Interlaboratory agreement study of a double set of PCR plasmid primers for detection of Chlamydia trachomatis in a variety of genitourinary specimens

Differentiation of Chlamydia trachomatis lymphogranuloma venereum-related serovars from other serovars using multiplex allele-specific polymerase chain reaction and high-resolution melting analysis

Lymphogranuloma venereum (LGV) is a sexually transmitted infection caused by Chlamydia trachomatis serovars L1, L2 and L3. Consequently, more specific and sensitive detection methods that are rapid and inexpensive are necessary to differentiate between C. trachomatis serovars. The purpose of this study was to identify and differentiate LGV-related C. trachomatis serovars from rectal swabs using high-resolution melting analysis (HRMA) and multiplex allele-specific polymerase chain reaction (MAS-PCR). Fifteen clinical samples from patients in Sydney were first screened and confirmed as C. trachomatis by using the COBAS®AMPLICOR PCR analyser. The same samples were assayed for C. trachomatis and LGV by HRMA and MAS-PCR of the polymorphic membrane protein H ( pmpH) gene. Both methods indicated that two of 15 samples were serovar L2 and the remainder (13/15) other C. trachomatis serovars. Both HRMA and MAS-PCR are inexpensive, rapid, easy methods that are useful tools for the identification of LGV in clinical and research laboratories.

Use of PCR and reverse line blot hybridization assay for rapid simultaneous detection and serovar identification of Chlamydia trachomatis

The aim of this study was to develop and evaluate multiplex and nested PCR-reverse line blot (RLB) hybridization assays for detection and serovar identification of Chlamydia trachomatis. Two sets of primers targeting the VD2 region of the omp1 gene and one set targeting the cryptic plasmid were designed for use in multiplex (both targets) and nested PCR (omp1 only). For the RLB assay, labeled omp1 amplicons were hybridized to a membrane containing probes specific for 15 C. trachomatis serovars. The assays were used to test 429 clinical specimens, which had been previously tested for C. trachomatis using the COBAS AMPLICOR system. Specimens were tested without knowledge of the COBAS AMPLICOR result. Of 205 specimens that were positive by COBAS AMPLICOR, 201 (98%) were positive by multiplex PCR-RLB and 188 (92%) were also positive by omp1 nested PCR-RLB. In addition, three of 224 COBAS AMPLICOR-negative specimens were positive by omp1 nested PCR-RLB. One hundred sixty-six of 191 (87%) specimens in which C. trachomatis serovars were identified contained only one serovar and 25 (13%) contained two or three serovars. Serovars D, E, and F were found in 31 (16%), 83 (43%), and 51 (27%) specimens, respectively. Serovar E (41%) was the most commonly identified single serovar. Serovars J and K were found alone uncommonly (<2% each), but 18 of 25 (72%) specimens with multiple C. trachomatis serovars contained one or both (10 specimens) of these serovars. The nested (ompI) PCR-RLB is a specific and sensitive method for simultaneous detection and serovar identification of C. trachomatis, which can reliably identify mixed C. trachomatis serovars. It is suitable for use in epidemiological studies.

Application of nucleic acid amplification in clinical microbiology

The use of nucleic acid amplification methods in routine clinical microbiology laboratories is becoming increasingly widespread. The theory of polymerase chain reaction is described, including discussion of suitable microbal targets, extraction of nucleic acid from clinical samples, choice of primers, optimization of the process, laboratory design, contamination, and other problems as well as quality control. Other nucleic acid amplification methods such as ligase chain reaction, self-sustained sequence replication, strand displacement amplification, and branched DNA signal amplification are described and the choice of technology is discussed.

An algorithm to detect Chlamydia trachomatis by polymerase chain reaction on specimens extracted for enzyme immunoassay

Amplification assays for detecting Chlamydia trachomatis have been shown to be more sensitive than enzyme immunoassay (EIA) by many investigators. In this study, we have developed an algorithm for performing PCR (COBAS AMPLICOR) on selected specimens extracted for EIA (ACCESS) with sample-to-cutoff (s/co) values between 0.25 and 0.99. Furthermore, we have shown that these specimens can be utilized for PCR without encountering any inhibition problems. In our investigation, 230 out of 6,558 urethral and cervical swabs submitted for C. trachomatis screening by EIA over a period of 9 months, had s/co values ranging between of 0.25 and 0.99. Ninety (39.1%) of these specimens tested positive by PCR. These specimens were stable and gave reproducible PCR results before and after storage for a period of 9 months. This testing algorithm offers an effective way of detecting C. trachomatis with selective use of PCR while increasing the sensitivity of the EIA screening system.

Multiplex AMPLICOR PCR screening for Chlamydia trachomatis and Neisseria gonorrhoeae in women attenting non-sexually transmitted disease clinics. The European Chlamydia Epidemiology Group

A new PCR kit (AMPLICOR CT/NG; Roche Diagnostic Systems, Inc., Branchburg, N.J.) was used as a screening tool for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae in first-void urine (FVU) specimens from 3,340 asymptomatic women attending European health care units for contraceptive advice or pregnancy termination. All samples were kept frozen (-20 degrees C) prior to testing. Chlamydia-positive samples were retested once by the plasmid-based PCR kit and also by a major outer membrane protein (MOMP) primer-based PCR. Discrepancies were resolved by using the direct immunofluorescence test (DIF) with the centrifuged sediment of the FVU specimens. Samples positive for N. gonorrhoeae were retested by chromosomal primer-based PCR and verified by a 16S RNA PCR. Of the samples tested, 1.8% were considered inhibitory by using the internal amplification control. Of 81 samples positive for C. trachomatis, 74 samples were positive by both plasmid- and MOMP-based PCRs, 6 samples were positive by plasmid-based PCR and DIF, and one sample was positive by both MOMP-based PCR and DIF. Nine samples (0.3%) were positive for N. gonorrhoeae by the chromosomal primer-based PCR; however, none of the results could be confirmed. The test offers the unique ability to identify inhibition of amplification with the optional internal control.

The use of a polymerase chain reaction assay for the detection of bovine herpesvirus 1 in semen during a natural outbreak of infectious bovine rhinotracheitis

Nasal swabs from two bulls at an artificial insemination (AI) station were submitted to our laboratory. The animals showed clinical signs of Infectious bovine rhinotracheitis (IBR), although the station was supposedly free of bovine herpesvirus 1 (BHV1). DNA of BHV1 was detected using a polymerase chain reaction (PCR). Subsequently nasal swabs from 100 animals that could have been in contact were submitted. BHV1 DNA was detected in swabs from 23 animals. Using the PCR, BHV1 could only be detected in a limited number of semen samples over a period of two months prior to the outbreak or two months after the outbreak. Also, not all animals that shed BHV1 from the nose harboured detectable BHV1 in the semen. Finally BHV1 was detected in the semen of one bull, approximately six weeks before seroconversion. Presently the PCR is being used as a means of quality control of fresh semen from bulls that are seropositive for BHV1. We are able to produce a result within 6 h after the semen samples have been submitted, allowing the AI-station manager to take measures before semen distribution in the event of a positive reaction. So far 11 out of 318 samples were shown to contain BHV1 DNA. In order to be able to interpret these results an interlaboratory comparative study is proposed. In countries endemically infected with BHV1 the PCR can be a cost-effective method to minimize the risk of transmitting virus by semen.

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.

Detection of Chlamydia trachomatis by a ligase chain reaction amplification method

BACKGROUND AND OBJECTIVES

The ligase chain reaction is an in vitro DNA amplification technique that exponentially amplifies selected DNA sequences.

GOAL

To evaluate a ligase chain reaction assay for the detection of Chlamydia trachomatis cryptic plasmid DNA (LCx Chlamydia) in patients routinely attending a sexually transmitted disease center in Italy.

STUDY DESIGN

Urethral or cervical swabs were obtained from 501 consecutive patients (334 men and 167 women). The samples were assayed in parallel with LCx Chlamydia and conventional tissue culture; discordant results were further assayed by direct immunofluorescence and a ligase chain reaction with alternate primers.

RESULTS

After resolution of discordant results, the LCx method showed a sensitivity, specificity, positive predictive value, and negative predictive value of 100%, 99.3%, 96.7%, and 100% in men; 100%, 100%, 100%, and 100% in women; and 100%, 99.5%, 97.1%, and 100% overall, respectively. By comparison, the sensitivity of tissue culture was 81.4% in men, 50% in women, and 77.6% overall.

CONCLUSIONS

The automated LCx method is sensitive, fast, and accurate and represents a useful diagnostic tool for C. trachomatis infection, even in low and medium prevalence populations.

Chlamydia infection in street youth: Need for more aggressive screening programs

OBJECTIVES

To determine, first, the sexual practices among street youth in the Ottawa-Carleton, Ontario region; second, the percentage of street youth who report previous sexually transmitted disease (STD) screening; and third, the rate of previous infection with Chlamydia trachomatis in this population.

METHODS

This prospective street youth pilot study was cross-sectional in design. Street youth aged 15 to 20 years were recruited through a drop-in centre or shelter in Ottawa, Ontario between August and October 1993. Information on demographics, substance use, current sexual practices and STD screening and infection history were obtained through a structured face to face interview and a 75-item questionnaire. Past C trachomatis infection was determined by microimmunofluorescence assay with purified antigens of C trachomatis (serovars A to K), Chlamydia psittaci (avian strain 6BC) and Chlamydia pneumoniae (TW-183 strain).

RESULTS

Ninety-eight per cent of the youth approached participated. Of the 100 street youth (61 males, mean age 17.8 years; 39 females, mean age 17.1 years), 94% were sexually active, with 21% of males and 26% of females having had four or more different sexual partners in the previous year. Only 27% of males and 8% of females reported consistent condom use with all partners all of the time. Thirty per cent of males and 50% of females reported previous STD testing. Of the 100 street youth, 22 (16 males and six females) had had previous C trachomatis infection by serotesting, but only three of 16 (19%) of these males and three of six (50%) of these females reported previous STD testing. None of the 22 recalled previous diagnosis or treatment for any STD.

CONCLUSIONS

These street youth reported a high prevalence of risky sexual behaviour, and this supports the national STD guidelines for targeted screening in this population. The current screening guidelines for C trachomatis in this population do not reach the majority of street youth.

Comparison of PCR/nucleic acid hybridization and EIA for the detection of Chlamydia trachomatis in different populations in a regional centre

Culture on McCoy cell monolayers has been accepted as the reference method for the detection of Chlamydia trachomatis. Recent studies have shown that polymerase chain reaction (PCR)/nucleic acid hybridization based methods have increased sensitivity over culture while still retaining specificity. In situations where organism viability is of concern, due to factors such as transportation delays, culture is inappropriate. Regional laboratories therefore have not been able to utilize the reference method and have been forced to use less reliable methods. The aims of our study were to assess the feasibility of performing PCR to diagnose infections due to C. trachomatis in a regional laboratory using a new commercial kit--Amplicor (Roche Molecular Systems, Branchburg, NJ) and to compare the current enzyme-immunoassay (EIA) based-methods used in our laboratory (VIDAS [bioMerieux Vitek, Hazelwood MO] and IDEIA [Novo Nordisk Diagnostics, Cambridge, UK]) against PCR. Thirteen positive Amplicor specimens were found in 267 urine specimens collected from asymptomatic adolescent males and females. All 13 were confirmed positive using major outer membrane protein gene PCR (MOMP). VIDAS and IDEIA showed 100% correlation to each other but only detected 5/13 positives. Of 140 consecutive patients attending the regional sexual health clinic, 13 were Amplicor positive, 11/13 MOMP positive and 10/13 positive by VIDAS. Five of 254 patients attending the hospital antenatal clinic were positive by Amplicor, all being confirmed by MOMP. No PCR inhibition was detected in a random sample of 100 varied negative Amplicor tests using a modification of the Amplicor kit. No contamination was experienced. The Amplicor kit was shown to be suitable for use in the routine clinical laboratory with minimal disruption to workflow. For regional laboratories this kit should provide more accurate results than EIA based methods, particularly in the detection of asymptomatic persons.

Diagnosis of genital Chlamydia trachomatis infections in asymptomatic males by testing urine by PCR

An enzyme-linked immunosorbent assay (EIA) (MikroTrak; Syva) was compared with PCR (Amplicor; Roche) for detection of Chlamydia trachomatis in first-void urine (FVU) from 184 men attending a skin and venereal disease clinic. The prevalence of C. trachomatis in the population studied was 18.5%. Discrepant results between Syva EIA and Roche PCR were retested by using major outer membrane protein primer-based PCR. After retesting, the sensitivity, the specificity, and the positive and negative predictive values for the Syva EIA were 85.3, 100, 100, and 77.5%, respectively, and those for the Roche PCR 100, 100, 100, and 100%, respectively. It was concluded that PCR provides a highly sensitive and specific noninvasive screening method for genital chlamydial infection in asymptomatic men.

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.