Typing Chlamydia trachomatis by detection of restriction fragment length polymorphism in the gene encoding the major outer membrane protein

Helicobacter pylori Infection of the Gastric Mucosa and Ocular Adnexa-Lack of Association With Ocular Adnexal Lymphoma

PURPOSE

Helicobacter pylori could theoretically induce ocular adnexal lymphoma (OAL) via 2 mechanisms: the first is that of infection within the ocular adnexa and the second is that of infection within the gastric mucosa, leading to the malignant transformation of lymphocytes that migrate to the ocular adnexa, forming a primary "ectopic" cancer. This study investigated if an association exists between gastric H. pylori or ocular adnexal H. pylori and OAL.

METHODS

Prospective case-control study including cases with OAL and controls with nonlymphomatous pathologies. Gastric H. pylori infection was assessed via serologic antibody testing. Ocular adnexal infection was assessed via polymerase chain reaction testing for H. pylori and Chlamydia psittaci within ocular adnexal samples.

RESULTS

Seventy-two patients were enrolled, of whom 18 had lymphoma and 54 nonlymphomatous pathologies. H. pylori antibodies were present in 5 cases (28%) and 18 controls (33%) (95% CI, 0.24%-2.50%, p = 0.78). All ocular adnexal specimens were negative for H. pylori and C. psittaci infection. The only relevant statistically significant difference between cases and controls was a history of gastric ulcer (95% CI, 1.23%-44.80%, p = 0.03).

CONCLUSIONS

In the study's population, infection of gastric mucosa with H. pylori does not appear to influence the development of OAL. Also, H. pylori or C. psittaci infection within the ocular adnexa does not appear to influence the development of OAL. In the study's practice, authors do not recommend antibiotic administration or routine gastroscopy for patients with OAL. The authors do recommend referral of OAL patients with gastric symptoms to a gastroenterologist.

Highly diverse MLVA-ompA genotypes of rectal Chlamydia trachomatis among men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network

OBJECTIVES

In this prospective study, we aimed to determine the distribution of genotypes by multilocus variable number tandem repeat (VNTR) analysis plus analysis of the ompA gene (MLVA-ompA) of rectal Chlamydia trachomatis among men who have sex with men (MSM) attending Brighton Genitourinary Medicine (GUM) Clinic and to examine any correlations with clinical variables, including HIV status, and to isolate rectal C. trachomatis cultures maximising the possibility of obtaining complete genotyping data.

METHODS

Samples were assigned genotypes by PCR and sequencing of the markers of the MLVA-ompA genotyping system. Rectal C. trachomatis was isolated in cell culture using McCoy cells. Data regarding demographics, HIV status, rectal symptoms and history of sexually transmitted infections, including C. trachomatis, were collected.

RESULTS

1809 MSM attending the clinic between October 2011 and January 2013 took part in the study, 112 (6.2%) of whom had rectal samples that tested positive for C. trachomatis. 85/112 (75.9%) C. trachomatis-positive rectal samples were assigned 66 different genotypes. Two distinct genotype subclusters were identified: subcluster 1 consisted of more HIV-negative men than subcluster 2 (p=0.025), and the MLVA-ompA genotypes in these subclusters reflected this. Isolates were successfully cultured from 37 of the 112 specimens, from which 27 otherwise unobtainable (from direct PCR) MLVA-ompA genotypes were gained.

CONCLUSIONS

The most prevalent genotypes were G, E and D representing some overlap with the heterosexual distribution in UK. Subcluster 1 consisted of more 'heterosexual genotypes' and significantly more HIV-negative men than subcluster 2, associated with 'MSM genotypes'. There was a higher diversity of C. trachomatis strains among MSM in Brighton than observed in other cities.

Semen Quality of Men With Asymptomatic Chlamydial Infection

We have shown previously that the in vitro exposure of spermatozoa to elementary bodies (EBs) of Chlamydia trachomatis can lead to sperm death over a number of hours of incubation. As such, we have hypothesized that the ejaculates of men with a chlamydial infection could contain increased numbers of nonmotile (dead) spermatozoa if they are exposed to EBs prior to ejaculation. To test this hypothesis, the ejaculates of 642 men undergoing diagnostic semen analysis as part of ongoing infertility investigations with their partner were examined. All men were without symptoms of genitourinary infections and semen analysis was performed according to World Health Organisation (WHO) 1999 methods after a 3-5 day abstinence period. In addition to semen analysis, nested plasmid polymerase chain reaction (PCR) was undertaken on the ejaculate to detect the presence of C trachomatis DNA. A total of 31 semen specimens (4.9%) were found to be positive, and in 28 of these, the diagnosis was confirmed using the ligase chain reaction (LCR). Men whose ejaculates were PCR positive for chlamydial DNA had a significantly (P <.05) higher mean concentration of leukocytes (1.71 +/- 2.20 x 10(6) per mL) and a higher mean ejaculate volume (3.45 +/- 1.52 mL) than in those whose ejaculates were PCR negative (leukocyte concentration: 0.67 +/- 2.59 x 10(6) per mL; volume 2.93 +/- 1.38 mL). Leukocytospermia was twice as common in men that were PCR positive for chlamydial DNA (P <.05) but it was not always associated with the presence of chlamydial DNA in semen. However, there was no difference in the mean percent motility between the 2 groups and the proportion of asthenozoospermia also did not differ. Because these results do not confirm the hypothesis proposed from our in vitro experiments, further work needs to be undertaken to understand whether human spermatozoa are actually exposed to elementary bodies of C trachomatis in an infected individual prior to ejaculation.

Genotyping markers used for multi locus VNTR analysis with ompA (MLVA-ompA) and multi sequence typing (MST) retain stability in Chlamydia trachomatis

We aimed to evaluate the stability of the Chlamydia trachomatis multi locus VNTR analysis (MLVA-ompA) and multi sequence typing (MST) systems through multiple passages in tissue culture. Firstly, we analyzed the stability of these markers through adaptation of C. trachomatis to tissue culture and secondly, we examined the stability of a four-locus MLVA-ompA and a five-locus MST system after multiple passages in tissue culture. Marker sequences were monitored through successive chlamydial developmental cycles to evaluate the stability of the individual DNA markers through many bacterial divisions and this, in turn, informed us of the usefulness of using such typing systems for short and long-term molecular epidemiology. Southampton genitourinary medicine (GUM) clinic isolates from endocervical swabs collected from C. trachomatis positive women were passaged through tissue culture. MLVA-ompA typing was applied to primary swab samples and to the same samples after C. trachomatis had been passaged through cell culture (eight passages). Sequence data from time-zero and passage-eight isolates were aligned with reference sequences to determine the stability of the markers. The Swedish new variant (nvCT) underwent 72 passages in cell culture and the markers of the two schemes were similarly analyzed. Analysis of genetic markers of the MLVA-ompA typing system before and after the isolates were introduced to tissue culture showed no change in the dominant sequence. The nvCT that had been passaged 72 times over the duration of a year also showed no variation in the dominant sequence for both the genotyping schemes. MLVA-ompA and MST markers are stable upon adaptation of C. trachomatis to tissue culture following isolation of strains from primary endocervical swab samples. These markers remain stable throughout multiple rounds of cell-division in tissue culture, concomitant with the incubation period and appearance of symptoms normally associated with host-infection. Both genotyping schemes are, therefore, suitable for epidemiology of C. trachomatis.

C. trachomatis in female reproductive tract infections and RFLP-based genotyping: a 16-year study from a tertiary care hospital

Presence of Chlamydia trachomatis in endocervix was determined in 2466 women attending a tertiary care hospital in New Delhi, India over a period of 16 years, using a monoclonal-based direct immunofluorescence assay, tissue culture isolation, and a conventional PCR assay. Chlamydia antigen could be detected in 391 out of 2466 (15.85%) of patients studied; in 27.27% women with PID, 16.74% women with cervicitis, 16.03% women with infertility, and 12.06% women with adverse pregnancy outcomes, respectively. There was a statistically significant decreasing trend in Chlamydia antigen positivity between the years 1994–1999 and 2000–2004; the apparent decline in antigen positivity between the years 2000–2004 and 2005–2010 was not statistically significant. Antigen detection assay detected equal number of positives as the PCR assay; tissue culture isolation demonstrated lower positivity. In a few representative specimens from cervicitis patients, genotyping was done using RFLP pattern analysis of C. trachomatis MOMP gene amplified by PCR assay, all of these belonged to Chlamydia trachomatis serovar E.

Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay

Current typing methods of Chlamydia (C.) trachomatis are mainly based on the diversity of the ompA gene, which is coding for the major outer membrane protein A. The present study aimed at facilitating genotyping of strains of this obligate intracellular human pathogen by developing a DNA microarray assay using the ArrayTube™ format for individual samples and the ArrayStrip™ format for higher throughput. The new test is exploiting multiple discriminatory sites by involving a total of 61 oligonucleotide probes representing genotype-specific polymorphisms in variable domains 1, 2 and 4 of the ompA gene. After multiplex amplification of these domains using biotinylated primers, the sample is hybridized in the microarray vessel under highly stringent conditions. The resulting binding pattern is genotype specific, thus allowing direct identification. We were able to show that DNA from each of the currently accepted genotypes (serovars) yielded a unique, theoretically expected and distinct hybridization pattern. The assay was also shown to be highly sensitive as a dilution containing the equivalent of 1 inclusion-forming unit was still correctly genotyped. In addition, when 62 clinical samples were examined and compared to PCR-RFLP typing results, the genotype was correctly identified by the DNA microarray in all cases. The present test is easy to handle and economically affordable, and it allows genotyping of C. trachomatis to be accomplished within a working day, thus lending itself for epidemiological studies and routine diagnosis.

Phylogenetic analysis of Chlamydia trachomatis Tarp and correlation with clinical phenotype

Chlamydia trachomatis is the leading cause of infectious blindness worldwide and is the most commonly reported pathogen causing sexually transmitted infections. Tarp (translocated actin recruiting phosphoprotein), a type III secreted effector that mediates actin nucleation, is central to C. trachomatis infection. The phylogenetic analysis of tarP from reference strains as well as ocular, genital, and lymphogranuloma venereum (LGV) clinical isolates demonstrated an evolutionary relationship with disease phenotype, with LGV and ocular isolates branched into clades that were separate from the urogenital isolates. The sequence analysis of Tarp indicated a high degree of variability and identified trends within clinical groupings. Tarps from LGV strains contained the highest number of tyrosine-rich repeat regions (up to nine) and the fewest (two) predicted actin binding domains. The converse was noted for Tarp proteins from ocular isolates that contained up to four actin binding domains and as few as one tyrosine-rich repeat region. The results suggest that Tarp is among the few known genes to play a role in C. trachomatis adaptations to specific niches within the host.

Promoters for Chlamydia type III secretion genes show a differential response to DNA supercoiling that correlates with temporal expression pattern

Type III secretion (T3S) is important for the establishment and maintenance of a chlamydial infection. The genes encoding T3S components in Chlamydia are transcribed as separate temporal classes, but the mechanisms that regulate the timing of their expression are not understood. In this study, we demonstrate that promoters for 10 predicted T3S transcriptional units are each transcribed in vitro by the major form of chlamydial RNA polymerase but not by an alternative form of RNA polymerase containing sigma(28). Since changes in DNA supercoiling during chlamydial development have been proposed as a mechanism for temporal gene regulation, we examined the in vitro response of T3S promoters to altered superhelical density. Promoters for three T3S genes that are upregulated at mid times were activated in response to increased DNA supercoiling. In contrast, promoters for three late T3S genes were not sensitive to changes in superhelical density. This differential response to changes in DNA topology is similar to the pattern that has been reported for representative mid and late chlamydial genes that are unrelated to the T3S system. Based on these results, we propose that the temporal expression of T3S genes in Chlamydia is controlled by general mechanisms that regulate sigma(66)-dependent gene expression during the developmental cycle. Our results are consistent with a model in which T3S genes that are upregulated in mid cycle are activated together with other mid genes in response to increased DNA supercoiling.

Predicting phenotype and emerging strains among Chlamydia trachomatis infections

Single nucleotide polymorphisms can be used for epidemiologic and evolutionary studies worldwide.

Chlamydia trachomatis is a global cause of blinding trachoma and sexually transmitted infections (STIs). We used comparative genomics of the family Chlamydiaceae to select conserved housekeeping genes for C. trachomatis multilocus sequencing, characterizing 19 reference and 68 clinical isolates from 6 continental/subcontinental regions. There were 44 sequence types (ST). Identical STs for STI isolates were recovered from different regions, whereas STs for trachoma isolates were restricted by continent. Twenty-nine of 52 alleles had nonuniform distributions of frequencies across regions (p<0.001). Phylogenetic analysis showed 3 disease clusters: invasive lymphogranuloma venereum strains, globally prevalent noninvasive STI strains (ompA genotypes D/Da, E, and F), and nonprevalent STI strains with a trachoma subcluster. Recombinant strains were observed among STI clusters. Single nucleotide polymorphisms (SNPs) were predictive of disease specificity. Multilocus and SNP typing can now be used to detect diverse and emerging C. trachomatis strains for epidemiologic and evolutionary studies of trachoma and STI populations worldwide.

Genital Chlamydia trachomatis infections

Chlamydia trachomatis infections affect young, sexually active persons. Risk factors include multiple partners and failure to use condoms. The incidence of infection has increased in the past 10 years. Untreated C. trachomatis infections are responsible for a large proportion of salpingitis, ectopic pregnancy, infertility and, to a lesser extent, epididymitis. Screening is a possible intervention to control the infection, which is often asymptomatic. The emergence of lymphogranuloma venereum proctitis in men who have sex with men, in Europe, and of a variant with a deletion in the cryptic plasmid, in Sweden, are new features of C. trachomatis infections in the last years. A diagnosis is best made by using nucleic acid amplification tests, because they perform well and do not require invasive procedures for specimen collection. Single-dose therapy has been a significant development for treatment of an uncomplicated infection of the patient and his or her sexual partner.

Highly discriminative genotyping of Chlamydia trachomatis using omp1 and a set of variable number tandem repeats

This article reports the development of a method for genotyping Chlamydia trachomatis, using PCR and sequencing of omp1, supplemented with three new variable number tandem repeat (VNTR) loci of C. trachomatis. Typeability, reproducibility and discriminatory power were assessed using four groups of samples: two groups (I and II) of C. trachomatis-positive patients and their positive partner(s), one group (III) of patients with recurrent or persistent C. trachomatis infections, and one group (IV) comprising samples containing a newly discovered mutant strain with a 377-bp deletion in the cryptic plasmid, the new variant C. trachomatis (nvCT). The VNTR loci (designated CT1335, CT1299, and CT1291) were all single nucleotide repeats chosen for maximal mutability and variation. In the study material, nine variants of CT1335, eight variants of CT1299 and five variants of CT1291 were found. The discriminatory power (D) of omp1 in the present material was D(omp1) = 0.69. Ds for VNTRs CT1335, CT1299 and CT1291 were 0.53, 0.74 and 0.74, respectively. The resolution power of the omp1-VNTR assay was 0.94. Stability over time of the VNTRs was investigated and found to be adequate for epidemiological studies. Using this genotyping assay, it was confirmed that the nvCT strain was indeed a clone. These results indicate that, with this novel method, strains of C. trachomatis can be individually identified, and epidemiological associations established.

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.

Development of real-time PCR assays for genotyping of Chlamydia trachomatis

We have developed and validated a nested real-time PCR (NRT-PCR) for the genotyping of Chlamydia trachomatis and used it specifically for the typing of either eight genovars from D to K or three genovars of lymphogranuloma venereum (LGV). The 11 probes used in the NRT-PCR correctly identified the DNA from D to K and LGV reference strains and did not cross-react with the DNA from 26 strains representing the bacterial pathogens and commensals of the oropharynx, genital tract, and rectum. The NRT-PCR had a 95% probability of detection at four genome copies (confidence interval, three to six copies) of C. trachomatis per reaction. One hundred cervical and urethral swab specimens containing C. trachomatis DNA from 63 women and 37 men were used to validate the method. The results from the NRT-PCR and the DNA sequencing of amplicons generated from the omp1 gene showed 100% correlation for these samples. The assay also identified the LGV-II genotype in 24 of 48 rectal swab specimens containing C. trachomatis DNA that were obtained from men having sex with men. The Sexually Transmitted Bacteria Reference Laboratory, London, independently confirmed these results using group-specific LGV real-time PCR and restriction fragment length polymorphism analysis. Compared with the NRT-PCR, non-NRT-PCR was found to be less sensitive: it typed C. trachomatis DNA in only 80% of the genital samples and 90% of the rectal swab samples. This is the first successful demonstration of the use of real-time PCR for the genotype-specific typing of C. trachomatis strains that cause sexually transmitted diseases.

Distribution study of Chlamydia trachomatis serovars among high-risk women in China performed using PCR-restriction fragment length polymorphism genotyping

This was one of the first epidemiological studies in China focused on genital Chlamydia trachomatis serotype distribution in high-risk female populations using omp1 gene-based restriction fragment length polymorphism analysis. One thousand seven hundred seventy cervical swab samples from women attending sexually transmitted disease clinics and female sex workers in six cities in China (Shenzhen and Guangzhou in southern China, Nanjing and Shanghai in eastern China, and Nanning and Chengdu in southwestern China) were subjected to serovar genotyping. The proportion of omp1 genes successfully amplified in 240 C. trachomatis plasmid-positive samples was 94.2% (226/240). Serotypes E (n = 63; 27.9%), F (n = 53; 23.5%), G (n = 28; 12.4%), and D (n = 25; 11.1%) were most prevalent. Though there was no significant difference in the geographic distribution of C. trachomatis, serotype E was predominant in the South (32.1%) and East (27.1%), while serotype F was predominant in the Southwest (28.3%). Serotype F infection was associated with young age and single status. Serovar G was associated with lower abdominal pain; 47.5% of asymptomatic patients were infected with serovar E. These results provide information on distribution of genital C. trachomatis serotypes among high-risk women in China and indicate that high-risk women, including those who are asymptomatic, can be infected with multiple serovars of C. trachomatis, revealing exposure to multiple sources of infection. Although the scope for generalizations is limited by our small sample size, our results showing clinical correlations with genotypes are informative.

In vivo and in vitro studies of Chlamydia trachomatis TrpR:DNA interactions

We previously reported that Chlamydia trachomatis expresses the genes encoding tryptophan synthase (trpBA) and the tryptophan repressor (trpR). Here we employ primer extension analysis to identify the transcriptional origins of both trpR and trpBA, allowing for the identification of the putative operator sequences for both trpR and trpBA. Moreover we demonstrate that native recombinant chlamydial TrpR binds to the predicted operator sequence upstream of trpR. A restriction endonuclease protection assay was designed and used to demonstrate that 5-fluorotryptophan was the only tryptophan analogue capable of activating binding of native recombinant chlamydial TrpR to its operator. Additionally, 5-fluorotryptophan was the only analogue that repressed expression of trpBA at a level analogous to L-tryptophan itself. Based on these findings, a mutant selection protocol was designed and a C. trachomatis isolate containing a frameshift mutation in trpR was isolated. This chlamydial mutant synthesizes a truncated TrpR protein that cannot regulate expression of trpBA and trpR in response to changes in tryptophan levels. These findings provide the first genetic proof that TrpR acts as a negative regulator of transcription in C. trachomatis.

In vitro effects of spectinomycin and ceftriaxone alone or in combination with other antibiotics against Chlamydia trachomatis

The in vitro effects of spectinomycin and ceftriaxone, alone or in combination with erythromycin, ofloxacin, and doxycycline, against Chlamydia trachomatis were investigated by the checkerboard method and compared by Ridit (reference identical unit) analysis. A combination of spectinomycin with erythromycin or doxycycline was found to be more effective than that of ceftriaxone.

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.

Current problems of perinatal Chlamydia trachomatis infections

Chlamydia trachomatis has been recognized as a pathogen of trachoma, nongonococcal urethritis, salpingitis, endocervicitis, pelvic inflammatory disease, inclusion conjunctivitis of neonates, follicular conjunctivitis of adults, infantile pneumonia and associated conditions. Chlamydial infections during pregnancy may also cause a variety of perinatal complications. Different antigenic strains of C. trachomatis from endocervical, nasopharyngeal and conjunctival origins have been associated with different clinical conditions. Control programs emphasizing early diagnosis, targeted screening, and effective treatment will lead to an eventual decline in the incidence of perinatal chlamydial infection. This review focuses on current problems of perinatal C. trachomatis infections in the aspects of microbiological and immunological pathogenesis.

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.

Screening of volunteer students in Yaounde (Cameroon, Central Africa) for Chlamydia trachomatis infection and genotyping of isolated C. trachomatis strains

The prevalence of Chlamydia trachomatis infection was 3.78% out of 1,277 volunteer students screened by direct fluorescence assay and Cobas Amplicor PCR. The infection was associated with the nonuse or inconsistent use of condoms in women (P = 0.026) and a previous sexually transmitted infection in men (P = 0.023). The most frequent genotypes determined by sequencing the omp1 genes of 25 clinical isolates were E (44%) and F (20%), and some strains harbored mutations, but E genotype strains did not.

Genotyping of Chlamydia trachomatis strains from cultured isolates and nucleic acid amplification test-positive specimens

Urogenital strains of Chlamydia trachomatis are divided into several serogroups (D-K). Since these serovars are represented with differing prevalence in the population a serotyping of strains is necessary, when characterising the epidemiological situation. The aim of this study was the genotyping of C. trachomatis strains, the comparison of the results with those of serotyping, and the genotyping of positive specimens using commercial nucleic acid amplification tests (NAAT). The Chlamydia trachomatis major outer membrane protein gene (omp1) from 55 isolated strains and 36 NAAT-positive specimens was amplified by polymerase chain reaction (PCR). The restriction fragment length polymorphism (RFLP) patterns of these amplicons were compared with those of reference strains. The genotypes E and F were found to be most prevalent. The results are discussed considering other studies, genovariants and epidemiology.

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.

Genotyping of Chlamydia trachomatis would improve contact tracing

BACKGROUND

The reported number of Chlamydia trachomatis genital infections has increased 15% annually since 1997 in Sweden. Inaccurate partner notification might be one reason.

GOAL

The goals were to determine if genotyping of C trachomatis would improve partner notification and to study the duration of infection.

STUDY DESIGN

Sexual networks were constructed. C trachomatis isolates from 231 individuals attending the Orebro STD clinic during 1 year were typed by sequencing of the omp1 gene.

RESULTS

All individuals were traced and diagnoses were established in 30 of 161 networks. More than one genotype was seen in seven networks. The mean duration of C trachomatis infection in each network was calculated to be 23 weeks.

CONCLUSION

Genotyping could be a useful tool in partner notification when there are discrepant or uncommon genotypes. Limited clinic catchment areas create information difficulties that obstruct accurate contact tracing.

Prevalence of Chlamydia trachomatis in human immunodeficiency virus-infected women in Cuba

To determine the prevalence rates and serovar distribution of Chlamydia trachomatis cervical infections in Cuban women, two different groups were selected. Group I consisted of 60 human immunodeficiency virus (HIV-1) seropositive women from different regions of Cuba and group II of 60 randomly selected women HIV seronegative and apparently healthy. C. trachomatis was detected in cervical scrapes by mean of nested polymerase chain reaction (PCR) specific for major out membrane protein. The overall prevalence rate of C. trachomatis in cervical scrapes determined by nested PCR was 10% in group I and the estimated prevalence was 6.6% for group II; 83.3% of HIV seropositive women with C. trachomatis infection reported history of pelvic inflammatory disease followed by cervicitis (50%). The control group C. trachomatis-infected women referred a history of cervicitis in 75% of cases. Other reports in the latter group included infertility and pelvic inflamatory disease in 50%. The present study is the first report of C. trachomatis prevalence in Cuba. It showed that there was not significantly difference in the prevalence rate of C. trachomatis between both groups.

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.

Chlamydia trachomatis - the agent

Chlamydiae are obligate intracellular bacteria, parasitizing eukaryotic cells. Chlamydia trachomatis, C. psittaci and C. pneumoniae are the three species of chlamydiae pathogenic to humans. C. trachomatis shows a tropism for the genital and conjunctival epithelia and consists of 19 different serovars which are pathogenic predominantly for the urogenital tract.A distinguishing feature of chlamydiae is their transition between the infectious elementary body that enters the host cell and the non-infectious reticulate body that replicates intracellularly within an inclusion that does not fuse with lysosomes. Chlamydiae depend for some functions upon the host cell; in particular, chlamydiae have little capacity for generating energy. The complete sequence of the 1000-kb chromosome of C. trachomatis is known, as are most of the genes located on the 7.5-kb cryptic plasmid. Recently, several concepts about the biology and the metabolic pathways of C. trachomatis have been revised in relation to the genome sequence, and different novel proteins have been described.

Typing of Chlamydia trachomatis strains from urine samples by amplification and sequencing the major outer membrane protein gene (omp1)

OBJECTIVES

To develop a novel protocol for the extraction, amplification, and sequencing of Chlamydia trachomatis MOMP gene (omp1) from urine, a non-invasive source, and apply it to an epidemiological study on the distribution of C trachomatis strains in a population of pregnant women in Thailand.

METHODS

The C trachomatis DNA was extracted from culture stocks and urine using a slightly modified commercially available kit, the High Pure PCR Template Preparation Kit (Roche Molecular Biochemicals, IN, USA). The PCR and sequencing primers used for the amplification and sequencing of the omp1 were designed based on the nucleotide sequence of multiple C trachomatis strains found in GenBank. The protocol for the extraction, amplification, and sequencing was tested on laboratory culture stocks of reference strains of all C trachomatis serovars and on urine samples collected in a cross sectional study designed to assess the prevalence of C trachomatis infections in the cities of Bangkok and Chiang Rai, Thailand.

RESULTS

The omp1 gene was successfully amplified and sequenced from 18 laboratory C trachomatis reference strains and from 45 C trachomatis positive urine clinical samples collected from asymptomatic pregnant women. Among clinical samples, we found nine different C trachomatis genotypes: F (11, 25%), D (10, 22.6%), H (5, 11.7%), K (5, 11.7%), E (4, 9.3%), Ia (3, 7%), B (3, 7%), Ja (2, 4.5%), and G (1, 2.3%). One specimen generated an omp1 DNA sequence pattern indicating the presence of a mixed infection with at least two different serovars.

CONCLUSIONS

Urine is a convenient and reliable source for genotyping C trachomatis strains. A clear advantage of urine over traditional samples, such as cervical swabs, is that urine is a non-invasive source which makes collection easier and thus facilitates the enrolment of patients in clinical and epidemiological studies. In addition to typing, urine is increasingly used for diagnosis of C trachomatis infection by several commercially available nucleic acid amplification assays which represents a distinct advantage for collecting, transport, storage, and laboratory handling of samples.

Prevalence of Chlamydophila abortus infection in domesticated ruminants in Taiwan

This study is to (1) investigate the prevalence of Chlamydophila abortus infection in cows and goats in Taiwan, and (2) compare the genetic properties of Taiwanese isolates with abortion strains from other sources. Approximately 71% of aborted cows and 58% of aborted does had IgG against C. abortus in their sera. The seroprevalence rate in cows may be overestimated, because a certain degree of cross-reactivity with C. pecorum cannot be ruled out. Only 22.7% (from aborted cows) and 33.3% (from aborted dogs) of vaginal swabs that tested positive by polymerase chain reaction led to successful isolation of C. abortus by inoculation into chicken embryos, equivalent to 7.1% and 7.9% of isolation rates, respectively. The major outer membrane protein gene of 15 Taiwanese abortion isolates was compared with that of various strains by restriction fragment length polymorphism (RFLP) and nucleotide sequencing. Restriction enzyme CfoI was able to distinguish Taiwanese ruminant isolates, which have identical RFLP patterns, from C. felis (feline) and C. psittaci (avian) strains. Taiwanese isolates had 98.8-100% homology with known ruminant abortion strains and were phylogenetically closest to bovine LW508 strain.

Characterization of Chlamydia trachomatis omp1 genotypes among sexually transmitted disease patients in Sweden

A method for detection and genotyping of genital Chlamydia trachomatis infections based on omp1 gene amplification and sequencing was developed. DNA was extracted from urogenital or urine samples using a Chelex-based method, and an approximately 1,100-bp-long fragment from the omp1 gene was directly amplified and sequenced. Genotyping was performed by BLAST similarity search, and phylogenetic tree analysis was used to illustrate the evolutionary relationships between clinical isolates and reference strains. The method was used to determine the genotypes of C. trachomatis in 237 positive urogenital and/or urine specimens collected at a Swedish sexually transmitted disease clinic during 1 year. The most common genotypes corresponded to serotypes E (47%) and F (17%). The omp1 gene was highly conserved for genotype E (106 of 112 samples without any mutation) and F (41 of 42 samples without any mutation) strains but appear slightly less conserved for genotypes G (n = 6) and H (n = 6), where the sequences displayed one to four nucleotide substitutions relative to the reference sequence. Genotyping of samples collected at the follow-up visit indicated that two patients had become reinfected, while three other patients suffered treatment failure or reinfection. One woman appeared to have a mixed infection with two different C. trachomatis strains. This omp1 genotyping method had a high reproducibility and could be used for epidemiological characterization of sexually transmitted Chlamydia infections.

Analysis of genetic heterogeneity in Chlamydia trachomatis clinical isolates of serovars D, E, and F by amplified fragment length polymorphism

Amplified fragment length polymorphism (AFLP) fingerprinting of clinical isolates of Chlamydia trachomatis serovars D, E, and F showed a low percentage of genetic heterogeneity, but clear differences were found. Isolates from index patients and partners had identical AFLP patterns and AFLP markers. Characterization of these AFLP markers could give more insight into the differences in virulence and clinical course of C. trachomatis infections.

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).

Restriction fragment length polymorphism analysis using random chromosomal gene probes for epidemiological analysis of Campylobacter jejuni infections

We have evaluated the ability of a new genotyping method for Campylobacter jejuni based on restriction fragment length polymorphisms using random chromosomal gene probes. DNAs from C. jejuni strains digested with each of three restriction enzymes, HhaI, HaeIII, and HpaII, were analyzed by Southern hybridization using each of two unrelated cosmid clones, P14 and P15 (respectively containing 30- and 35-kb genomic DNA fragments of C. jejuni strain OH4384). The method reported provides a stable and discriminating means for identifying C. jejuni strains and should be useful for epidemiological analyses.

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.

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.

The in situ polymerase chain reaction for detection of chlamydia trachomatis

The in situ polymerase chain reaction (PCR) is a technique that has important applications in the diagnosis of viral and bacterial diseases. This study investigated an in situ PCR assay established to detect the presence of Chlamydia trachomatis in endocervical swabs. In addition, histological sections of endocervical squamous cell carcinoma were analyzed because previous studies had revealed a significant association with C. trachomatis. A total of 20 cervical neoplasms (squamous cell carcinoma in situ; n = 10; invasive squamous cell carcinoma; n = 10) and endocervical smears taken from five patients with and without inflammatory changes were analyzed by conventional PCR. Chlamydial DNA was found in 10 histological samples (six carcinomas in situ, four invasive carcinomas) and in one endocervical swab from a patient with known C. trachomatis infection. Positive specimens were used for establishing an in situ PCR assay (IS-PCR). After IS-PCR, these samples showed dense cytoplasmic staining of endocervical cells (smears) and non-neoplastic epithelial cells (cervical neoplasms). The other tumor samples and smears did not demonstrate positive PCR reaction. The results indicate that in situ PCR is an effective technique for localizing C. trachomatis in target cells because IS-PCR detection of chlamydial DNA correlated with histological and cytological features.

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.

Two new serovars of Chlamydia psittaci from North American birds

Five Chlamydia psittaci isolates (1 turkey, 1 psittacine, 1 human, and 2 pigeon isolates) failed to react with serovar-specific monoclonal antibodies to known avian and mammalian C. psittaci serovars and were presumed to represent 1 or more new serovars. The isolates were characterized using restriction endonuclease analysis of the whole genome, polymerase chain reaction-restriction fragment length polymorphism of the major outer membrane protein genome, monoclonal antibody comparisons, and growth in tissue culture. Monoclonal antibodies were produced to the human isolate (MP) and to the psittacine isolate (VS225). The monoclonal antibody results show that the isolates represent 2 new avian serovars (serovars E and F). The restriction fragment length polymorphism analysis of the major outer membrane protein genome demonstrated that the isolates are distinct. The whole genome restriction endonuclease analysis data and the growth patterns in tissue culture indicate that the new serovars are similar to avian serovars recognized previously. A subspecies monoclonal antibody that reacted with serovars A and B also reacted with serovar E, indicating that these serovars are closely related. The results show that these isolates represent 2 new avian serovars, making them the fifth and sixth avian serovars identified in North American birds.

Differentiation of Chlamydia psittaci and C. pecorum strains by species-specific PCR

Sequence analyses 5' ends of the 60-kDa cysteine-rich outer membrane protein genes (Omp2) of Chlamydia psittaci and Chlamydia pecorum strains indicate that these species have approximately 70% nucleotide identity. On the basis of this sequence information, PCR primers were designed to allow the specific amplification of DNA extracted from C. psittaci S26/3 (abortion strain), P94/1 (pigeon strain), and C. pecorum W73 (fecal strain) in one reaction tube. By using nested reactions (with primers PCR-D1 and PCR-D2 followed by the specific primers and PCR-D2), 0.6, 0.2, and 8 inclusion-forming units of S26/3, P94/1 (both diluted in tissue culture-negative placental material), and W73 (diluted in culture-negative fecal material) per ml, respectively, were detected. The differentiation of C. psittaci and C. pecorum strains of ovine and bovine origins was carried out, and the results were in agreement with those obtained from AluI restriction enzyme analysis of DNA amplified from corresponding strains by PCR. This approach allows the simultaneous detection and typing of C. psittaci and C. pecorum strains and the identification of samples containing both species.

The application of genotyping techniques to the epidemiological analysis of Campylobacter jejuni

Campylobacter jejuni serogroup reference strains and collections of sporadic and outbreak-associated isolates were examined for restriction fragment length polymorphisms (RFLPs), using C. jejuni random chromosomal and 16S rRNA gene probes. A collection of 48 Penner (HS) and 14 Lior (HL) serogroup reference strains, plus 10 clinical isolates, generated 35 RFLP and 26 ribotype patterns. In combination the two loci generated 48 distinct genotypes. Both probes were able to differentiate between certain random isolates of the same HS/HL serogroups but greater discrimination was obtained with RFLP than with ribotyping. Genotyping distinguished accurately between related and unrelated strains when applied to several outbreaks. Genotypic analysis of C. jejuni by restriction fragment length polymorphisms is a valuable technique for epidemiological typing. Chromosomal variation detected by the two unlinked probe loci provides some information about the genetic relationship between isolates.

Prevalence and serovar distribution of asymptomatic cervical Chlamydia trachomatis infections as determined by highly sensitive PCR

The prevalence rates and serovar distributions of Chlamydia trachomatis cervical infections were investigated in two different groups of women. Group I consisted of 393 asymptomatic young women (aged 17 to 30 years) who were invited to participate in a C. trachomatis screening program. Group II consisted of 734 randomly selected patients (aged 17 to 68 years) attending an inner-city gynecological outpatient clinic. C. trachomatis was detected in cervical scrapes by PCR specific for endogenous plasmid. These plasmid PCR-positive samples were subsequently subjected to genotyping by C. trachomatis-specific omp1 PCR-based restriction fragment length polymorphism analysis (J. Lan, J. M. M. Walboomers, R. Roosendaal, G. J. van Doornum, D. M. MacLaren, C. J. L. M. Meijer, and A. J. C. van den Brule, J. Clin. Microbiol. 31:1060-1065, 1993). The overall prevalence rates of C. trachomatis found in patients younger than 30 years were 9.2 and 11.8% in groups I and II, respectively. A clear age dependency was seen in group II, with the highest prevalence rate (20%) found in patients younger than 20 years, while the rate declined significantly after 30 years of age (5.9%). In women younger than 30 years, the genotyping results showed that serovars E, I, and D (in decreasing order) were frequent in group I, while serovars F, E, and G (in decreasing order) were predominantly found in group II. The study shows that C. trachomatis infections are highly prevalent in asymptomatic young women. The different serovar distributions found most likely reflect the different compositions of the study groups, but additional analysis of the case histories of individual patients suggests that certain serovars might be associated with symptomatic (i.e., serovar G) or asymptomatic (i.e., serovars D and I) infections.

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.