Use of a commercial PCR kit for detecting Chlamydia trachomatis

Prevalence of Chlamydia infection among women visiting a gynaecology outpatient department: evaluation of an in-house PCR assay for detection of Chlamydia trachomatis

Background

Screening women for Chlamydia trachomatis infection in developing countries is highly desirable because of asymptomatic infection. The existing diagnostic methods in developing countries are not effective and their sensitivity fall below 45.0% which leads to further spread of infection. There is an urgent need for improved and cost effective diagnostic tests that will reduce the burden of sexually transmitted infections in the developing world.

Methods

Prevalence of C. trachomatis infection among women visiting gynaecology department of Hindu Rao hospital in Delhi, India was determined using Roche Amplicor Multi Well Plate kit (MWP) as well as using in-house PCR assay. We used 593 endocervical swabs for clinical evaluation of the in-house developed assay against Direct Fluorescence Assay (DFA; Group I n = 274) and Roche Amplicor MWP kit (Group II, n = 319 samples) and determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) of the in-house developed assay.

Results

We detected 23.0% positive cases and there was a higher representation of women aged 18-33 in this group. An in-house PCR assay was developed and evaluated by targeting unique sequence within the gyrA gene of C. trachomatis. Specificity of the reaction was confirmed by using genomic DNA of human and other STI related microorganisms as template. Assay is highly sensitive and can detect as low as 10 fg of C. trachomatis DNA. The resolved sensitivity of in-house PCR was 94.5% compared with 88.0% of DFA assay. The high specificity (98.4%) and sensitivity (97.1%) of the in-house assay against Roche kit and availability of test results within 3 hours allowed for immediate treatment and reduced the risk of potential onward transmission.

Conclusions

The in-house PCR method is cost effective (~ 20.0% of Roche assay) and hence could be a better alternative for routine diagnosis of genital infection by C. trachomatis to facilitate improved screening and treatment management.

Comparison of an in-house PCR assay, direct fluorescence assay and the Roche AMPLICOR Chlamydia trachomatis kit for detection of C. trachomatis

To improve the control of Chlamydia trachomatis infection in India, a rapid, specific and cost-effective method is much needed. We developed an in-house PCR assay by targeting a unique genomic sequence encoding a protein from the C. trachomatis phospholipase D endonuclease superfamily that produces an amplified fragment of 368 bp. The specificity of the primers was confirmed using genomic DNA from other sexually transmitted disease-causing and related micro-organisms and from humans. The assay was highly sensitive and could detect as low as 10 fg C. trachomatis DNA. Clinical evaluation of the in-house-developed PCR was carried out using 450 endocervical specimens that were divided in two groups. In group I (n=274), in-house PCR was evaluated against the direct fluorescence assay. The resolved sensitivity of the in-house PCR method was 97.22 % compared with 88 % for the direct fluorescent antibody assay. In group II (n=176), the in-house PCR was compared with the commercial Roche AMPLICOR MWP CT detection kit. The resolved sensitivity of the in-house PCR assay reported here was 93.1 % and the specificity was 97.46 %, making it a cost-effective alternative for routine diagnosis of genital infection by C. trachomatis. The method should facilitate early detection leading to better prevention and treatment of genital infection in India.

Strategies for control of trachoma: observational study with quantitative PCR

BACKGROUND

Antibiotics are an important part of WHO's strategy to eliminate trachoma as a blinding disease by 2020. At present, who needs to be treated is unclear. We aimed to establish the burden of ocular Chlamydia trachomatis in three trachoma-endemic communities in Tanzania and The Gambia with real-time quantitative PCR.

METHODS

Conjunctival swabs were obtained at examination from 3146 individuals. Swabs were first tested by the qualitative Amplicor PCR, which is known to be highly sensitive. In positive samples, the number of copies of omp1 (a single-copy C trachomatis gene) was measured by quantitative PCR.

FINDINGS

Children had the highest ocular loads of C trachomatis, although the amount of pooling in young age groups was less striking at the site with the lowest trachoma frequency. Individuals with intense inflammatory trachoma had higher loads than did those with other conjunctival signs. At the site with the highest prevalence of trachoma, 48 of 93 (52%) individuals with conjunctival scarring but no sign of active disease were positive for ocular chlamydiae.

INTERPRETATION

Children younger than 10 years old, and those with intense inflammatory trachoma, probably represent the major source of ocular C trachomatis infection in endemic communities. Success of antibiotic distribution programmes could depend on these groups receiving effective treatment.

Detection of Chlamydia trachomatis in genital swabs: comparison of commercial and in house amplification methods with culture

AIMS

To evaluate the sensitivity of the Roche Cobas, Roche Amplicor plate kit, ligase chain reaction (LCR), and an in house polymerase chain reaction (PCR) by titration of purified elementary bodies (EB) and also to test 245 urethral and endocervical specimens for Chlamydia trachomatis by the four assays as well as conventional culture.

STUDY DESIGN

EB titrations were run in duplicate in each commercial assay and six times in the in house PCR. Clinical samples were aliquoted and tested by each assay and were considered positive if C trachomatis was detected by two or more separate tests or if the sample was either culture or immunofluorescence positive. Major outer membrane protein (MOMP) specific primers were used as a confirmatory assay for the in house PCR.

RESULTS

The in house PCR, Roche Cobas Amplicor, LCR, and Amplicor plate kit gave detection limits of approximately 1, 1-2, 2, and 2-4 EBs respectively. By the criteria described above for definition of a C trachomatis positive result in clinical samples we identified 23 true positives among the 245 clinical specimens. The in house PCR detected all 23 giving a sensitivity of 100% and a specificity of 98%. The Roche Cobas Amplicor, Roche Amplicor plate kit, and LCR detected 21, 19, and 19 of these respectively giving sensitivities of 87.5%, 82%, and 82% respectively and specificities of 99.5%, 99%, and 100% respectively. The culture gave a sensitivity of 78% and specificity of 100%.

CONCLUSION

All four amplification assays had a greater sensitivity than the culture used routinely in this laboratory. The in house plasmid PCR had the greatest sensitivity and when combined with confirmation by immunofluorescence detected the greatest number of positives. This increased sensitivity is likely to have been achieved by the use of a DNA purification step and of nested primers in the amplification stage and their combined use in routine diagnostic assays for chlamydia might increase the frequency of C trachomatis detections. However, this assay is much less user friendly than the two semiautomated commercial assays investigated in this study.

Use of a single swab in multi-microbe or flex trans transport medium for detection of Chlamydia trachomatis by Roche Amplicor PCR and culture in specimens from two different patient populations

The Roche Amplicor PCR increased the detection of Chlamydia trachomatis compared with culture in promptly processed clinical specimens from a local clinic (100 and 86.5%, respectively) and in samples with delayed processing transported from distant facilities (100 and 72.7%, respectively). A single swab collected in culture transport medium was used. Two media, Multi-Microbe and Flex Trans, were tested and found to be equally acceptable.

Differences in the sensitivity of the Amplicor Chlamydia trachomatis PCR assay

PURPOSE

To evaluate the use of the Amplicor PCR assay in two European centres (Amsterdam and Vienna) as a standard for amplification assays in comparative studies.

STUDY DESIGN

Both centres used the Amplicor PCR assay and their own standard diagnostic methods as the reference assay. Discrepant results were further analysed by an Omp1-PCR assay. In total 805 female patients and 614 male patients were included in the studies.

RESULTS

The prevalence of Chlamydia trachomatis infections in female patients was 10.0% in Amsterdam and 2.5% in Vienna and in male patients 13.7% and 10.8%, respectively. The mean sensitivity of the Amplicor PCR assay with cervical specimens from female patients was 92.5% and the mean specificity was 99.2%. For the reference assays the mean values were 87.5% and 100.0% respectively. The mean sensitivity of the Amplicor PCR assay with urine specimens from male patients was 70.3% and the mean specificity was 97.6%. For the reference assays these values were 64.9% and 100.0% respectively. The mean sensitivity of the Amplicor PCR assay with urethral specimens from male patients was 67.6% and the mean specificity was 98.5%. For the reference assays these values were 62.2% and 100.0% respectively. Of all specimens together, 1.0% showed an OD value between 0.25 and 0.5 in the Amplicor PCR assay and had to be retested. The sensitivity of the Amplicor PCR assay was less than could be expected from previous studies comparing amplification assays under similar conditions. Also, the sensitivity of the Amplicor PCR assay varied considerably between study centres using urine specimens from male patients-45.9% and 94.6%, respectively.

CONCLUSION

The Amplicor PCR assay cannot be considered as a standard for amplification assays in comparative studies.

Rapid and simple diagnosis of the two common alpha 1-proteinase inhibitor deficiency alleles Pi*Z and Pi*S by DNA analysis

We describe a simple DNA-based method to assign the two common alpha 1-proteinase inhibitor (alpha 1-antitrypsin) deficiency alleles in the Pi-system (Pi*Z and Pi*S). Two sets of mutated primers are used in the polymerase chain reaction (PCR), followed by a restriction enzyme digest of the products. The mutated forward primers create a Taq I site only if the wildtype alleles (mostly M or subtypes) are present and not in the presence of the Pi*Z or Pi*S alleles. The reverse primers are mutated for an invariant Taq I site which serves as an internal control site in order to assure the completion of the restriction enzyme digest. The digested PCR products can be clearly resolved by 2.5% MetaPhore-agarose gel electrophoresis. This simple PCR probing of the most common alpha 1-antiproteinase deficiency alleles can be routinely applied either to samples showing quantitatively decreased alpha 1-antiproteinase values in serum or to blood spots of Guthrie cards used for mass screening purposes. In addition, this method may provide the opportunity for a simple, rapid, and reliable prenatal diagnosis of alpha 1-antiproteinase deficiency in special cases.

Periodic health examination, 1996 update: 2. Screening for chlamydial infections. Canadian Task Force on the Periodic Health Examination

OBJECTIVE

To update the 1984 recommendations of the Canadian Task Force on the Periodic Health Examination on the routine screening of asymptomatic patients for infection with Chlamydia trachomatis.

OPTIONS

Screening, with the use of culture or nonculture tests, of the general population, of certain high-risk groups or of all pregnant women; or no routine screening.

OUTCOMES

Rates of asymptomatic and symptomatic chlamydial infection, perinatal complications, longterm complications of infection (i.e., pelvic inflammatory disease, infertility and ectopic pregnancy), coinfection with other sexually transmitted diseases, disease spread, hospital care, complications of therapy and costs of infection and of screening.

EVIDENCE

Search of MEDLINE for articles published between Jan. 1, 1983, and Dec. 31, 1995, with the use of the major MeSH heading "chlamydial infections," references from recent review articles and recommendation by other organizations.

VALUES

The evidence-based methods of the Canadian Task Force on the Periodic Health Examination were used. Advice from reviewers and experts and recommendations of other organizations were taken into consideration. Prevention of symptomatic disease and decreased overall costs were given high values.

BENEFITS, HARMS AND COSTS

The greatest potential benefits of screening asymptomatic patients for chlamydial infections are the prevention of complications, especially infertility and perinatal complications, and the prevention of disease spread. There is no evidence that screening of the general population for chlamydial infections leads to a reduction in complications, and screening may increase costs. However, there is evidence that annual screening of selected high-risk groups and of pregnant women during the first trimester is beneficial in preventing symptoms and reducing the overall cost resulting from infection.

RECOMMENDATIONS

There is fair evidence to support screening and treatment of pregnant women during the first trimester (grade B recommendation) as well as annual screening and treatment of high-risk groups (sexually active women less than 25 years of age, men or women with new or multiple sexual partners during the preceding year, women who use nonbarrier contraceptive methods and women who have symptoms of chlamydial infection: cervical friability, mucopurulent cervical discharge or intermenstrual bleeding; grade B recommendation). There is fair evidence to exclude routine screening of the general population (grade D recommendation).

VALIDATION

These recommendations are similar to those of the US Preventive Services Task Force and the US Centers for Disease Control and Prevention, Atlanta.

SPONSOR

These guidelines were developed and endorsed by the Canadian Task Force on the Periodic Health Examination, which is funded by Health Canada and the National Health Canada and the National Health Research and Development Program. The principal author (H.D.D.) was supported in part by the Ontario Ministry of Health and the Canadian Infectious Diseases Society Lilly Fellowship.

Evaluation of a commercial polymerase chain reaction assay for Chlamydia trachomatis and suggestions for improving sensitivity

A commercial polymerase chain reaction (PCR) assay (Amplicor, Roche) for Chlamydia trachomatis was compared with a direct fluorescent antibody (DFA) test using urethral and cervical samples, many of which on the basis of prior testing by DFA contained small rather than large numbers of elementary bodies. Urine samples were collected from patients in a sequential unselected manner. Of 244 clinical specimens (138 male urethral and cervical; 106 male and female urine), 66 were positive by both DFA and PCR and 141 were negative by both tests. Nine samples were DFA negative and PCR positive, and 28 samples were DFA positive and PCR negative. However, 24 (86%) of the latter samples contained fewer than ten elementary bodies. When serial dilutions of laboratory stock strains (serovars E and H) were tested, the DFA test detected Chlamydia trachomatis at a dilution tenfold greater than the PCR. Furthermore, of five DFA-positive clinical samples, three that were PCR negative when tested according to the manufacturer's instructions were positive when they were diluted less. A modification of the PCR assay along these lines might improve sensitivity.

Comparison of antigen detection, polymerase chain reaction and culture for detection of Chlamydia trachomatis in genital infection

An in-house polymerase chain reaction (PCR) test using ribosomal RNA gene primers was compared with chlamydia antigen detection (DIF) and culture for the detection of Chlamydia trachomatis. Five hundred and forty-eight fresh (unstored) genital swabs and 174 urines (collected at the same time) from patients attending a sexually-transmitted diseases clinic were examined. PCR, DIF and culture detected chlamydia in 43, 35 and 42 swabs respectively from the 43 resolved positive cases. The specificity on the resolved negative specimens was 100% for each of the tests. From the urines, PCR and DIF detected the organism in 16 and 15 cases respectively of the 23 resolved positive males tested but in only 2 and 3 cases respectively of the 9 resolved positive females tested. Specificities were 100% in all cases. Both of the non-culture tests manifested problems with urine due to inhibitory activity (in PCR test) or excessive debris (in DIF test) in about 5% of the specimens. Culture of the urines yielded sensitivities of 40% in the males and 22% in the females. Overall PCR was more sensitive than either culture or DIF on both urethral and cervical swabs and urines. The urines yielded less than three-quarters the number of positives that was obtained from the swabs and were considered to be an unsatisfactory specimen for chlamydial diagnosis. It is concluded that PCR is a satisfactory alternative to culture on genital swabs and may be preferable in situations where the viability of the organisms is in question. DIF remains useful because of its speed and simplicity but is insufficiently sensitive to be relied upon by itself.

Role of confirmatory PCRs in determining performance of Chlamydia Amplicor PCR with endocervical specimens from women with a low prevalence of infection

The role of confirmatory PCR assays for determining the performance of Chlamydia Amplicor PCR for endocervical specimens from women with a low prevalence of infection was evaluated. An endocervical swab was collected from 770 women and tested by culture or direct fluorescent antibody (DFA) staining. A second swab was tested by Chlamydia Amplicor PCR (Roche Molecular Systems, Branchburg, N.J.). Discordant results were resolved by three confirmatory PCRs: one targeting the plasmid by using different primers and two directed to the major outer membrane protein (MOMP) gene. Of the 30 swabs that were positive by culture or DFA (3.9%), 27 were positive by Amplicor PCR. An additional five swabs were positive by Amplicor PCR but negative by culture or DFA. Both plasmid and MOMP confirmatory PCRs identified the five culture-DFA negatives and the three Amplicor negatives as true positives. The three specimens originally classified as negative by Amplicor PCR were positive on repeat Amplicor testing. After resolution of the discordant results by confirmatory PCR testing, the sensitivity of the initial Amplicor PCR was 91.4% (32 of 35 specimens), changing to 100% after storage and repeat testing. The specificity of Amplicor PCR was 100% (735 of 735 specimens). Our results demonstrated that plasmid and MOMP confirmatory PCRs worked equally well in resolving false-positive and false-negative Amplicor PCR results. Some specimens may contain inhibitors of Amplicor PCR which may disappear with time.