MCRNA - Clinical: Chlamydia trachomatis, Miscellaneous Sites, by Nucleic Acid Amplification (GEN-PROBE)

Test Catalog

Test Name

Test ID: MCRNA    
Chlamydia trachomatis, Miscellaneous Sites, by Nucleic Acid Amplification (GEN-PROBE)

Useful For Suggests clinical disorders or settings where the test may be helpful

Detection of Chlamydia trachomatis

Testing Algorithm Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

This test is used for specimens that are not FDA approved for this assay. Acceptable non-FDA-approved specimen types are ocular, oral, anal or rectal swabs, and peritoneal fluid.

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Chlamydia is caused by the obligate intracellular bacterium Chlamydia trachomatis and is the most prevalent sexually transmitted bacterial infection in the United States.(1,2) In 2010, 1.3 million documented cases were reported to the CDC.(2) Given that 3 out of 4 infected women and 1 out of 2 infected men will be asymptomatic initially, the actual prevalence of disease is thought to be much greater than reported. The organism causes genitourinary infections in women and men and may be associated with dysuria and vaginal, urethral, or rectal discharge. In women, complications include pelvic inflammatory disease, salpingitis, and infertility. Approximately 25% to 30% of women who develop acute salpingitis become infertile.(2) Complications among men are rare, but include epididymitis and sterility. Rarely, genital chlamydial infection can cause arthritis with associated skin lesions and ocular inflammation (Reiter syndrome). C trachomatis can be transmitted from the mother during delivery and is associated with conjunctivitis and pneumonia. Finally, C trachomatis may cause hepatitis and pharyngitis in adults.

 

Once detected, the infection is easily treated by a short course of antibiotic therapy. Annual chlamydia screening is now recommended for all sexually active women age 25 years and younger, and for older women with risk factors for infection, such as a new sex partner or multiple sex partners. The CDC also recommends that all pregnant women be given a screening test for Chlamydia infection.(2) Repeat testing for test-of-cure is not recommended after treatment with a standard treatment regimen unless patient compliance is in question, reinfection is suspected, or the patient's symptoms persist. Repeat testing of pregnant women, 3 weeks after completion of therapy, is also recommended to ensure therapeutic cure.(2)

 

Culture was previously considered to be the gold standard test for diagnosis of C trachomatis infection.(2) However, organisms are labile in vitro, and precise specimen collection, transportation, and processing conditions are required to maintain organism viability, which is necessary for successful culturing. In comparison, nucleic acid amplification testing (NAAT) provides superior sensitivity and specificity and is now the recommended method for diagnosis in most cases.(3-5) Immunoassays and nonamplification DNA tests are also available for C trachomatis detection, but these methods are significantly less sensitive and less specific than NAAT.(2)

 

Improved screening rates and increased sensitivity of NAAT testing have resulted in an increased number of accurately diagnosed cases.(2) Early identification of infection enables sexual partners to seek testing and treatment as soon as possible and reduces the risk of disease spread. Prompt treatment reduces the risk of infertility in women.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Negative

Interpretation Provides information to assist in interpretation of the test results

A positive result indicates the presence of rRNA Chlamydia trachomatis. This assay does detect plasmid-free variants of C trachomatis.

 

A negative result indicates that rRNA for C trachomatis was not detected in the specimen.

 

The predictive value of an assay depends on the prevalence of the disease in any particular population. In settings with a high prevalence of sexually transmitted disease, positive assay results have a high likelihood of being true positives. In settings with a low prevalence of sexually transmitted disease, or in any setting in which a patient's clinical signs and symptoms or risk factors are inconsistent with chlamydial urogenital infection, positive results should be carefully assessed and the patient retested by other methods, if appropriate.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

This report is intended for use in clinical monitoring or management of patients; it is not intended for use in medico-legal applications.

 

Appropriate specimen collection and handling is necessary for optimal assay performance.

 

Results should be interpreted in conjunction with other laboratory and clinical information.

 

A negative test result does not exclude the possibility of infection. Improper specimen collection, concurrent antibiotic therapy, presence of inhibitors, or low numbers of organisms in the specimen (ie, below the sensitivity of the test) may cause false-negative test results.

 

In low-prevalence populations, positive results must be interpreted carefully as false-positive results may occur more frequently than true-positive results in this setting.

 

In general, this assay should not be used to assess therapeutic success or failure, since nucleic acids from these organisms may persist for 3 weeks or more following antimicrobial therapy.

 

 

No interference is expected with swab specimens due to:

-Blood

-Lubricants and spermicides

  

This assay does not detect Chlamydia pneumoniae.

Supportive Data

Accuracy/Diagnostic Sensitivity and Specificity:

 

Accuracy

 

1. Clinical Specimens:

Non-FDA approved specimen types were collected in GEN-PROBE APTIMA collection devices according to the manufacturer’s instructions and tested using the GEN-PROBE APTIMA Combo 2 assay on the Tigris DTS System. Results were compared to those obtained by other CLIA-certified laboratories using the GEN-PROBE Tigris system. All specimens were within product insert stability requirements at the time of testing on the GEN-PROBE Tigris system. Clinical specimens were stored frozen until the time of testing. 

 

Non-FDA Approved Sources for detection of Chlamydia trachomatis (see additional spiking data below):

Oral/Throat

 

Reference result

Aptima Unisex

 

Positive

Negative

Total

APTIMA

(Mayo)

Positive

11

0

11

Negative

2

29

31

Total

13

29

42

 

Anorectal

Reference result

Aptima Unisex

Positive

Negative

Total

APTIMA

(Mayo)

Positive

11

0

11

Negative

0

21

21

Total

11

21

32

 

Peritoneal Fluid

Reference result

Aptima Unisex

Positive

Negative

Total

APTIMA

(Mayo)

Positive

0

0

0

Negative

0

10

10

Total

0

10

10

           

2. Spiked Specimens:  

Analyte-negative ocular (n=32), oropharyngeal (n=36), anorectal (n=19) and peritoneal fluid (n=30) specimens were spiked at the approximate limit of detection (LoD) and tested to supplement clinical specimen validation data (see analytical sensitivity validation data below).

 

Percent concordance by specimen type:

Source

Positives

(Number tested)

Negatives

(Number tested)

Concordance

Oropharyngeal (throat)

36 (36)

0 (0)

100%

Anorectal

19 (19)

0 (0)

100%

Peritoneal Fluid

30 (30)

0 (0)

100%

Ocular

32 (32)

35 (35)

100%

 

3. M5 media:

One milliliter of M5 media was added to GEN-PROBE APTIMA Specimen Transfer Kit collection devices and then spiked at the approximate LoD for C trachomatis. This was performed to determine if M5 media interfered with detection of C trachomatis, and to determine if future specimens submitted in M5 media could be tested in this manner. Thirty-one specimens were spiked near the LoD, while 14 specimens had M5 media added, but no organism was spiked into the sample.

M5 Media

Positives

Number  Tested

Negatives

Number Tested

Agreement

 

31 (31)

14 (14)

100%

 

4. Total Accuracy (Clinical and spiked specimens combined):

Source

Collection Device*

Total Tested**

Sensitivity

Specificity

Positive

(Number tested)

Negative (Number tested)

Oropharyngeal (Throat)

Unisex

49 (51)

29 (29)

96%

100%

Anorectal

Unisex

30 (30)

21 (21)

100%

100%

Peritoneal fluid

Unisex

30 (30)

10 (10)

100%

100%

Ocular

Unisex

32 (32)

35 (35)

100%

100%

 

* All collection devices are manufactured by GEN-PROBE for use with the Aptima assay.

** Positive and negative status are based on the result by the comparator method (clinical specimens) or expected result (spiked specimens).

 

Analytical Sensitivity/LoD:

The LoD of this assay was established at 3 ifu (inclusion forming units) using a quantified whole organism control from Zeptometrix. The LoD was confirmed in all non-FDA approved specimens that will be accepted for testing with this assay (oropharyngeal/throat, ocular, and miscellaneous anogenital specimens). At least thirty clinical specimens of each source grouping were spiked with C trachomatis (CT) at 3 ifu/assay. Results are as follows:

 

Specimen

Type

LoD

Number Positive

(Number tested)

% Positive

Oral/Throat

3 ifu

36 (36)

100

Ocular

3 ifu

32 (32)

100

Anogenital

3 ifu

31 (31)

100

Peritoneal fluid

3 ifu

30 (30)

100

 

According to the package insert, the LoD for detection of C trachomatis (CT) using FDA-approved specimens and collection devices is 1 ifu per assay, with a range of 3 to 0.1 ifu per assay. Therefore, the LoD for non-FDA approved specimens falls within this range and is considered acceptable.

 

Analytical Specificity:

To augment the specificity panel performed by GEN-PROBE as outlined in the APTIMA product insert, an additional panel was tested by the GEN-PROBE Tigris DTS System using the APTIMA COMBO 2 Assay. Negative patient matrix specimens collected in GEN-PROBE collection devices were spiked with specificity panel organisms and tested. Organisms were chosen based on their ability to cause disease similar to C trachomatis, or be normal flora in non-FDA approved specimen sources. The assay did not cross-react with any members of the specificity panel.

Clinical Reference Recommendations for in-depth reading of a clinical nature

1. Centers for Disease Control and Prevention. 2014. Recommendations for the laboratory-based detection of chlamydia trachomatis and neisseria gonorrhoeae, 2014. MMWR Morb Mortal Wkly Rep 2014;63:1-18

2. Centers for Disease Control and Prevention: Sexually Transmitted Diseases Treatment Guidelines, 2010. MMWR Morb Mortal Wkly Rep 2010;59:RR12

3. Crotchfelt KA, Pare B, Gaydos C, Quinn TC: Detection of Chlamydia trachomatis by the GEN-PROBE AMPLIFIED Chlamydia trachomatis Assay (AMP CT) in urine specimens from men and women and endocervical specimens from women. J Clin Microbiol 1998 Feb;36(2):391-394

4. Gaydos CA, Quinn TC, Willis D, et al: Performance of the APTIMA Combo 2 assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in female urine and endocervical swab specimens. J Clin Microbiol 2003 Jan;41(1):304-309

5. Chernesky MA, Jang DE: APTIMA transcription-mediated amplification assays for Chlamydia trachomatis and Neisseria gonorrhoeae. Expert Rev Mol Diagn 2006 Jul;6(4):519-525