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Shimada M, Hino F, Yamamoto J, Mukai H, Hosobe T, Onodera S, Hoshina S, Machida K. [Evaluation of the simultaneous detection system for Chlamydia trachomatis/Neisseria gonorrhoeae DNA by the isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN)]. RINSHO BYORI. THE JAPANESE JOURNAL OF CLINICAL PATHOLOGY 2003; 51:1061-7. [PMID: 14679783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
The isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) is a new isothermal DNA amplification method composed of exo Bca DNA polymerase, RNaseH and DNA-RNA chimeric primers. We developed the simultaneous detection system for Chlamydia trachomatis/Neisseria gonorrhoeae DNA, combined with luminescence detection by a probe hybridization. In the performance tests, this system was able to detect 10 to 100 copies of C. trachomatis/N. gonorrhoeae DNA for only 3.5 hours, and was highly specific to C. trachomatis/N. gonorrhoeae without any cross-reaction to C. pneumoniae, N. lactamica, N. sicca or N. meningitidis. When we tested 60 clinical samples of urine and cervical swabs, the interpretive results were completely consistent with those obtained by Roche PCR system. Of 13 positive samples by the ICAN and PCR systems for C. trachomatis, four were negative by EIA method(IDEIA Chlamydia). These results indicate that the ICAN system is an efficient and sensitive system to simultaneously detect C. trachomatis/N. gonorrhoeae DNA.
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627
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Vernikos GS, Gkogkas CG, Promponas VJ, Hamodrakas SJ. GeneViTo: visualizing gene-product functional and structural features in genomic datasets. BMC Bioinformatics 2003; 4:53. [PMID: 14594459 PMCID: PMC280652 DOI: 10.1186/1471-2105-4-53] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Accepted: 10/31/2003] [Indexed: 11/17/2022] Open
Abstract
Background The availability of increasing amounts of sequence data from completely sequenced genomes boosts the development of new computational methods for automated genome annotation and comparative genomics. Therefore, there is a need for tools that facilitate the visualization of raw data and results produced by bioinformatics analysis, providing new means for interactive genome exploration. Visual inspection can be used as a basis to assess the quality of various analysis algorithms and to aid in-depth genomic studies. Results GeneViTo is a JAVA-based computer application that serves as a workbench for genome-wide analysis through visual interaction. The application deals with various experimental information concerning both DNA and protein sequences (derived from public sequence databases or proprietary data sources) and meta-data obtained by various prediction algorithms, classification schemes or user-defined features. Interaction with a Graphical User Interface (GUI) allows easy extraction of genomic and proteomic data referring to the sequence itself, sequence features, or general structural and functional features. Emphasis is laid on the potential comparison between annotation and prediction data in order to offer a supplement to the provided information, especially in cases of "poor" annotation, or an evaluation of available predictions. Moreover, desired information can be output in high quality JPEG image files for further elaboration and scientific use. A compilation of properly formatted GeneViTo input data for demonstration is available to interested readers for two completely sequenced prokaryotes, Chlamydia trachomatis and Methanococcus jannaschii. Conclusions GeneViTo offers an inspectional view of genomic functional elements, concerning data stemming both from database annotation and analysis tools for an overall analysis of existing genomes. The application is compatible with Linux or Windows ME-2000-XP operating systems, provided that the appropriate Java Runtime Environment is already installed in the system.
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628
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Jendro MC, Raum E, Schnarr S, Köhler L, Zeidler H, Kuipers JG, Martin M. Cytokine profile in serum and synovial fluid of arthritis patients with Chlamydia trachomatis infection. Rheumatol Int 2003; 25:37-41. [PMID: 14593490 DOI: 10.1007/s00296-003-0393-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2003] [Accepted: 08/17/2003] [Indexed: 11/28/2022]
Abstract
Chlamydia trachomatis (Ct)-induced arthritis (CtIA) is characterized by persistent Ct infection, which stimulates secretion of cytokines in vitro. We therefore investigated whether CtIA patients have a unique cytokine profile in synovial fluid or serum in vivo. Because underlying Ct infection is overlooked in a high percentage of patients with initially diagnosed undifferentiated oligoarthritis (UOA), we examined whether determination of cytokines might also be of diagnostic relevance for this arthritis form. Matched serum and synovial fluid specimens from 26 patients with CtIA were analyzed and compared to those from 34 patients with UOA in whom Ct infection was excluded and those of nine patients with rheumatoid arthritis (RA). In 15 CtIA patients, Ct DNA from synovial fluid could be amplified by polymerase chain reaction. The following cytokine or cytokine antagonists were measured by enzyme-linked immunosorbent assay: interleukin (IL)-1beta, tumor necrosis factor (TNF)-alpha, IL-6, IL-1 receptor antagonist, and soluble TNF receptor p75. No statistically significant differences in cytokine levels between patients with CtIA or the other arthritis forms were detected. Also, comparison between CtIA patients with (n = 17) and without Chlamydia DNA (n = 9) in synovial fluid revealed no significant differences for these cytokines. Cytokine levels in serum and synovial fluid were not different between CtIA, UOA without Ct infection, and RA patients. The intracellular presence of Ct was not associated with a specific profile of these cytokines in vivo.
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Starnbach MN, Loomis WP, Ovendale P, Regan D, Hess B, Alderson MR, Fling SP. An Inclusion Membrane Protein fromChlamydia trachomatisEnters the MHC Class I Pathway and Stimulates a CD8+T Cell Response. THE JOURNAL OF IMMUNOLOGY 2003; 171:4742-9. [PMID: 14568950 DOI: 10.4049/jimmunol.171.9.4742] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During its developmental cycle, the intracellular bacterial pathogen Chlamydia trachomatis remains confined within a protective vacuole known as an inclusion. Nevertheless, CD8(+) T cells that recognize Chlamydia Ags in the context of MHC class I molecules are primed during infection. MHC class I-restricted presentation of these Ags suggests that these proteins or domains from them have access to the host cell cytoplasm. Chlamydia products with access to the host cell cytoplasm define a subset of molecules uniquely positioned to interface with the intracellular environment during the pathogen's developmental cycle. In addition to their use as candidate Ags for stimulating CD8(+) T cells, these proteins represent novel candidates for therapeutic intervention of infection. In this study, we use C. trachomatis-specific murine T cells and an expression-cloning strategy to show that CT442 from Chlamydia is targeted by CD8(+) T cells. CT442, also known as CrpA, is a 15-kDa protein of undefined function that has previously been shown to be associated with the Chlamydia inclusion membrane. We show that: 1) CD8(+) T cells specific for an H-2D(b)-restricted epitope from CrpA are elicited at a significant level (approximately 4% of splenic CD8(+) T cells) in mice in response to infection; 2) the response to this epitope correlates with clearance of the organism from infected mice; and 3) immunization with recombinant vaccinia virus expressing CrpA elicits partial protective immunity to subsequent i.v. challenge with C. trachomatis.
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630
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Schouenborg P. [Mycoplasma genitalium--a reply]. Ugeskr Laeger 2003; 165:4134; author reply 4134-5. [PMID: 14619068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
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631
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Burton MJ, Holland MJ, Faal N, Aryee EAN, Alexander NDE, Bah M, Faal H, West SK, Foster A, Johnson GJ, Mabey DCW, Bailey RL. Which members of a community need antibiotics to control trachoma? Conjunctival Chlamydia trachomatis infection load in Gambian villages. Invest Ophthalmol Vis Sci 2003; 44:4215-22. [PMID: 14507864 DOI: 10.1167/iovs.03-0107] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Trachoma is the leading cause of infectious blindness worldwide. Control strategies target antibiotic therapy to individuals likely to be infected with Chlamydia trachomatis on the basis of clinical signs. However, many studies have found chlamydial infection in the absence of clinical disease. It has been unclear whether such individuals represent a significant reservoir of infection. In the current study, a quantitative polymerase chain reaction (PCR) assay was used to investigate the distribution and determinants of chlamydial infection load in an endemic community, and the findings were used to evaluate the potential effectiveness of different control strategies. METHODS Members of a trachoma-endemic community (n = 1319) in a rural area of The Gambia were examined for signs of disease, and tarsal conjunctival swab samples were collected. C. trachomatis was initially detected by qualitative PCR. The load of infection was then estimated by real-time quantitative PCR. RESULTS Chlamydial infection was detected in 7.2% of the population. The distribution of infection load was skewed, with a few individuals having high loads. Only 24% of infected individuals had signs of active trachoma. Infection loads were higher in those with clinically active disease and were highest among those with severe inflammatory trachoma. High infection loads were associated with having no accessible latrine and living with a person with active disease. CONCLUSIONS In this low-prevalence setting, infected individuals without signs of active trachoma constitute a significant reservoir of infection. Treatment of a defined unit of people who live with someone with clinically active trachoma would effectively target antibiotic treatment to infected people without signs of disease.
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632
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Berg ES, Skaug K. Liposome encapsulation of the internal control for whole process quality assurance of nucleic acid amplification-based assays. J Microbiol Methods 2003; 55:303-9. [PMID: 14500022 DOI: 10.1016/s0167-7012(03)00165-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A system intended for whole process quality assurance of nucleic acid amplification assays was developed based on the use of liposomes as cell-mimicking vehicles for the internal control, allowing introduction of the internal control directly into the crude biological specimens. By the proof of principle testing, the Roche Cobas Amplicor CT assay was chosen as model system and the Roche CT/NG Internal Control was thus loaded into the liposomes. The liposome/DNA particles were spiked into a Chlamydia trachomatis-positive urine specimen. A quantitative "in-house" duplex real-time C. trachomatis PCR assay showed that liposomes having Blue Dextran 2000 polysaccharide co-entrapped were the most suited particles as they were efficiently deposited by the centrifugation carried out according to the Roche urine specimen preparation procedure. Furthermore, it was demonstrated that the liposome/DNA particles might be used for whole process quality assurance of Amplicor assay without major modifications of the assay protocol. An additional feature of the use of these liposomes was that the pellet became blue coloured and that might facilitate a thorough removal of the urine supernatant without increasing the risk of disturbance of the pellet. Principally, the liposome/internal control system is versatile and seems to be applicable for whole process quality control of amplification-based assays for detection of various pathogens.
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633
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Pannekoek Y, Westenberg SM, Eijk PP, Repping S, van der Veen F, van der Ende A, Dankert J. Assessment of Chlamydia trachomatis infection of semen specimens by ligase chain reaction. J Med Microbiol 2003; 52:777-779. [PMID: 12909654 DOI: 10.1099/jmm.0.05187-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diagnostic potential of the Chlamydia trachomatis ligase chain reaction system (LCx) to assess the presence of C. trachomatis in urine and semen specimens was evaluated. Paired urine and semen specimens from 153 asymptomatic male partners of subfertile couples attending our Center for Reproductive Medicine were examined by LCx. As controls, 19 semen samples from four donors who were participating in the programme for artificial insemination were used. Of these, 12 samples had previously been shown to be C. trachomatis-positive by an in-house PCR. C. trachomatis was detected by LCx in seven of 153 (5 %) urine samples. None of the 153 semen samples tested positive by LCx. Also, none of the 12 C. trachomatis-containing control semen samples were positive by LCx. By in-house PCR, seven urine specimens and two of 153 (1 %) semen samples tested positive. The corresponding urine samples of these male partners were also C. trachomatis-positive, as well as the 12 C. trachomatis-containing samples from donors. In conclusion, LCx is not sensitive enough to assess the presence of C. trachomatis in semen specimens; therefore, this method is not recommended to routinely screen semen specimens from donors who participate in programmes for artificial insemination or male partners of subfertile couples for C. trachomatis.
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634
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Wood H, Fehlner-Gardner C, Berry J, Fischer E, Graham B, Hackstadt T, Roshick C, McClarty G. Regulation of tryptophan synthase gene expression in Chlamydia trachomatis. Mol Microbiol 2003; 49:1347-59. [PMID: 12940992 DOI: 10.1046/j.1365-2958.2003.03638.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We previously reported that Chlamydia trachomatis expresses the genes encoding tryptophan synthase (trpA and trpB). The results presented here indicate that C. trachomatis also expresses the tryptophan repressor gene (trpR). The complement of genes regulated by tryptophan levels in C. trachomatis is limited to trpBA and trpR. trp gene expression was repressed if chlamydiae-infected HeLa cells were cultured the presence of tryptophan and induced if grown in tryptophan-depleted medium or in the presence of IFN-gamma. Furthermore, expression of the trp genes in strains which encode a functional tryptophan synthase is repressed when infected cells are cultured in the presence of the tryptophan precursor indole. Results from experiments with cycloheximide, an inhibitor of eukaryotic protein synthesis, indicate that in addition to the absolute size of the intracellular tryptophan pool, host competition for available tryptophan plays a key role in regulating expression of the trp genes. The tryptophan analogue, 5-fluorotryptophan, repressed trp gene expression and induced the formation of aberrant organisms of C. trachomatis. The growth-inhibitory properties of 5-fluorotryptophan could be reversed with exogenous tryptophan but not indole. In total, our results indicate that the ability to regulate trp gene expression in response to tryptophan availability is advantageous for the intracellular survival of this organism. Furthermore, the fact that C. trachomatis has retained the capacity to respond to tryptophan limitation supports the view that the in vivo antichlamydial effect of IFN-gamma is via the induction of the tryptophan-degrading enzyme, indoleamine 2,3-dioxygenase.
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635
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Wei H, Wu SX, Yu JL, Yang J, Liu GX. [Development of a gap ligase chain reaction for detection of Chlamydia trachomatis in newborn infants]. ZHONGHUA ER KE ZA ZHI = CHINESE JOURNAL OF PEDIATRICS 2003; 41:578-81. [PMID: 14744376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
OBJECTIVE To establish a gap ligase chain reaction (G-LCR) assay for the detection of Chlamydia trachomatis (Ct) in neonates with pneumonia. METHODS A G-LCR DNA amplification assay that targeted the outer major membrane protein gene (omp1) of Ct was developed to detect Ct. The sensitivity and specificity of the G-LCR test was examined by the use of highly purified elementary bodies (EBs). Nasopharyngeal swabs taken from 328 neonates with pneumonia were analyzed by Gap-LCR and cell culture. RESULTS The detection limit of G-LCR was 2 EBs. G-LCR could detect five species of Ct and was not cross-reacted with C psittaci and other bacteria. The prevalence of Ct in 328 neonates with pneumonia, using an expanded gold standard of a positive cell culture or two confirmed positive non-culture tests, was 21% (69/328). After analysis of discrepant results, the sensitivity, specificity, and positive and negative predictive values for the G-LCR were 98.6%, 100%, 100% and 99.6%, respectively; whereas those for culture were 86.9%, 100%, 100% and 96.6%, respectively. CONCLUSION This study demonstrated that the G-LCR was a highly sensitive nonculture technique and good alternative test for the detection of chlamydial infections.
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636
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Schwebke JR, Hook EW. High rates of Trichomonas vaginalis among men attending a sexually transmitted diseases clinic: implications for screening and urethritis management. J Infect Dis 2003; 188:465-8. [PMID: 12870131 DOI: 10.1086/376558] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2002] [Accepted: 03/05/2003] [Indexed: 11/03/2022] Open
Abstract
Trichomonas is a cause of nongonococcal urethritis (NGU); however, studies of its prevalence in men have been hampered by the lack of sensitive diagnostics. DNA amplification allows for reappraisal of the extent of infection in men. Men attending a sexually transmitted diseases clinic were tested for trichomonas, chlamydia, and gonorrhea. The prevalence of these pathogens was 17%, 19.6%, and 17.7% respectively. In men with NGU, 19.9% were infected with trichomonas. These data have implications for treatment of NGU and control of trichomoniasis.
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637
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Culler EE, Caliendo AM, Nolte FS. Reproducibility of positive test results in the BDProbeTec ET system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Clin Microbiol 2003; 41:3911-4. [PMID: 12904416 PMCID: PMC179826 DOI: 10.1128/jcm.41.8.3911-3914.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests such as the BDProbeTec ET (BDPT) system are more prone to reproducibility problems than are antigen detection tests and culture. A repeat testing algorithm for all samples with method other than acceleration (MOTA) scores greater than or equal to the cutoff value (2000) was developed for the BDPT system and applied in a clinical laboratory setting. All positive samples were retested, and if the result of the second test was below the cutoff value, a third test was performed to resolve the discrepancy. Overall, 11 (5.3%) of 207 samples initially positive for Chlamydia trachomatis and 11 (10.7%) of 103 samples initially positive for Neisseria gonorrhoeae were not confirmed by repeat testing of the original sample. Poor reproducibility was associated with low-positive MOTA scores (2000 to 9999) for both analytes. Only 21 (80.8%) of 26 low-positive samples in the C. trachomatis test and 4 (33.3%) of 12 low-positive samples in the N. gonorrhoeae test retested as positive. The reproducibility of both tests with samples with initial MOTA scores of >or=10000 increased to 96.7%. The data suggest that retesting of low-positive samples is warranted and could reduce the number of potentially false-positive test results.
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638
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Schachter J, McCormack WM, Chernesky MA, Martin DH, Van Der Pol B, Rice PA, Hook EW, Stamm WE, Quinn TC, Chow JM. Vaginal swabs are appropriate specimens for diagnosis of genital tract infection with Chlamydia trachomatis. J Clin Microbiol 2003; 41:3784-9. [PMID: 12904390 PMCID: PMC179798 DOI: 10.1128/jcm.41.8.3784-3789.2003] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Because self-collected vaginal swabs (VS) are potentially very useful for screening asymptomatic women for Chlamydia trachomatis infection, a multicenter study evaluated that specimen with nucleic acid amplification tests (NAATs). The objective was to determine whether VS are equal to Food and Drug Administration (FDA)-cleared specimens (cervical swabs and first-catch urines [FCU]) for diagnosing genital chlamydial infection. All NAATs then commercially available (October 1996 to October 1999) were used (ligase chain reaction [LCx Probe System; Abbott Laboratories, Abbott Park, Ill.]; PCR [Amplicor; Roche Molecular Systems, Branchburg, N.J.]; and transcription-mediated amplification, [Amplified CT Assay; Gen-Probe Inc., San Diego, Calif.]). NAATs were performed on FCU, urethral, cervical, self- and clinician-collected VS. Sensitivity was compared to isolation using cervical and urethral swabs. Agreement of NAAT results between VS and cervical swabs or FCU was calculated. Specimens from 2,517 15- to 25-year-old asymptomatic women attending clinics at nine different centers were evaluated. Results with self- and clinician-collected VS were equivalent and were at least as good as results with FCU and cervical swabs. Across all sites, summary specificities for all specimens were >99%. Among culture-positive women, NAAT sensitivity with VS (93%) was as high as or higher than NAAT sensitivity with cervical swabs (91%) or FCU (80.6%) or culture of cervical swabs (83.5%). VS are appropriate specimens for diagnosing chlamydial genital tract infection by NAATs. That patients can efficiently collect them offers important benefits for screening programs. It would be beneficial for public health programs if the NAAT manufacturers sought FDA clearance for this specimen.
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639
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Solomon AW, Holland MJ, Burton MJ, West SK, Alexander NDE, Aguirre A, Massae PA, Mkocha H, Muñoz B, Johnson GJ, Peeling RW, Bailey RL, Foster A, Mabey DCW. Strategies for control of trachoma: observational study with quantitative PCR. Lancet 2003; 362:198-204. [PMID: 12885481 DOI: 10.1016/s0140-6736(03)13909-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Antibiotics are an important part of WHO's strategy to eliminate trachoma as a blinding disease by 2020. At present, who needs to be treated is unclear. We aimed to establish the burden of ocular Chlamydia trachomatis in three trachoma-endemic communities in Tanzania and The Gambia with real-time quantitative PCR. METHODS Conjunctival swabs were obtained at examination from 3146 individuals. Swabs were first tested by the qualitative Amplicor PCR, which is known to be highly sensitive. In positive samples, the number of copies of omp1 (a single-copy C trachomatis gene) was measured by quantitative PCR. FINDINGS Children had the highest ocular loads of C trachomatis, although the amount of pooling in young age groups was less striking at the site with the lowest trachoma frequency. Individuals with intense inflammatory trachoma had higher loads than did those with other conjunctival signs. At the site with the highest prevalence of trachoma, 48 of 93 (52%) individuals with conjunctival scarring but no sign of active disease were positive for ocular chlamydiae. INTERPRETATION Children younger than 10 years old, and those with intense inflammatory trachoma, probably represent the major source of ocular C trachomatis infection in endemic communities. Success of antibiotic distribution programmes could depend on these groups receiving effective treatment.
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640
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Belland RJ, Zhong G, Crane DD, Hogan D, Sturdevant D, Sharma J, Beatty WL, Caldwell HD. Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis. Proc Natl Acad Sci U S A 2003; 100:8478-83. [PMID: 12815105 PMCID: PMC166254 DOI: 10.1073/pnas.1331135100] [Citation(s) in RCA: 373] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlamydia trachomatis is one of the most common bacterial pathogens and is the etiological agent of debilitating sexually transmitted and ocular diseases in humans. The organism is an obligate intracellular prokaryote characterized by a highly specialized biphasic developmental cycle. We have performed genomic transcriptional analysis of the chlamydial developmental cycle. This approach has led to the identification of a small subset of genes that control the primary (immediate-early genes) and secondary (late genes) differentiation stages of the cycle. Immediate-early gene products initiate bacterial metabolism and potentially modify the bacterial phagosome to escape fusion with lysosomes. One immediate early gene (CT147) is a homolog of the human early endosomal antigen-1 that is localized to the chlamydial phagosome; suggesting a functional role for CT147 in establishing the parasitophorous vacuole in a nonfusogenic pathway. Late gene products terminate bacterial cell division and constitute structural components and remodeling activities involved in the formation of the highly disulfide cross-linked outer-membrane complex that functions in attachment and invasion of new host cells. Many of the genes expressed during the immediate-early and late differentiation stages are Chlamydia-specific and have evolutionary origins in eukaryotic lineages.
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642
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Dreses-Werringloer U, Padubrin I, Köhler L, Hudson AP. Detection of nucleotide variability in rpoB in both rifampin-sensitive and rifampin-resistant strains of Chlamydia trachomatis. Antimicrob Agents Chemother 2003; 47:2316-8. [PMID: 12821487 PMCID: PMC161851 DOI: 10.1128/aac.47.7.2316-2318.2003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 656-bp PCR fragment from rpoB was sequenced from five rifampin-resistant Chlamydia trachomatis variants selected in vitro from a wild-type parent with a surprising level of genetic variability in this region. Three variants (MIC, 4 microg/ml) showed Ala522-->Val in cluster I (codons 507 to 533), which harbors mutations in most rifampin-resistant bacteria. Two high-level resistance variants (MICs, 64 and 256 microg/ml) showed His526-->Tyr in cluster I with additional genetic variation, some of which resulted in amino acid substitutions. None of the latter was situated in clusters related to rifampin resistance in other bacteria.
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643
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Verkooyen RP, Noordhoek GT, Klapper PE, Reid J, Schirm J, Cleator GM, Ieven M, Hoddevik G. Reliability of nucleic acid amplification methods for detection of Chlamydia trachomatis in urine: results of the first international collaborative quality control study among 96 laboratories. J Clin Microbiol 2003; 41:3013-6. [PMID: 12843035 PMCID: PMC165323 DOI: 10.1128/jcm.41.7.3013-3016.2003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first European Quality Control Concerted Action study was organized to assess the ability of laboratories to detect Chlamydia trachomatis in a panel of urine samples by nucleic acid amplification tests (NATs). The panel consisted of lyophilized urine samples, including three negative, two strongly positive, and five weakly positive samples. Ninety-six laboratories in 22 countries participated with a total of 102 data sets. Of 204 strongly positive samples 199 (97.5%) were correctly reported, and of 506 weakly positive samples 466 (92.1%) were correctly reported. In 74 (72.5%) data sets correct results were reported on all samples, and 17 data sets (16.7%) showed either one false-negative or one false-positive result. In another 11 data sets, two or more incorrect results were reported, and two data sets reported a false-positive result on one negative sample. The Roche COBAS Amplicor test was performed in 44 (43%) data sets, the Abbott LCx assay was performed in 31 (30%) data sets, the Roche Amplicor manual assay was performed in 9 (9%) data sets, an in-house PCR was performed in 9 (9%) data sets, the Becton Dickinson ProbeTec ET assay was performed in 5 (4.9%) data sets, and the GenProbe TMA assay was performed in 4 (3.9%) data sets. The results of the Roche Amplicor manual (95.6% correct), COBAS Amplicor (97.0%), and Abbott LCx (94.8%) tests were comparable (P = 0.48). The results with the in-house PCR, BD ProbeTec ET, and GenProbe TMA tests were reported correctly in 88.6, 98, and 92.5% of the tests, respectively. Freeze-drying of clinical urine specimens proved to be a successful method for generating standardized, stable, and easy-to-transport samples for the detection of C. trachomatis by using NATs. Although the results, especially the specificity, for this proficiency panel were better than most quality control studies, sensitivity problems occurred frequently, underlining the need for good laboratory practice and reference reagents to monitor the performance of these assays.
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644
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Vinayagamoorthy T, Mulatz K, Hodkinson R. Nucleotide sequence-based multitarget identification. J Clin Microbiol 2003; 41:3284-92. [PMID: 12843076 PMCID: PMC165273 DOI: 10.1128/jcm.41.7.3284-3292.2003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MULTIGEN technology (T. Vinayagamoorthy, U.S. patent 6,197,510, March 2001) is a modification of conventional sequencing technology that generates a single electropherogram consisting of short nucleotide sequences from a mixture of known DNA targets. The target sequences may be present on the same or different nucleic acid molecules. For example, when two DNA targets are sequenced, the first and second sequencing primers are annealed to their respective target sequences, and then a polymerase causes chain extension by the addition of new deoxyribose nucleotides. Since the electrophoretic separation depends on the relative molecular weights of the truncated molecules, the molecular weight of the second sequencing primer was specifically designed to be higher than the combined molecular weight of the first sequencing primer plus the molecular weight of the largest truncated molecule generated from the first target sequence. Thus, the series of truncated molecules produced by the second sequencing primer will have higher molecular weights than those produced by the first sequencing primer. Hence, the truncated molecules produced by these two sequencing primers can be effectively separated in a single lane by standard gel electrophoresis in a single electropherogram without any overlapping of the nucleotide sequences. By using sequencing primers with progressively higher molecular weights, multiple short DNA sequences from a variety of targets can be determined simultaneously. We describe here the basic concept of MULTIGEN technology and three applications: detection of sexually transmitted pathogens (Neisseria gonorrhoeae, Chlamydia trachomatis, and Ureaplasma urealyticum), detection of contaminants in meat samples (coliforms, fecal coliforms, and Escherichia coli O157:H7), and detection of single-nucleotide polymorphisms in the human N-acetyltransferase (NAT1) gene (S. Fronhoffs et al., Carcinogenesis 22:1405-1412, 2001).
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Caldwell HD, Wood H, Crane D, Bailey R, Jones RB, Mabey D, Maclean I, Mohammed Z, Peeling R, Roshick C, Schachter J, Solomon AW, Stamm WE, Suchland RJ, Taylor L, West SK, Quinn TC, Belland RJ, McClarty G. Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates. J Clin Invest 2003; 111:1757-69. [PMID: 12782678 PMCID: PMC156111 DOI: 10.1172/jci17993] [Citation(s) in RCA: 224] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
We previously reported that laboratory reference strains of Chlamydia trachomatis differing in infection organotropism correlated with inactivating mutations in the pathogen's tryptophan synthase (trpBA) genes. Here, we have applied functional genomics to extend this work and find that the paradigm established for reference serovars also applies to clinical isolates - specifically, all ocular trachoma isolates tested have inactivating mutations in the synthase, whereas all genital isolates encode a functional enzyme. Moreover, functional enzyme activity was directly correlated to IFN-gamma resistance through an indole rescue mechanism. Hence, a strong selective pressure exists for genital strains to maintain a functional synthase capable of using indole for tryptophan biosynthesis. The fact that ocular serovars (serovar B) isolated from the genital tract were found to possess a functional synthase provided further persuasive evidence of this association. These results argue that there is an important host-parasite relationship between chlamydial genital strains and the human host that determines organotropism of infection and the pathophysiology of disease. We speculate that this relationship involves the production of indole by components of the vaginal microbial flora, allowing chlamydiae to escape IFN-gamma-mediated eradication and thus establish persistent infection.
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646
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Oehme A, Gaschler G, Straube E. Genotyping of Chlamydia trachomatis strains from cultured isolates and nucleic acid amplification test-positive specimens. Int J Med Microbiol 2003; 293:225-8. [PMID: 12868660 DOI: 10.1078/1438-4221-00238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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647
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Singh V, Salhan S, Das BC, Mittal A. Predominance of Chlamydia trachomatis serovars associated with urogenital infections in females in New Delhi, India. J Clin Microbiol 2003; 41:2700-2. [PMID: 12791909 PMCID: PMC156538 DOI: 10.1128/jcm.41.6.2700-2702.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.
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648
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Baseviciene I, Labanauskas L, Vysniauskaite N. [Early diagnosis of genital Chlamydia trachomatis infection among adolescent girls]. MEDICINA (KAUNAS, LITHUANIA) 2003; 39:138-43. [PMID: 12626866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
UNLABELLED Genital Chlamydia trachomatis infection is the most frequently found sexually transmitted disease among sexually active adolescent 15-19-year-old girls. In general, infection caused by C. trachomatis tends to be less abrupt in onset, clinical course is usually characterized as asymptomatic or with mild symptoms. If is although the cause of moderate to severe complications (infertility, pelvic inflammatory diseases) at a later age. OBJECTIVE To study the prevalence of chlamydia infection and the possibilities and of early detection among adolescent girls. METHODS Four hundred eighty seven 15-19-year-old girls were questioned by anonymous questionnaire. All 240 sexually active girls were advised to come for the investigation to the Clinic of Pediatrics of Kaunas University of Medicine Hospital. Fifty nine girls underwent inspection of the genitalia, had a speculum and bimanual pelvic examination, test of CT/NG DNA hybridisation for C. trachomatis from vagina. Smears from urethra vagina and cervix were taken. RESULTS Test for C. trachomatis infection was positive in 11 (18%) by CT/NG DNA hibridisation from vagina. Detection of bad smelling discharge from vagina together with nonspecific changes in vaginal and cervical mucosa, mount and methylene blue prepared smears could reliably predict the diagnosis of C. trachomatis infection. CONCLUSION We found high prevalence of C. trachomatis infection among adolescent girls. Only clinical symptoms together with nospecifical test were reliable predictors of the final diagnosis, enabling to start the early treatment.
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Klein M, Kötz A, Bernardo K, Krönke M. Detection of Chlamydia pneumoniae-specific antibodies binding to the VD2 and VD3 regions of the major outer membrane protein. J Clin Microbiol 2003; 41:1957-62. [PMID: 12734234 PMCID: PMC154690 DOI: 10.1128/jcm.41.5.1957-1962.2003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although Chlamydia pneumoniae is an important human pathogen, the antigens eliciting a specific humoral immune response remain elusive. We scrutinized several recombinant chlamydial surface proteins for species-specific recognition by a panel of human sera previously tested for the presence of anti-C. pneumoniae and anti-C. trachomatis antibodies by microimmunofluorescence and enzyme-linked immunosorbent assay. The 15-kDa cysteine-rich protein (CrpA), porin-b (PorB), 9-kDa outer membrane protein (OMP3), 60-kDa outer membrane protein (OMP2), and four fragments of the major outer membrane protein (MOMP) representing each variable domain (VD) were overexpressed in Escherichia coli, affinity purified, and employed for Western blot analysis. None of the sera tested contained antibodies recognizing PorB and OMP3 of C. pneumoniae. Sera from C. pneumoniae-immune patients cross-reacted with OMP2 of C. trachomatis, and sera from C. trachomatis-immune patients cross-reacted with CrpA of C. pneumoniae, indicating that some of chlamydial surface molecules share antigenic epitopes. In contrast, the VD2, as well as the VD3, regions of the MOMP of C. pneumoniae were only recognized by C. pneumoniae-positive sera, suggesting the existence of species-specific epitopes. The identification of such epitopes of cell surface molecules provides new insights into C. pneumoniae-specific immune responses and may be of value for the improvement of C. pneumoniae-specific diagnostic assay systems based on defined recombinant antigens.
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Golden MR, Astete SG, Galvan R, Lucchetti A, Sanchez J, Celum CL, Whittington WLH, Stamm WE, Holmes KK, Totten PA. Pilot study of COBAS PCR and ligase chain reaction for detection of rectal infections due to Chlamydia trachomatis. J Clin Microbiol 2003; 41:2174-5. [PMID: 12734272 PMCID: PMC154739 DOI: 10.1128/jcm.41.5.2174-2175.2003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2002] [Revised: 02/12/2003] [Accepted: 02/18/2003] [Indexed: 11/20/2022] Open
Abstract
We tested rectal specimens from men who have sex with men for Chlamydia trachomatis by using COBAS PCR (Roche Diagnostics) and ligase chain reaction LCR (Abbott laboratories) and compared three PCR specimen-processing procedures. Chlamydiae were detected by one or more procedures in 22 of 186 specimens. All three PCR tests were positive for 17 specimens, all of which also tested positive by LCR.
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