as sensitive as cervical swab specimens and there is no difference in specificity. Cervical samples are acceptable when pelvic examinations are done, but vaginal swab specimens are an appropriate sample type even when a full pelvic exam is being performed.
Source: APHL Laboratory Diagnostic Testing for Chlamydia trachomatis and Neisseria gonorrhoeae, Expert Consultation Meeting Summary Report, January 13‐15, 2009
Self-collected vaginal swab specimens perform at least as well as with other approved specimens using NAATs, and women find this screening strategy highly acceptable.
Source: Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010

8. Oropharyngeal and rectal swab specimens
Not cleared for use with any nucleic acid amplification tests
Some public and private laboratories have established performance specifications for using NAATs with oropharyngeal and rectal swab specimens
- Allows results to be used for clinical management as an LDT
As mentioned earlier the CDC issued recommendations in July of 2009 for screening of at-risk men who have sex with men (MSM) at least annually for urethral and rectal gonorrhea and chlamydia, and for pharyngeal gonorrhea.
The challenge has been that there are no NAATs cleared by the FDA for testing with these types of specimens.
Some laboratories have validated these specimen types for use in their lab as laboratory developed tests (LDTs).
The APHL website provides a checklist for STD performance specifications and example protocols for the validation of these specimen types.
Sexually Transmitted Diseases Treatment Guidelines, 2010; CDC, December 17, 2010

9. cobas® CT/NG v2.0 Test The true solution for efficiency, confidence &
cost-effectiveness
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10. cobas CT/NG v2.0 Test The true solution for efficiency, confidence & cost-effectiveness
cobas x 480 instrument –
automated nucleic acid extraction
cobas z 480 analyzer
automated amplification
and detection
cobas CT/NG v2.0 test
As you may know, the cobas CT/NG v2.0 test was designed for the cobas 4800 system, which is comprised of the cobas x 480 instrument (which automates nucleic acid extraction and purification) and the cobas z 480 analyzer (which performs real-time PCR testing).
cobas 4800 system
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11. Only system with primary vial loading for all specimen types
De-cap primary vial & load
Fully automated
sample extraction and result generation
Specimen types for symptomatic/asymptomatic patients that have been validated using the cobas CT/NG v2.0 test:
Endocervical swabs*
Vaginal swabs (clinician- or self- collected in a clinical setting)*
Male and female urine (stabilized with the cobas® PCR Urine Sample kit)
Cervical specimens collected in ThinPrep® PreservCyt® Solution
When we say our system is easy to use, that’s what we mean.
We hear that all the time from customers – who appreciate having a test and system that requires very little training.
Just as important, our system is the ONLY one that features primary vial loading for all specimen types, including:
Endocervical swabs
Vaginal swabs – collected by the patient OR by the clinician
Urine – from males or females
Cervical specimens collected in ThinPrep PreservCyt solution
And after specimens are loaded, the cobas 4800 system requires the least amount of hands-on time of ALL competitive systems…
*In cobas® PCR Media collected with the cobas PCR Female Swab sample kit
Note: cobas PCR Media provides room-temperature specimen stability for up to one year.
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12. Lowest hands-on time & faster turnaround time when compared to other systems1
The data is clear. For roughly the same number of reportable results, our system requires the least amount of hands-on time – AND it delivers results with faster turnaround time than nearly all other systems.
(Note that the cobas 4800 system’s turnaround time is clearly better than either Hologic system.)
Source: Argent Global Services. CT/NG Comparison Study Data on file.
1Argent Global Services. CT/NG Comparison Study Data on file.
10 November page © 2014 Roche

13. Easy-to-use, easy-to-train test & system A truly smart answer is at hand for your laboratory
cobas x 480 instrument
automated nucleic acid extraction
cobas z 480 analyzer
Real-time amplification & detection
Easy-to-use system
~ 4 mins daily maintenance
No daily decontamination by bleaching components required
Easy-to-use test
No reagent preparation
Assay specific reagents provided in bar-coded vials
To summarize: our system and test are truly easy to use and easy to train. There’s no need to prep reagents OR to decontaminate system components each day with bleach solution.
10 November page © 2014 Roche

14. Chlamydia trachomatis Neisseria gonorrhoeae
Only third-generation test with dual-targets for CT, NG and internal controls
Chlamydia trachomatis
Neisseria gonorrhoeae
Internal Control
Detects both cryptic plasmid and ompA gene Major Outer Membrane Protein (MOMP) targets
Detects all major serovars of CT and the Swedish CT mutant (nvCT)
Detects variants that may harbor deletions in the cryptic plasmid
Detects variants that do not carry the cryptic plasmid
Detects both the Direct Repeat (DR9) sequence A and the Direct Repeat (DR9) sequence B targets
Target region is repeated x3 in the NG genome and has 2 highly conserved sequence variations
Detects combinations of both target variations
No cross-reactivity with commensal Neisseria or other bacterial species has been observed
Two individual IC plasmids provide consistent signal with high target input
First, unlike all other competitive tests, ONLY our test includes dual targets for CT, NG and internal controls.
It is a multiplex assay that uses different dyes to detect targets in 3 different optical channels of the cobas® z 480 analyzer.
Chlamydia is detected in channel 1
Gonorrhea is detected in channel 2
Internal control in channel 4
You can order a combo test or individual CT or NG tests.
Dual-probe, single-tube multiplex assay design with automatic internal control
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15. Sensitivity of new NG target delivers true confidence
Collection site NG
strains
DR9A
DR9A/DR9B Hybrid
DR9B
Japanese Collection
147
University of Washington
129
101 26 2
RMSCC NG Panel 1 94 77 17
RMSCC NG Panel II 87 71 14
Australia collection 81 80 1
Staten Serum Institute in Denmark 51 39 7 5
Total
589
515 65 9
All 589 culture isolates were positive for the presence of DR9
There are geographical differences on the prevalence of DR9A or DR9B
The cobas CT/NG test was designed to detect each of the 2 conserved NG sequence variations (DR9A and DR9B) contained within the triple repeat DR9. A large, geographically diverse NG culture panel (n=589) was tested with the prototype DR9 assay to describe the prevalence of DR9A and DR9B sequences. The findings of the prevalence studies of DR9A and DR9B are summarized in the table shown here.
All 589 NG culture isolates were positive for the presence of DR9.
84.5% of NG culture isolates contain only DR9A sequences in the triple DR9 repeat.
11.0% of NG culture isolates contain a combination of DR9A and DR9B sequences in the triple repeat.
1.5% of NG culture isolates contain only DR9B sequences in the DR9 triple repeat.
Geographical differences were observed in the prevalence of DR9A and DR9B sequences within the DR9 triple repeat.
The DR9B sequence was not observed in Japan.
The presence of the DR9B sequence is rare in Australia.
The DR9B sequence was observed most in NG culture isolates from Denmark.
DR9A and DR9B prototype assay testing results using geographically diverse NG culture panel
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16. High specificity of new NG target eliminates the need for confirmatory testing
Neisseria commensal sps
N Tested
cobas 4800 NG result
N. canis 1
neg
N. cinerea 10
N. elongata
N. flavescens 2
N. lactamica 20
N. meningitidis 36
N. mucosa 9
N. polysacchareae 5
N. sicca 8
N. subflava 37
N. weaveri
Moraxella (Branhamella) catarrhalis 14
Total
144
N. gonorrhea isolates 76
All positive
All 144 non-gonococcal isolates provided negative results
All 76 gonococci provided positive results
The specificity of the new NG target eliminates the need for confirmatory testing.
At Queensland Paediatric Infectious Diseases Laboratory (QPID), a panel of Neisseria species (223 isolates) was used to further investigate the specificity and conservation of the target sequences used by the cobas CT/NG v2.0 test.
The panel species are described in the table shown here.
All 144 non-gonococcal isolates provided negative results and all 76 gonococci provided positive results.
QPID Neisseria species culture panel
10 November page © 2014 Roche

17. cobas CT/NG v2.0 Test Reliable sensitivity & specificity for all specimen types1
Sample Type CT NG N
Sens %
Spec %
Endocervical Swab
2,926
94.9%
99.4%
5,104
96.6%
99.9%
Female Urine
2,945
94.0%
99.6%
5,127
95.6%
99.7%
Vaginal Swab (Clinician-collected)
1,902
98.2%
99.1%
3,138
100.0%
Vaginal Swab
(Self-collected)
2,037
97.6%
99.3%
96.7%
PreservCyt (Pre-ThinPrep)
2,937
94.2%
5,131
PreservCyt (Post-ThinPrep)
2,878
93.7%
99.5%
4,868
Male Urine
738
98.4%
99.2%
The cobas CT/NG v2.0 test delivers true confidence because of its reliable sensitivity and specificity for all specimen types.
Sensitivity, specificity, and predictive values of the cobas CT/NG v2.0 Test for CT and NG (as defined by patient infection status) are presented here by gender and specimen type.
Performance estimates for CT and NG detection were similar between symptomatic and asymptomatic subjects.
Source: cobas CT/NG v2.0 Test package insert, 2013.
1cobas CT/NG v2.0 Test package insert, 2013.
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18. Only test with AmpErase enzyme & internal controls to minimize false positives & negatives
True confidence
Designed with layers of safeguards for accurate results
The cobas CT/NG v2.0 test delivers true confidence because it’s designed with layers of safeguards to help ensure accurate results.
10 November page © 2014 Roche

19. Definitive results in high- & low-prevalence populations1CT NG
PPV (%)
NPV (%) 1
69.0
99.9
82.0
100.0 3
87.2
99.8
93.3 5
92.0
99.7
96.0 10
96.1
99.3
98.0 15
97.5
99.0
98.8
99.5 20
98.2
98.5
99.1 30
98.9 50
94.4
97.2
The prevalence of CT and NG in patient populations depends on a variety of factors, including age, gender, the presence of symptoms, clinic type and test method.
Hypothetical positive and negative predictive values (PPV & NPV) derived from disease prevalence of 1% to 50% for the cobas CT/NG v2.0 test are shown here.
The prevalence of CT observed with the cobas® CT/NG v2.0 test during a multi-center clinical trial ranged from 5.0% to 8.9% in females, and from 11.3% to 25.2% in males; the prevalence of NG ranged from 0.9% to 2.3% in females, and from 1.5% to 21.6% in males.
Source: cobas CT/NG v2.0 Test package insert, 2013.
1cobas CT/NG v2.0 Test package insert, 2013.
10 November page © 2014 Roche

20. Dependable results virtually eliminate costly retests
New generation “kinetic” algorithm for results eliminates need to visually analyze growth curves
Eliminates the guessing game by providing clear results
Consistency checks
No gray zone area
Algorithm based on 250,000 curves
Algorithm result correspondence >99.95%
Because of its new-generation “kinetic algorithm,” our test can deliver results that are clearly positive, negative or invalid.
This helps minimize emotional burden on patients—and can reduce costs associated with unnecessary treatment and/or retesting.
10 November page © 2014 Roche