Generic selectors
Exact matches only
Search in title
Search in content
Post Type Selectors
Filter by Categories
15th National Conference of the IAOMFP, Chennai, 2006
Abstracts from current literature
Acne in India: Guidelines for management - IAA Consensus Document
Art & Psychiatry
Association Activities
Association Notes
Award Article
Book Review
Brief Report
Case Analysis
Case Letter
Case Letters
Case Notes
Case Report
Case Reports
Clinical and Laboratory Investigations
Clinical Article
Clinical Studies
Clinical Study
Conference Oration
Conference Summary
Continuing Medical Education
Cosmetic Dermatology
Current Best Evidence
Current Issue
Current View
Derma Quest
Dermato Surgery
Dermatosurgery Specials
Dispensing Pearl
Do you know?
Drug Dialogues
Editor Speaks
Editorial Remarks
Editorial Report
Editorial Report - 2007
Editorial report for 2004-2005
Fourth All India Conference Programme
From Our Book Shelf
From the Desk of Chief Editor
Get Set for Net
Get set for the net
Guest Article
Guest Editorial
How I Manage?
IADVL Announcement
IADVL Announcements
IJDVL Awards
IJDVL Awards 2018
IJDVL Awards 2019
IJDVL Awards 2020
IJDVL International Awards 2018
Images in Clinical Practice
In Memorium
Inaugural Address
Knowledge From World Contemporaries
Leprosy Section
Letter in Response to Previous Publication
Letter to Editor
Letter to the Editor
Letter to the Editor - Case Letter
Letter to the Editor - Letter in Response to Published Article
Letter to the Editor - Observation Letter
Letter to the Editor - Study Letter
Letter to the Editor - Therapy Letter
Letter to the Editor: Articles in Response to Previously Published Articles
Letters in Response to Previous Publication
Letters to the Editor
Letters to the Editor - Letter in Response to Previously Published Articles
Letters to the Editor: Case Letters
Letters to the Editor: Letters in Response to Previously Published Articles
Medicolegal Window
Miscellaneous Letter
Net Case
Net case report
Net Image
Net Letter
Net Quiz
Net Study
New Preparations
News & Views
Observation Letter
Observation Letters
Original Article
Original Contributions
Pattern of Skin Diseases
Pediatric Dermatology
Pediatric Rounds
Presedential Address
Presidential Address
Presidents Remarks
Report of chief editor
Report of Hon : Treasurer IADVL
Report of Hon. General Secretary IADVL
Research Methdology
Research Methodology
Resident page
Resident's Page
Resident’s Page
Residents' Corner
Residents' Corner
Residents' Page
Review Article
Review Articles
Reviewers 2022
Revision Corner
Self Assessment Programme
Seminar: Chronic Arsenicosis in India
Seminar: HIV Infection
Short Communication
Short Communications
Short Report
Special Article
Specialty Interface
Study Letter
Study Letters
Symposium - Contact Dermatitis
Symposium - Lasers
Symposium - Pediatric Dermatoses
Symposium - Psoriasis
Symposium - Vesicobullous Disorders
Symposium Aesthetic Surgery
Symposium Dermatopathology
Symposium-Hair Disorders
Symposium-Nails Part I
Symposium-Nails-Part II
Systematic Review and Meta-Analysis
Systematic Reviews and Meta-analyses
Systematic Reviews and Meta-analysis
Therapeutic Guideline-IADVL
Therapeutic Guidelines
Therapeutic Guidelines - IADVL
Therapy Letter
Therapy Letters
View Point
What’s new in Dermatology

Translate this page into:

Original Article
PMID: 17664762

Use of polymerase chain reaction (PCR) for detection of Chlamydia trachomatis infection in cervical swab samples

Jayanti Mania-Pramanik, UM Donde, Anurupa Maitra
 Institute for Research in Reproduction (ICMR), Jehangir Merwanji Street, Parel, Mumbai - 400 012, India

Correspondence Address:
Jayanti Mania-Pramanik
Institute for Research in Reproduction (ICMR), Jehangir Merwanji Street, Parel, Mumbai - 400 012
How to cite this article:
Mania-Pramanik J, Donde U M, Maitra A. Use of polymerase chain reaction (PCR) for detection of Chlamydia trachomatis infection in cervical swab samples. Indian J Dermatol Venereol Leprol 2001;67:246-250
Copyright: (C)2001 Indian Journal of Dermatology, Venereology, and Leprology


A polymerase chain reaction (PCR) based method has been set up for detection of Chlamydia trachomatis (C. trachomatis) infection in single cervical swab samples. A primer pair specific to the major outer membrane protein (MOMP) gene common to all serotypes of C. trachomatis was used. This method was validated for its sensitivity as well as specificity. A minimum Ing of DNA could be used for detection of the infection. Specificity of the method was confirmed by carrying out a sample dilution curve. The cervical swab samples analysed in the present study were in coded form for validation of the PCR with an established commercial ELISA (Chlamydiazyme). Both the sensitivity and specificity of PCR was 100% when the ELISA results of these samples were decoded. Thus, this PCR technique could be used for better diagnosis of C. trachomatis infection in comparison to the commercially available ELISA technique.
Keywords: Chlamydia trachomatis, PCR, Cervical swab sample


Chlamydia trachomatis (C. trachomatis) infection of the lower genital tract is one of the most prevalent sexually transmitted diseases in the world. Detecting chlamydial genital infection and preventing transmission and spread of this infection to the upper reproductive tract are a challenge for both clinicians and laboratory workers.[1] Genital infections caused by C. trachomatis are often asymptomaticz and early detection to avoid serious complications is of real value since effective treatment exists. Polymerase chain reaction (PCR) has recently been introduced for detection of C. trachomatis and studies have reported its superior sensitivity in comparison with culture,[3],[4],[5],[6] enzyme - linked immunosorbent assay[3],[5] or direct flurescein-conjugated antibody (DFA) staining.[7] Information regarding incidence and prevalence of laboratory confirmed C. trachomatis infection of the genital tract in India is limited to a few studies because of lack of proper laboratory facilities.[8],[9] In India reports on the use of PCR to detect C. trachomatis infection is restricted,[9] though this technique has been successfully used in clinical specimens elsewhere. In view of the sensitivity and broad applicability, we attempted to set up, a PCR based method to detect the C. trachomatis infection among the women population using individual single cervical swab samples. Subjects included were women attending the Gynaecology Department of two different hospitals in the city viz, the King Edward Memorial Hospital (KEM) and the Sir Hurkisondas Nurrotumdas Hospital (H.N. Hospital).

Materials and Methods

Specimens: Endocervical swab samples were obtained from patients attending the Gynaecology department of KEM Hospital, Parel and Sir H.N. Hospital, Prathana Samaj, Mumbai. Each swab was put in the sample collection vial containing the buffer (1 ml) supplied with the commercially available ELISA kit (Abbott′s Diagnostics, U.S.A.). Sample of each individual was screened in the hospital laboratory (Microbiology Department of KEM & Medical Research Society of Sir H.N. Hospital) using the ELISA kit for C. trachomatis. Some of these screened samples (n=30) were collected in coded form for PCR analysis to the author′s laboratory. Five of these 30 samples had a sample volume of 700µI each whereas in others (n=25) the volume of each sample was approximately 400 µl. Decoding of the supplied samples for infection by ELISA - based method was carried out after the PCR - based detection.

Preparation of samples for PCR: Several methods are available for DNA extraction. In the present study, we used two methods i.e., alkali lysis[10] and proteinase K treatment[11] in 5 of the samples where each sample volume was 700 µl. In other 25 samples, volume of each was 400 µl and DNA was extracted in these samples using the proteinase K treatment.

Primers: One pair of oligonucleotide primers specific for a 144 by region of the C. trachomatis gene coding for the major outer membrane protein (MOMP) was selected.[12] This primer pair was procured from Bangalore Genei, Bangalore. The sequences from 5′ to 3′ of these oligonucleotide primers are as follows:



PCR mixture and DNA amplification:

For PCR, Gene Amp(R) PCR reagents from Perkin Elmer, U.S.A. with AmpliTaq(R) DNA polymerase were used. A master mixture of these reagents was made for the samples along with positive and negative controls. The final reaction mixture of 50µI for each sample contained 0.5µM each primer; 100µM each of dAP, dCTP, dGTP and dTTP; 50 mM KCI; 10 mM Tris-HCI, pH 8.3; 1.5 mM MgCI2; 0.01% gelatin and 1.25 units of DNA polymerase (Thermus aquaticus) enzyme and 9ul of sample DNA. For positive PCR control whole bacteriophage Lambda DNA template along with primers amplifying a 500 by region were used. In 50 µl of PCR mixture, 0.5 ng of positive control was used, whereas for negative control 5 µl of autoclaved distilled water was used. Each microfuge tube containing the PCR mix of 50µI was mixed and subjected to 40 cycles of amplification. Each cycle was composed of sequential incubations of 94°C for 1 minute for DNA denaturation, 52°C for 1 minute for annealing primer to these templates, and 72°C for 2 minutes for DNA chain extension. At the end of 40 cycles, samples were kept for another 7 minutes at 72°C for completion of extension of DNA chain. The PCR product samples were immediately frozen for further analysis.

Amplified product detection: Visualisation of amplified product was carried out by agarose gel electrophoresis. A 10µI of post-PCR mixture was subjected to electrophoresis on 2% agarose gel in presence of ethidium bromide. A DNA ladder was also run simultaneously to confirm size of the amplified product.

Specificity of the amplified product

To confirm the specificity, the amplified DNA product was extracted directly from 30 µl of the post-PCR solution. Extraction was carried out with a DNA binding resin, using a kit supplied by Boehringer Mannheim, USA. The isolated DNA pellet was resuspended in 20 µl of TE buffer. A portion of the suspension (15 µl) was incubated with the endonuclease EcoRl. For this purpose, a mixture of 25 µI was prepared containing 15 µl of the isolated DNA product, 2 µl of EcoR1 endonuclease (80 units), 2.5 pl of enzyme specific buffer with 5.5 µl of autoclaved distilled water. The mixture for each sample was incubated for 3 hours at 37° C and then frozen till used for detection. This digested mixture (10 µl) along with the 5 µl of the undigested isolated DNA from each sample was then subjected to 2% agarose gel electrophoresis. An appropriate DNA ladder was also run simultaneously to determine the size of the bands obtained.

Detection level of the PCR: A standard of C. trachomatis (L2 strain, Elementary bodies from Scripps Organisation, USA) was used for determination of the minimum detection level of DNA for PCR amplification. For the purpose, various quantities of DNA (range: 0.001 µg to 5 µg) were taken for amplification. The amplification product of 144 by was detected as described earlier.

Quantitation of DNA with respect to epithelial cells for calculation of cell number in analysed samples and an expected yield of DNA, each sample after collection was observed under microscope to estimate the epithelial cells present. The samples were then processed for DNA extraction. Further quantification of each DNA was done by the optical density measurement obtained at 260 nm.

Discrepant - result analysis

If a specimen produced a PCR result discrepant with the comparison test Chlamydiazyme′ following decoding, PCR was repeated along with the confirmatory test with EcoR1 digestion. If the second amplification produced a result in agreement with the comparison test, the result from the initial amplification was not taken into consideration (not encountered during this study). A repeat positive PCR result indicated a ELISA (Ch\amy6azyme) false- negative result.


Similar results were obtained when 5 of the 30 samples were processed both by alkali lysis and proteinase K methods for DNA extraction. PCR amplification using these DNA samples showed that, of the 30 samples, 23 produced the specific 144 by DNA fragment. This 144 by DNA after digestion with EcoR1, produced the 103 by fragment. The minimum amount of DNA that could be amplified for detection of the required 144 by was observed to be 1 µg. [Figure - 1] shows the PCR amplification of 144 by C. trachomatis MOMP gene along with digested product of 103 bp. A serial amplification of DNA corresponding to 16 µg to 1 µg is also presented in the [Figure - 1]. A linearity in the amplification of the expected fragment from increasing concentrations of DNA was clearly evident from the [figure]. DNA quantification and microscopic examination of samples showed that using our method, approximately 90 epithelial cells correspond to 1 µg of DNA.

Correlation with ELISA assay

The results of PCR analysis were correlated with the ELISA assay carried out in the hospitals using the ELISA "Chlamydiazyme" (Abbott′s Diagnostics, U.S.A.) and presented in [Table - 1]. By ELISA, out of 30 samples tested, 20 were found to be positive for C. trachomatxs antigen. The PCR based technique detected 3 additional samples with positive C. trachomatis infection. All these 3 PCR - positive, Chlamydiazyme negative specimens were confirmed by repeat PCR assay along with the confirmatory test of EcoR, digestion. After resolution of 3 Chlamydiazyme negative specimens that were PCR positive, the Chlamydiazyme and PCR sensitivities were 86.96% and 100% respectively, compared with the total resolved positive specimens, whereas the specificities of both Ch\amy6azyme and PCR were 100%.


Detection of Chlamydia in patient specimens by DNA amplification has expanded the spectrum of pathogens amenable to PCR. The molecular biology of the Chlamydiae is incomplete. Few genes have been sequenced and little is known of the molecular aspects of its pathogenesis. Because of its relative abundance and antigenic importance, the major outer membrane proteins (MOMPs) of several isolates of C. trachomatis have been cloned and sequenced. The MOMPs have several regions of highly conserved nucleotide sequences, which have been used for primer selection.[12] These primers allow for generation of PCR fragments spanning several regions of the MOMP gene, with an internal restriction enzyme site. The primer pair which has been chosen in this study, has been able to identify the fermalinized serotypes of C. trachomatis culture products.[13] In the present study, these primer pairs also identified the 144 by sequence of MOMP gene of C. trachomatis infection present in individual cervical swab sample. Mumbai being a metropolitan city, patients coming to different hospitals (KEM Hospital, Parel and Sir H.N, Prathana Samaj, Mumbai) belong to different ethnic and socio-economic groups. These patients originated from different States. Thus the pair of primers used could successfully identify the infection present in single cervical swab samples of these individuals with mixed socio-economic backgrounds. The three cases which were positive by PCR but negative by ELISA, were the true positive as confirmed by repeat PCR and as is also reported PCR is superior in its sensitivity to ELISA.[3],[4],[5] In the first study, it was reported that the sensitivity of ELISA (Chlamydiazyme) when compared with PCR was 60%.[3] According to the other study, when PCR was compared with a direct specimen enzyme immuno assay (Chlamydiazyme) using 375 cervical specimens, PCR had a sensitivity and specificity of 100%, while the ELISA had a sensitivity of 58.8% and a specificity of 100%.[5] In the observation, both the sensitivity and specificity of the PCR is 100%, while the ELISA has a sensitivity of 86.96% and specificity of 100%.The choice of a reference method, when the true disease status is unknown is difficult. Since gene amplification methods are usually more sensitive than traditional methods like culture, ELISA, DFA, the use of these traditional methods as reference methods is not appropriate.[14] In the present study, the PCR results have been compared here with ELISA, as this was readily available and facility for culture or DFA were not available.

To achieve optimum sensitivity of the PCR assay, one has to emphasize the cycle number and quality of sample collected. In the present study, PCR was carried out for 40 cycles, so that any sample with low number of C. trachomatis genome could be optimally amplified for visualisation. Attention had been given on the quality of specimens collected.

This is an equally important aspect which has been given little attention compared to the tremendous amount of energy, time and money that has been spent on improving Chlamydia detection test.[15] In the present attempt, it was observed that sufficient number of epithelial cells should be present in the sample collected for DNA extraction and amplification. Sample dilution curve using different concentration of DNA showed that 1 µg is the minimum amount of DNA that could be used for amplification of the desired 144 by fragment. This corresponds to an approximately 90 epithelial cells present in the sample.

Direct and indirect costs due to Chlamydial infections are substantial and justify the screening with the use of a high performance diagnostic test like PCR.[16] Present observation demonstrates that C. trachomatis can be detected by this PCR-based method in Indian population with a greater sensitivity than ELISA, from cervical swabs in properly collected samples using an appropriate cycle number. It offers hope for more accurate diagnosis, which would lead to a better control of this infection and to a better prevention of pelvic inflammatory disease, ectopic pregnancies and tubal infertility.


The authors are grateful to Microbiology Department of KEM Hos-pital and Medical Research Society of Sir Hurkisondas Nurrotumdas Hospital, Prathana Samaj, Mumbai for providing the selected samples to carry out the assay. We acknowledge the constant support of Dr. H.S. Juneja, Director of this Institute for developing this.

Barnes RC. Laboratory diagnosis of human chlamydial infections. Clin Microbiol Rev 1989; 2 : 119-136.
[Google Scholar]
Schachter J. Chlamydia trachomatis infection : epidemiology and disease spectrum. Rec Adv Sex Transm Dis 1986 ; 3: 39-58.
[Google Scholar]
Osewaarde JM, Rieffe M, Rozenberg-Arska M, et al. Development and clinical evaluation of polymerase chain reaction tests for detection of Chlamydia trachomatis. J Clin Microbiol 1992; 30 : 2122-2128.
[Google Scholar]
Bass CA, Jungkind DL, Silverman NS, et. Clinical evaluation of a new polymerase chain reaction assay for detection of Chlamydia trachomatis in endocervical specimens. J Clin Microbiol 1993;31 2648-2653.
[Google Scholar]
Loeffelholz MJ, Lewinski CA, Silver SR, et al. Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction. J Clin Microbiol 1992;30 : 2847-2851.
[Google Scholar]
Kessler HH, Pierer K, Stuenzner D, et al. Rapid detection of Chlamydia trachomatis in conjunctival, pharyngeal and urethral specimens with a new polymerase chain reaction assay. Sex Trans Dis 1994;21: 191-195.
[Google Scholar]
Bobo L, Munoz B, Viscidi R, et al Diagnosis of Chlamydia trachomatis eye infection in Trnzania by polymerase chain reaction/ enzyme immumoassay. Lancet 1991;338 : 847-850.
[Google Scholar]
Sharma M, Nayak N, Malhotra S, et al. Chlamydiazyme test for rapid detection of Chlamydia trachomatis. Ind J Res 1989;89:87-91.
[Google Scholar]
Sapathy G, Mohanty S, Pani SP, et al.Chlamydia trachomatis in hydrocele fluid. Genitourin Med 1997; 73 : 503-505.
[Google Scholar]
Frost EH, Deslandes S, Bourgaux-Ramoisy D. Sensitive detection and typing of Chlamydia trachomatis using nested polymerase chain reaction. Genitourin Med 1993; 69: 290-294.
[Google Scholar]
Witkin SS, Jeremias 3, Toth M, et al. Detection of Chlamydia trachomatis by the polymerase chain reaction in the cervices of women with acute salpingitis. Am Obstet Gynecol 1993;168:1438-1442.
[Google Scholar]
Stephens RS, Sanchez-Pescador R, Wagar EA, et al. Diversity of Chlamydia trachomatis major outer membrane protein genes. J Bacteriol 1987 ; 169 : 3879-3885.
[Google Scholar]
Holland SM, Gaydos CA, Quinn TC. Detection and differentiation of Chlamydia trachomatis,Chlamydia psittaci and Chlamydia pneumoniae by DNA amplification.) Infec Dis 1990;162 : 984-987.
[Google Scholar]
Ossewaarde IM, van Doornum GJJ, Buimer M. Differences in the sensitivity of the Amplicor Chlamydia trachomatis PCR assay. Genitourin Med 1997;73 : 207-211.
[Google Scholar]
Taylor-Robinson D. Evaluation and comparison of tests to diagnose Chlamydia trachomatis genital infections. Hum Reprod 12 Natl Suppl. 1997; JBFS 2 : 113-120.
[Google Scholar]
Paavonen J. Is screening for Chlamydia trachomatis infection cost effective? Genitourin Med 1997;73 : 103-104.
[Google Scholar]
Show Sections