Rapid genotyping of theChlamydia trachomatismajor outer membrane protein by the polymerase chain reaction

Laboratory Methods in Molecular Epidemiology: Bacterial Infections

In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.

Sexually transmitted rectal infections in a cohort of 'men having sex with men'

PURPOSE

We assessed the prevalence and predictors of Chlamydia trachomatis, Neisseriagonorrhoeae and Mycoplasmagenitalium rectal infections in a population of 'men having sex with men' (MSM).

METHODOLOGY

From January to November 2017, 165 MSM attending a STI outpatients clinic in Bologna (Italy) and reporting unsafe anal intercourses were enrolled. An ano-rectal swab was collected from each patient: chlamydial and gonococcal infections were diagnosed by a commercial NAAT, whereas an in-house quantitative PCR was used for M. genitalium detection. In addition, 131 urine samples and 84 pharyngeal swabs underwent testing for C. trachomatis and N. gonorrhoeae. A molecular C. trachomatis typing, a serological screening for anti-Chlamydia IgG and IgA, as well as the assessment of HIV, HCV and syphilis infections, were performed.Results/Key findings. The prevalence of C. trachomatis, N. gonorrhoeae and M. genitalium rectal infections was 27.2, 25.4 and 4.8 %, respectively. Globally, 63.1 % of cases were asymptomatic and up to 80 % of chlamydial and gonococcal infections would have been missed if the rectal site had not been tested. All the patients with rectal M. genitalium carriage were asymptomatic and characterized by low bacterial loads (<2500 DNA copies/reaction). Lymphogranuloma venereum (LGV) prevalence was 12.1 % with a considerable proportion of asymptomatic infections (35 %). The presence of symptoms, age >30, HIV-positivity and elevated levels of anti-Chlamydia antibodies were the most significant predictors of LGV.

CONCLUSIONS

Sexually transmitted rectal infections are frequent and often asymptomatic among MSM. LGV prevalence is high in our country and there is increasing evidence of symptomless cases.

Frequency and genotypes of Chlamydia trachomatis in patients attending the obstetrics and gynecology clinics in Jalisco, Mexico and correlation with sociodemographic, behavioral, and biological factors

BACKGROUND

Chlamydia trachomatis is the causative agent of the most common bacterial sexually transmitted infection worldwide. The aim of this study was to investigate the frequency and genotypes of C. trachomatis in patients attending an obstetrics and gynecology clinic in Jalisco, Mexico and correlates them with sociodemographic, behavioral, and biological factors.

METHODS

C. trachomatis detection was performed in endocervical samples from 662 patients by direct fluorescence assay (DFA) and two PCR assays that amplified the phospholipase D endonuclease superfamily protein (PLDESP) and OmpA genes. Positive samples were genotyped using PCR-restriction fragment length polymorphism assays. Sociodemographic, behavioral, and biological data were collected.

RESULTS

The mean age of the study population was 31 (range, 14-78) years. C. trachomatis positivity was detected by DFA in 16.7% (n = 111), PLDESP gene amplification in 14.2% (n = 94), and OmpA gene amplification in 14.5% (n = 96) of the population. Eight C. trachomatis genotypes were detected: E (39.6%), F (29.2%), D (15.6%), K (6.3%), L2 (3.1%), G, J, and I (2.1% each). C. trachomatis infection was associated with age, marital status, pregnancy, and hormonal contraceptive use (all p = 0.01); intrauterine device use and previous premature birth (both p = 0.03); and infection during pregnancy, previous ectopic pregnancy, pelvic inflammatory disease (PID), and green vaginal discharge (all p = 0.04). C. trachomatis genotype K was more likely to be detected in women histories of ≥2 sexual partners, genotype F was more likely in pregnant women, genotype L2 was more likely in women with PID, genotype D was more likely in women who had had infection during previous pregnancies, and genotype E was more likely in those with previous ectopic pregnancies and green vaginal discharge (all p = 0.01).

CONCLUSIONS

The frequency of C. trachomatis in our population was higher than previously reported worldwide, but within the range reported for Mexico. Genotype E was detected most frequently in the study population. Infection by C. trachomatis and C. trachomatis genotypes K, F, D, and E was strongly associated with multiple sociodemographic, behavioral, and biological factors. C. trachomatis genotype L2 was detected in women with PID.

[Prevalence of Chlamydia trachomatis infection and factors with the risk of acquiring sexually transmitted infections in college students]

Chlamydia trachomatis genital infection is nowadays considered one of the most frequent causes of sexually transmitted infections (STI) in the world, mainly affecting the group of young people under 25 years old. The aim of this study was to determine the prevalence of C. trachomatis infection in newly admitted students to Universidad Nacional del Sur, Bahía Blanca, Argentina, and to evaluate the risk factors to acquire STI. For that purpose, 204 young college students with a mean age of 19 were involved in this study. Each participant delivered a sample of first-void urine and completed a questionnaire which was then submitted anonymously. The research for C. trachomatis was done on 114 valid samples through a technique of DNA amplification, whose molecular target was the gene ompA. Four cases of infection by C. trachomatis were detected with a prevalence of 3.5%. The risks factors associated to the infection were a history of 7 or more partners since the start of sexual activity and contact with a new sexual partner in the last 4 months. The prevalence of such infection reflects a moderate circulation of this microorganism in the studied population. This fact, along with some aspects shown by the questionnaire results, would characterize a population having a low risk profile for acquiring STIs. However, some other information obtained from the questionnaires gave some opposite evidence, which would alert us on the need of keeping watch, raising awareness and implementing preventive actions in this population.

Prevalence and predictors of Lymphogranuloma venereum in a high risk population attending a STD outpatients clinic in Italy

Background

We evaluated LGV prevalence and predictors in a high risk population attending a STI Outpatients Clinic in the North of Italy.

Methods

A total of 108 patients (99 MSM and 9 women), with a history of unsafe anal sexual intercourses, were enrolled. Anorectal swabs and urine samples were tested for Chlamydia trachomatis (CT) DNA detection by Versant CT/GC DNA 1.0 Assay (Siemens Healthcare Diagnostics Terrytown, USA). RFLP analysis was used for CT molecular typing.

Results

L2 CT genotype was identified in 13/108 (12%) rectal swabs. All LGV cases were from MSM, declaring high-risk sexual behaviour and complaining anorectal symptoms. Patients first attending the STI Outpatient Clinic received a significant earlier LGV diagnosis than those first seeking care from general practitioners or gastroenterologists (P = 0.0046).

LGV prevalence and characteristics found in our population are in agreement with international reports. Statistical analysis showed that LGV positive patients were older (P = 0.0008) and presented more STIs (P = 0.0023) than LGV negative ones, in particular due to syphilis (P < 0.001), HIV (P < 0.001) and HBV (P = 0.001).

Multivariate logistic regression analysis revealed that HIV and syphilis infections are strong risk factors for LGV presence (respectively, P = 0.001 and P = 0.010).

Conclusions

Even if our results do not provide sufficient evidence to recommend routine screening of anorectal swabs in high-risk population, they strongly suggest to perform CT NAAT tests and genotyping on rectal specimens in presence of ulcerative proctitis in HIV and/or syphilis-positive MSM. In this context, CT DNA detection by Versant CT/GC DNA 1.0 Assay, followed by RFLP analysis for molecular typing demonstrated to be an excellent diagnostic algorithm for LGV identification.

HIV and other sexually transmitted infections among men who have sex with men recruited by RDS in Buenos Aires, Argentina: high HIV and HPV infection

Background

The aim of this study was to estimate the prevalence of HIV and other STIs, among MSM from Buenos Aires (2007–2009).

Methods

Responding Driven Sampling was used for recruitment of MSM. Participants completed a structured web-based survey and provided biological samples.

Results

A total of 496 MSM were studied for HIV, HBV, HCV, and T pallidum infections. Chlamydia and HPV diagnoses were only performed in 98 and 109 participants, respectively. Prevalence of HIV was 17.3%, HBV 22.9%, HCV 7.5%, T pallidum 20.5%, HPV 83.5%, and C trachomatis 1.7%. In the year prior to the evaluation, 71% of the participants had had sex with men and/or trans and women (MMW) while 29% had not had sex with women (MM). Comparing MM to MMW, prevalence of HIV (30.7% vs. 11.9%, p<0.001), HBV (36.4% vs. 17.8%, p<0.001), T pallidum (32.1% vs. 15.7%, p<0.001), and HPV (88.3% vs. 70.4%, p = 0.039) were significantly higher among MM, whereas no significant differences were found for HCV and C trachomatis. The MM group had also significantly higher HIV incidence (5.60 vs. 4.28 per 100 persons-year, p = 0.032). HPV genotypes 16, 6, and 11 were the most frequently found; 40.7% of the MSM had more than one genotype and one high risk genotype was detected in 43.6% of participants.

Conclusions

Both MM and MMW are at high risk of infection for HIV and other STIs. Rates of HIV, HBV, T pallidum and HPV infections are higher in the MM group.

First report on sexually transmitted infections among trans (male to female transvestites, transsexuals, or transgender) and male sex workers in Argentina: high HIV, HPV, HBV, and syphilis prevalence

OBJECTIVES

Due to the scarce data on the prevalence of sexually transmitted infections (STIs) among male-to-female trans-sex workers (TSW) and male sex workers (MSW) in Argentina, the present study aimed to estimate the incidence of human immunodeficiency virus (HIV), and the prevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), and Treponema pallidum. Human papillomavirus (HPV) and Chlamydia trachomatis infections were tested among TSW.

METHODS

Two hundred and seventy-three TSW and 114 MSW were recruited by nongovernmental organizations. HIV incidence was estimated by STARHS (serologic testing algorithm for recent HIV seroconversion). HPV and C. trachomatis infections were tested in anal cells from TSW.

RESULTS

TSW showed significantly higher prevalences of HIV (34.1 vs. 11.4%), HBV (40.2 vs. 22.0%), and T. pallidum (50.4 vs. 20.4%) than MSW. TSW tested positive for HPV in 111/114 cases and for C. trachomatis in 4/80 cases. Investigation of HBV, HCV, HIV, and T. pallidum co-infections showed that 72% of TSW and 39% of MSW had at least one STI. T. pallidum was the most frequent mono-infection. The estimated HIV incidence was 10.7 per 100 person-years (95% confidence interval (CI) 3.8-17.7) for TSW and 2.3 per 100 person-years (95% CI 0-6.7) for MSW.

CONCLUSIONS

The high prevalence of STIs and the high incidence of HIV demonstrate the great vulnerability of these high-risk populations and indicate the urgent need for preventive strategies on intervention and facilitation of access to healthcare programs.

Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis

Background

The obligate intracellular growing bacterium Chlamydia trachomatis causes diseases like trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Several serovars and genotypes have been identified, but these could not be linked to clinical disease or outcome. The related Chlamydophila pneumoniae, of which no subtypes are recognized, causes respiratory infections worldwide. We developed a multi locus sequence typing (MLST) scheme to understand the population genetic structure and diversity of these species and to evaluate the association between genotype and disease.

Results

A collection of 26 strains of C. trachomatis of different serovars and clinical presentation and 18 strains of C. pneumoniae were included in the study. For comparison, sequences of C. abortus, C. psittaci, C. caviae, C. felis, C. pecorum (Chlamydophila), C. muridarum (Chlamydia) and of Candidatus protochlamydia and Simkania negevensis were also included. Sequences of fragments (400 – 500 base pairs) from seven housekeeping genes (enoA, fumC, gatA, gidA, hemN, hlfX, oppA) were analysed. Analysis of allelic profiles by eBurst revealed three non-overlapping clonal complexes among the C. trachomatis strains, while the C. pneumoniae strains formed a single group. An UPGMA tree produced from the allelic profiles resulted in three groups of sequence types. The LGV strains grouped in a single cluster, while the urogenital strains were distributed over two separated groups, one consisted solely of strains with frequent occurring serovars (E, D and F). The distribution of the different serovars over the three groups was not consistent, suggesting exchange of serovar encoding ompA sequences. In one instance, exchange of fumC sequences between strains of different groups was observed. Cluster analyses of concatenated sequences of the Chlamydophila and Chlamydia species together with those of Candidatus Protochlamydia amoebophila and Simkania negevensis resulted in a tree identical to that obtained with 23S RNA gene sequences.

Conclusion

These data show that C. trachomatis and C. pneumoniae are highly uniform. The difference in genetic diversity between C. trachomatis and C. pneumoniae is in concordance with a later assimilation to the human host of the latter. Our data supports the taxonomy of the order of Chlamydiales.

Lymphogranuloma venereum

Lymphogranuloma venereum (LGV) caused by Chlamydia trachomatis serovar L1-3 was formerly a rare sexually transmitted disease in western countries. Recently, an outbreak of LGV and LGV proctitis among men who have sex with men (MSM) was reported from the Netherlands. We report two cases from Dresden, Germany, of white HIV1-infected MSM who presented in November 2004 with genital ulcers along with inguinal lymphadenitis (case 1) and ulcerative proctitis (case 2). The clinical picture and high titers of serum IgG and IgA antibodies pointed to infection with Chlamydia trachomatis. Appropriate specimens were positive for Chlamydia trachomatis with culture and PCR. Subsequent genotyping of the major outer membrane protein (MOMP) by restricted fragment length polymorphism confirmed serovar L2. Treatment with doxycycline for 3-4 weeks was effective. The incidence of LGV is increasing among MSM in Europe. Since most of the reported cases have been HIV1-infected and ulcerative STDs enhance HIV transmission, both health care providers and patients should be more aware of LGV.

A multiplexed real-time PCR assay for rapid detection of Chlamydia trachomatis and identification of serovar L-2, the major cause of Lymphogranuloma venereum in New York

Lymphogranuloma venereum (LGV) is caused by a rare form of Chlamydia trachomatis that is difficult to diagnose, since culture is not readily available, and since other methods are not reliable or lack sensitivity. We report here a rapid, sensitive, and specific real-time multiplex polymerase chain reaction (PCR) assay capable of detecting C. trachomatis and identifying serovar L-2 in the same reaction, directly from rectal swabs. The analytical sensitivity of the assay was 25 genome copies for C. trachomatis, and 50 genome copies for L-2. The analytical specificity was 100%, as demonstrated with a diverse range of C. trachomatis serovars and other site-specific bacterial pathogens. With the use of a rapid DNA extraction method, a blinded validation of spiked rectal swabs correctly identified 30 samples containing C. trachomatis cells, L-2 DNA, or negative samples. The multiplexed PCR assay also identified serovar L-2 in 13 of 70 rectal swab samples taken from symptomatic patients. Twelve additional samples were positive for C. trachomatis only, and omp1 sequencing determined these samples as either serovar D, E, G, J, or K. This assay represents the first real-time PCR method capable of detecting C. trachomatis DNA, and of simultaneously identifying C. trachomatis infection as serovar L-2.

Combination of PCR targeting the VD2 of omp1 and reverse line blot analysis for typing of urogenital Chlamydia trachomatis serovars in cervical scrape specimens

In this study we developed and evaluated a new PCR-based typing assay, directed to the VD2 region of the omp1 gene, for the detection and typing of urogenital Chlamydia trachomatis infections. A nested VD2 PCR-reverse line blot (RLB) assay was developed for the typing of nine different urogenital serovars of C. trachomatis. The assay developed was tested with reference strains of C. trachomatis serovars and cervical scrapes of 86 Colombian women previously found to be positive for C. trachomatis by using plasmid PCR. Two sets of primers directed to the VD2 region of the omp1 gene of C. trachomatis were designed, and fragments of 220 and 166 bp were generated in the primary and nested PCRs, respectively. In addition, an RLB assay was developed to identify nine different urogenital serovars of C. trachomatis (Ba, D, E, F, G, H, I, J, and K) and group controls, including group B (Ba, D, and E), group C (I, J, K, and H), and an intermediate group (F and G). Using this assay, we were able to type 81 of the 86 samples (94.2%). Of these samples, 91.3% were single C. trachomatis infections, and 8.7% were multiple infections. The most common serovars identified were serovars D (22.2%), F (18.5%), G (13.6%), and E (12.3%). Of the women with multiple C. trachomatis infections, >50% contained both serovars D and E. The nested VD2 PCR-RLB developed is a simple, fast, and specific method for the identification of individual urogenital C. trachomatis serovars previously detected by using plasmid PCR. Moreover, it is an appropriate method for studying multiple C. trachomatis infections and for use in large epidemiological studies.

Restriction endonuclease patterns of the omp1 gene of reference Chlamydia trachomatis strains and characterization of isolates from Cameroonian students

Eighteen reference strains of Chlamydia trachomatis were differentiated by omp1 PCR- and nested PCR-based RFLP analysis, using two restriction digestions, one with AluI and the other with the three enzymes HpaII, EcoRI and HinfI. AluI digestion allowed the differentiation of 12 different profiles after CT1/CT5 PCR and 13 different profiles after the nested PCR. The triple hydrolysis permitted the identification of 15 different patterns. In all, 16/18 reference strains were clearly identified. These reference patterns were successfully used to genotype 34 of 35 (28 strains and 7 clinical specimens) samples from infected students, collected during a screening programme in Yaounde (Cameroon). Genotypes D, Da, E, F, G and J were found. The most prevalent omp1 genotype was E (n = 14; 40 %), followed by F (n = 7; 20 %). As RFLP patterns of reference strains are essential for typing clinical isolates, they will greatly facilitate C. trachomatis characterization in many resource-limited laboratories.

Predominance of Chlamydia trachomatis serovars associated with urogenital infections in females in New Delhi, India

Screening for Chlamydia trachomatis was done for 280 endocervical swab samples by PCR specific for endogenous plasmid. Age dependency was seen in symptomatic patients, with a high chlamydial prevalence rate (28%) found in younger women. Genotyping by restriction fragment length polymorphism analysis of omp1 PCR-positive samples showed serovars D, E, and F to be the most prevalent.

Microbiological aspects of the diagnosis of Chlamydia trachomatis

The available diagnostic methods for Chlamydia trachomatis infection comprise serology (indirect detection) and culture, antigen detection and nucleic acid amplification (direct detection). The rationale, applications, advantages and disadvantages of the methods and diagnostic targets are discussed. Compared to conventional methods, nucleic acid amplification tests have increased sensitivity. This allows samples to be taken at home by the patient herself and mailed directly to the laboratory. Public health strategies implying home sampling for asymptomatic men and women result in a lower prevalence and a lower risk of short-term complications in terms of pelvic inflammatory disease (PID). The importance of predictive values and the association with prevalence are highlighted.

Direct genotyping and nucleotide sequence analysis of VS1 and VS2 of the Omp1 gene of Chlamydia trachomatis from Moroccan trachomatous specimens

To determine the range of ocular strains of Chlamydia trachomatis circulating in southern Morocco, where trachoma is endemic, and to compare the value of the molecular methods for genotyping C. trachomatis, ocular specimens were subjected to a direct Omp1 PCR-restriction fragment length polymorphism (RFLP)-based analysis and direct sequencing. PCR-RFLP analysis shows that the Ba genotype represents the most frequent one (63%), followed by genotype A (45%), whereas no B or C genotypes were identified among the 53 out of 108 specimens that were strongly positive in the Omp1 CT1-CT5 PCR. Our results further show that the notion of interfamily and intrafamily transmission is very likely. To confirm the genotype identity of C. trachomatis as determined by PCR-RFLP, 16 selected specimens were sequenced across variable sequence 1 (VS1) and 2 (VS2). No discrepancies were found between PCR-RFLP typing and the genotype identity confirmed by nucleotide sequencing of the PCR product. Our results clearly indicate that both molecular methods of typing chlamydiae (i.e., PCR-RFLP and sequencing) are important and have specific applications for clinical epidemiological purposes. This is the case for individuals infected with more than one clonal population of C. trachomatis. The unambiguous nucleotide sequencing therefore defines an important epidemiologic descriptor for the infected patient whether the source is from a clonal population of organisms or whether it represents a more dynamic process of strain dominance or genetic change. Furthermore, Omp1 genotyping affords the necessary approach to epidemiologic investigations in areas of the world endemic for trachoma, where only one or two serovars are known to predominate.

High-resolution genotyping of Chlamydia trachomatis from recurrent urogenital infections

A method for Chlamydia trachomatis restriction fragment length polymorphism (RFLP) analysis and complete sequencing of omp1 was developed for use on samples collected at home, and results were compared. Genotyping by sequencing was superior to RFLP analysis. The omp1 gene in 31 clinical strains harbored few mutations compared to the same gene in ATCC reference strains. Follow-up samples obtained during a 24-week period from 31 patients showed recurrence with the same genotype in five cases and a new genotype in one case.

Urogenital Chlamydia trachomatis serovars in men and women with a symptomatic or asymptomatic infection: an association with clinical manifestations?

To determine whether certain Chlamydia trachomatis serovars are preferentially associated with a symptomatic or an asymptomatic course of infection, C. trachomatis serovar distributions were analyzed in symptomatically and asymptomatically infected persons. Furthermore, a possible association between C. trachomatis serovars and specific clinical symptoms was investigated. C. trachomatis-positive urine specimens from 219 asymptomatically infected men and women were obtained from population-based screening programs in Amsterdam. Two hundred twenty-one C. trachomatis-positive cervical and urethral swabs from symptomatically and asymptomatically infected men and women were obtained from several hospital-based departments. Serovars were determined using PCR-based genotyping, i.e., restriction fragment length polymorphism analysis of the nested-PCR-amplified omp1 gene. The most prevalent C. trachomatis serovars, D, E, and F, showed no association with either a symptomatic or asymptomatic course of infection. The most prominent differences found were (i) the association of serovar Ga with symptoms in men (P = 0.0027), specifically, dysuria (P < 0.0001), and (ii) detection of serovar Ia more often in asymptomatically infected people (men and women) (P = 0.035). Furthermore, in women, serovar K was associated with vaginal discharge (P = 0.002) and serovar variants were found only in women (P = 0.045).

Analysis of Chlamydia trachomatis serovars in endocervical specimens derived from pregnant Japanese women

The polymerase chain reaction (PCR) method has been employed to amplify a chlamydial genome encoding four variable segments of the major outer membrane protein and genotyping of different Chlamydia trachomatis serovars was successfully achieved by means of restriction fragment length polymorphism (RFLP) analysis and sequencing of amplified DNA. These methods were applied to identify the serotypes of C. trachomatis in endocervical specimens obtained from asymptomatic pregnant Japanese women at 28-30 weeks of gestation. Among the 218 specimens, 207 were serotyped 43 (19.3%) as serovar D, 53 (24.3%) as E, 24 (11.0%) as F, 39 (17.9%) as G, 15 (6. 9%) as H, 15 (6.9%) as I, five (2.3%) as J, nine (4.1%) as K and four (1.8%) as mixed. Among the 11 unclassified strains by RFLP, six (2.8%) were identified as serovar B variants and five (2.3%) were identified as D/IC-Cal-8. It was suggested that variants of endemic trachoma serovars also have affinity for the urogenital tract of Japanese pregnant women.

Rapid detection of the Chlamydiaceae and other families in the order Chlamydiales: three PCR tests

Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation.

Genotyping of Chlamydia trachomatis in urine specimens will facilitate large epidemiological studies

The serovars of Chlamydia trachomatis-positive urine specimens (n = 81; as detected by PCR and ligase chain reaction) were successfully analyzed in 94% of cases by omp1 PCR-based RFLP analysis. The use of urine specimens and this simple and sensitive typing method will greatly facilitate epidemiological studies of C. trachomatis serovar distribution in asymptomatic C. trachomatis infections in both females and males.

Plaque formation by and plaque cloning of Chlamydia trachomatis biovar trachoma

A new technique for the induction of plaque formation by Chlamydia trachomatis biovar trachoma applicable to the titration of infectivity and cloning of biovar trachoma was established. Three novel strains were cloned and confirmed to be free of glycogen inclusions. The lack of glycogen accumulation correlated with the absence of a 7.5-kb plasmid, which is highly conserved in other strains of C. trachomatis. Although the growth efficiency of these plasmid-free strains was slightly lower than that of plasmid-positive strains, possession of the plasmid and glycogen accumulation were not essential for the survival of C. trachomatis.

Serotyping and genotyping of genital Chlamydia trachomatis isolates reveal variants of serovars Ba, G, and J as confirmed by omp1 nucleotide sequence analysis

Urogenital isolates (n = 93) of Chlamydia trachomatis were differentiated into serovars and variants by serotyping with monoclonal antibodies and genotyping by restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified omp1 gene, respectively. The types of 87 of the 93 isolates (94%) were identical, as determined by both methods. Among these 87 isolates, 3 isolates were identified as the recently described new serovariant Ga/IOL-238 by omp1 nucleotide sequence analysis of the variable domains. Of the remaining six isolates, three isolates serotyped as both L2 and Ba but were identified as Ba/A-7 by genotyping by RFLP analysis of omp1. The omp1 nucleotide sequences of variable domains VD1, VD2, and VD4 of these urogenital Ba strains were identical to the sequences of the variable domains of Ba/J160, an ocular Ba type. The three remaining isolates were serotyped as J, but the patterns obtained by RFLP analysis of omp1, which were identical for the three isolates, differed from that of prototype serovar J/UW36. omp1 nucleotide sequence analysis revealed that these strains are genovariants of serovar J/UW36. Nucleotide sequence differences between serovar J/UW36 and this J genovariant, designated Jv, were found in both variable and constant domains. In conclusion, this study shows that the PCR-based genotyping of clinical C. trachomatis isolates by RFLP analysis of omp1 has a higher discriminatory power and is more convenient than serotyping. Variants of C. trachomatis serovars Ba, G, and J were identified and characterized.

Genotyping of Portuguese Chlamydia trachomatis urogenital isolates

OBJECTIVE

To determine the prevalence of the different Chlamydia trachomatis genotypes in Portuguese patients.

METHODS

Urogenital isolates (n = 240) derived from attenders of various clinics in the Lisbon area were differentiated into genovars by genotyping with restriction fragment length polymorphism (RFLP) analysis of the PCR amplified omp1 gene.

RESULTS

Genotype E was the most common for both men (47.9%) and women (43.8%). Genotypes D and F were the second most prevalent for men (11.3%) and genotype H was the second most prevalent for women (19.5%). Genotypes F, G, D, in women and H, G, I, in men, were found in a lower percentage of cases. Genotypes B, Ba, J, K, L1 and L2 were very rarely detected.

CONCLUSIONS

With one exception, the overall distribution of Chlamydia trachomatis genotypes in our study is similar to what has been observed in other western countries. The only exception is the unusual prevalence of genotype H among women. The clinical manifestations associated with this and other genotypes were similar.

Characterization of avian Chlamydia psittaci strains using omp1 restriction mapping and serovar-specific monoclonal antibodies

In the present study, 60 avian Chlamydia psittaci isolates were characterized using restriction fragment length polymorphism as well as serovar-specific monoclonal antibodies, enabling a comparison between the two characterization methods. Sixty avian C. psittaci isolates were characterized by Alul restriction mapping of the major outer membrane protein gene omp1 obtained after amplification by the polymerase chain reaction. The 60 avian C. psittaci strains were also characterized using serovar-specific monoclonal antibodies in a microimmunofluorescence test. Digestion of 60 avian C. psittaci omp1 amplicons by Alul generated 5 of the 6 known distinct restriction patterns (A, B, D, E and F). Restriction pattern C was not observed. Serotyping revealed 4 avian C. psittaci serovars (A, B, C and D). None of the 60 isolates was typed as serovar E. AluI restriction patterns A, B, D and E corresponded in 98% of the cases to serovars A, B, C and D, respectively. One isolate, classified as serovar A, generated restriction pattern F instead of A. Genotyping enabled a more precise differentiation of avian C. psittaci serovar A strains. Serovar A strains were divided into two groups according to their Alul restriction pattern (A or F). For epidemiological studies, genotyping can thus be a highly valuable alternative to serotyping, especially when applied directly to the clinical samples.

Genotyping of Chlamydia trachomatis serovars derived from heterosexual partners and a detailed genomic analysis of serovar F

OBJECTIVE

To investigate C trachomatis serovars in contact-traced heterosexual partners.

METHODS

Urogenital Chlamydia trachomatis isolates (n = 112) derived from 35 heterosexual patients (index patients) and their 37 chlamydia positive partners (contact patients) were differentiated into serovars by genotyping with restriction fragment length polymorphism (RFLP) analysis of the PCR amplified omp1 gene. In order to investigate whether different strains within the frequently prevalent serovar F were transmitted, two pairs of serovar F (n = 4) were further analysed by genomic DNA fingerprinting with arbitrary primer PCRs (AP-PCRs).

RESULTS

Identical C trachomatis serovars were found in 31 of the 35 pairs, serovars E, F, D, and G being most prevalent. In the remaining four pairs different serovars (either D, E, F or G) were found between the index and the contact patients. By AP-PCR analysis the strains of serovar F were found to be identical between the index and the contact patients, but were different between the two pairs in all AP-PCRs used.

CONCLUSION

A majority of heterosexual partners, once traced positive for C trachomatis infections, are infected with identical serovars. Identical strains of serovar F found in partners as found by DNA fingerprinting confirms the sexual transmission of C trachomatis.

Detection by multiplex polymerase chain reaction and typing of Chlamydia trachomatis isolates

The multiplex polymerase chain reaction (PCR) was applied for the detection of the Chlamydia trachomatis chromosome and plasmid. The multiplex PCR demonstrated a sensitivity of 0.8 fg of chlamydial DNA, corresponding to the detection of about 5 copies of the plasmid. Analysis of 195 genital specimens collected randomly from a female population, showed that the multiplex PCR is more sensitive and rapid than culturing for detecting Chlamydia trachomatis. Moreover, sequencing of the II variable domain of the omp1 gene, directly from DNA of the clinical specimens, appears to be a simple and rapid method for determining serovar isolates.

Comparison of the Amplicor Chlamydia trachomatis test and cell culture for the detection of urogenital chlamydial infections

OBJECTIVE

To compare the polymerase chain reaction (PCR) Amplicor Chlamydia trachomatis test with the cell culture method, in diagnosing urogenital chlamydial infections.

SUBJECTS

439 patients (327 women and 112 men) attending one STD clinic and Family Planning and Gynaecological Clinics in Lisbon, Portugal, between November 1993 and March 1994.

METHODS

In women, two endocervical swab samples were collected: one for PCR Amplicor and one for standard culture technique. Men were asked to submit 20 ml of urine (first pass urine) for PCR Amplicor and one urethral specimen was taken for culture. The order of collection of the specimens was rotated every 50 patients. Discrepant results were further analysed by a second PCR with primers directed against the C trachomatis major outer membrane protein (MOMP) and by direct fluorescent antibody (DFA).

RESULTS

After analysis of discrepancies, the adjusted sensitivity and specificity of PCR on endocervical specimens were 92.9% and 100% and the positive and negative predictive values were 100% and 99.7% respectively; on the urine samples these values were 100%, 99.1%, 100% and 99.1%, respectively.

CONCLUSION

These results indicate that the PCR Amplicor test is a rapid sensitive and specific assay for the detection of C trachomatis in urogenital infections and provides a non-invasive technique for screening chlamydia infection in men.

Evidence that the novel microorganism 'Z' may belong to a new genus in the family Chlamydiaceae

The purpose of this study was to investigate possible phylogenetic relationships of a new microorganism called 'Z'. The organism was previously shown to be similar to chlamydia in its growth cycle and some of its metabolic requirements, but different in others and in its major outer membrane protein. In this study we report the sequencing of 'Z"s 16S ribosomal DNA and comparison of the sequence with that of other microorganisms, including chlamydia and rickettsiae. While chlamydial species have 95.5% sequence identity among themselves, 'Z' had 83% identity with them, and 73% identity with certain rickettsia-like organisms. Based on the sequence analyses and taking into account physiologic considerations, we believe that 'Z' may belong to a novel genus in the family Chlamydiaceae.

Usefulness of omp1 restriction mapping for avian Chlamydia psittaci isolate differentiation

Sixty-five avian Chlamydia psittaci isolates collected worldwide, including 27 previously characterized reference strains, were analysed by restriction mapping of the major outer membrane protein gene (omp1) obtained after DNA amplification by PCR. They were compared to 2 ruminant isolates, a feline pneumonitis and a guinea pig inclusion conjunctivitis (GPIC) isolate. According to their omp1 restriction patterns, avian strains were heterogeneous in that they exhibited 6 and 4 distinct patterns using AluI and MboII restriction enzymes, respectively, thus defining 7 groups. However, 84% of the studied strains belonged to groups 1 to 4, which share a specific fragment triplet of 411, 282 and 102 base pairs in their AluI digestion patterns. Comparisons with serological classifications showed a strict correlation and allowed further intraserovar differentiation. Furthermore, this classification based upon a single gene (omp1) roughly correlated with the data obtained by RFLP of native DNA and DNA/DNA hybridization studies. There was no host or geographic specificity in the pattern exhibited by these strains. The ruminant, feline pneumonitis and GPIC C. psittaci isolates were clearly distinguished from each other and the avian strains. Moreover, this method was clearly able to identify dubiously designated strains as well as mixtures of isolates within a single sample. In conclusion, this PCR approach based upon omp1 restriction mapping enables the differentiation of avian C. psittaci isolates and can be proposed as a taxonomic and epidemiologic tool.

Improved PCR sensitivity for direct genotyping of Chlamydia trachomatis serovars by using a nested PCR

Successful amplification of omp1 DNA by PCR is crucial in the genotyping of Chlamydia trachomatis when directly performed with clinical samples (J. Lan, J. M. M. Walboomers, R. Roosendaal, G. J. van Doornum, D. M. McLaren, C. J. L. M. Meijer, and A. J. C. van den Brule, J. Clin. Microbiol. 31:1060-1065, 1993). Several primers flanking the four variable domains of the omp1 gene were selected and tested for sensitivity in several nested PCRs with serial dilutions of serovar G. The optimal sensitivity obtained was 0.1 to 0.01 inclusion-forming units, similar to that obtained in the C. trachomatis plasmid PCR. With this approach, any C. trachomatis PCR-positive sample can be typed.

Differentiation of Escherichia coli strains using randomly amplified polymorphic DNA analysis

Fifty-nine Escherichia coli strains isolated from 54 unrelated patients over a six-year period, as well as the reference strain of the species, were studied by analysis of randomly amplified polymorphic DNA (RAPD) to assess the usefulness of this genotyping approach in molecular epidemiology. Using a 10-mer oligonucleotide primer, 28 different RAPD fingerprints were distinguished among the 60 strains previously delineated in 36 ribotypes by EcoRI and HindIII digests. The patterns were reproducible and stable after in vitro and in vivo studies. Some strains harbouring an identical ribotype exhibited distinct RAPD fingerprints. Thus, these data illustrate the usefulness of the association of two genetic markers in assessing the relationship between strains. Interestingly, among the RAPD patterns, several bands were present only in the highly virulent carboxylesterase type B2 strains, which are more homogeneous than the carboxylesterase type B1 strains. Because of its simplicity and rapidity, RAPD analysis appears to be a highly valuable tool for studying E. coli molecular epidemiology.

Homogeneity of the major outer membrane protein gene of feline Chlamydia psittaci

Thirteen feline Chlamydia psittaci strains isolated in various countries over a 50-year period were examined by restriction mapping of the major outer membrane protein (MOMP) gene obtained after DNA amplification by the polymerase chain reaction and compared with avian, ovine and guinea pig inclusion conjunctivitis (GPIC) C psittaci strains. All the feline isolates produced a unique AluI pattern distinct from the other C psittaci strains and were characterised by a typical fragment doublet of 185/180 base pairs. Such a homogeneity argues for their genetic relatedness and suggests their clonal origin. These data demonstrate the usefulness of MOMP-gene restriction mapping in C psittaci typing.

Evaluation of molecular typing for epidemiological study of Chlamydia trachomatis genital infections

Molecular typing and serotyping were compared for 150 Chlamydia trachomatis strains isolated from genital sources, belonging to 10 different serovars. Because of the general agreement of the two methods, molecular omp1 genotyping was applied to the epidemiological study of C. trachomatis isolates from genital infections in Bordeaux (France), during a 29-month period. The most prevalent omp1 genotypes were E (51.7%), F (17.3%), D (8.8%), and G (8.4%). Restriction enzyme analysis allowed identification of a serovar D variant (Dv), whereas serovar E strains were homogeneous.

Molecular typing of Chlamydia trachomatis by random amplification of polymorphic DNA

The random amplification of polymorphic DNA (RAPD) was used for epidemiological typing of Chlamydia trachomatis strains. DNA samples from 39 C. trachomatis, 1 C. pneumoniae and 2 C. psittaci strains were screened by the use of 4 single 10-mer primers. Different and reproducible banding profiles were observed on agarose gel electrophoresis. No common profiles were recorded for strains from different Chlamydia species. All C. trachomatis strains of trachoma biovar were distinguished from lymphogranuloma venereum biovar. Moreover, serotypes A to C were separated from serotypes D to K, and some groups of strains sharing the same serotype D to K were further subdivided by RAPD. Conversely, strains of different serotypes could produce identical patterns of amplification, indicating that RAPD did not reflect serotyping. The patterns of amplified products were compared to the restriction fragment length polymorphism of the omp1 gene after amplification and to DNA fingerprinting by use of ribosomal RNA or randomly cloned DNA probes. RAPD seemed to be an alternative molecular typing procedure for epidemiological study and strain identification in urogenital infections due to serotypes D to K.

Complete sequence of the major outer membrane protein-encoding gene of Chlamydia trachomatis serovar Da

The complete nucleotide sequence of the gene omp1 encoding the major outer membrane protein (MOMP) of Chlamydia trachomatis serovar Da was determined following amplification by the polymerase chain reaction. The most closely related complete sequence published to date is that encoding the C. trachomatis L1 MOMP. When the L1 and Da MOMP deduced amino acid (aa) sequences were compared, 16 single-aa differences located mostly in the variable domains I, II, and IV were detected. These regions contain the B-cell epitopes. Additional differences were found in the constant domains I and II, thought to participate in the T-cell response.

DNA fingerprinting of Chlamydia trachomatis by use of ribosomal RNA, oligonucleotide and randomly cloned DNA probes

DNA fingerprinting of 15 reference strains and 24 clinical isolates of Chlamydia trachomatis, 2 strains of C. psittaci and one strain of C. pneumoniae was studied by use of universal 16 + 23S RNA from Escherichia coli, 16S rDNA-directed oligonucleotide and randomly cloned chlamydial DNA probes. The rRNA-gene restriction patterns (ribotypes) enabled the differentiation of chlamydial species. Following DNA cleavage by restriction endonuclease PvuII, lymphogranuloma venereum and trachoma biovars of C. trachomatis could be differentiated. An oligonucleotide, designed to hybridize the C. trachomatis 16S rDNA, also allowed for both species-specific identification and biovar typing of C. trachomatis human strains. Molecular typing system using 3 lambda clones containing C. trachomatis serotype E random DNA inserts, combined to ribotyping, revealed 12 groups of variable banding patterns within C. trachomatis, and could provide an alternative epidemiological tool.

Development and clinical evaluation of a polymerase chain reaction test for detection of Chlamydia trachomatis

A polymerase chain reaction (PCR) for the detection of Chlamydia trachomatis was developed and evaluated. Two primer-probe sets were designed; one detected a specific sequence of the plasmid, and the other detected the gene encoding the major outer membrane protein. Both sets reacted species specifically and amplified sequences from all human serovars. A simple protocol was used for sample pretreatment. The PCR was optimized by addition of tetramethylammonium chloride and bovine serum albumin. The results of the PCR with the plasmid primer-probe set were compared with those of culture and the Chlamydiazyme and Gen-Probe PACE 2 tests for urogenital specimens from 220 patients. The rates of prevalence of infection with C. trachomatis were 22.7, 16.4, 15.0, and 14.5%, respectively. The sensitivities of the Chlamydiazyme and Gen-Probe PACE 2 assays compared with culture were 66.7 and 61.1%, respectively, and their sensitivities compared with PCR were 60.0 and 60.0%, respectively. The sensitivity of culture compared with PCR was 70.0%. Forty-eight of the 50 specimens positive by PCR with the plasmid primer-probe set could be confirmed by PCR with the major outer membrane protein primer-probe set or culture. It is concluded that the PCR is the most sensitive technique for laboratory detection of C. trachomatis.