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Xiu L, Li Y, Zhang C, Li Y, Zeng Y, Wang F, Peng J. A molecular screening assay to identify Chlamydia trachomatis and distinguish new variants of C. trachomatis from wild-type. Microb Biotechnol 2020; 14:668-676. [PMID: 33277967 PMCID: PMC7936308 DOI: 10.1111/1751-7915.13724] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/15/2020] [Accepted: 11/16/2020] [Indexed: 01/13/2023] Open
Abstract
Chlamydia trachomatis is the most common sexually transmitted pathogen globally, causing serious health problems and representing a burden on public health. A new variant of C. trachomatis (nvCT) that carries mutations (C1514T, C1515T and G1523A) in the 23S rRNA gene has eluded detection in Aptima Combo 2 assays. This has led to false negatives in diagnostics tests and poses a challenge for C. trachomatis diagnostics on a global level. In this study, we developed a simple and cost‐effective assay to identify C. trachomatis, with a potential application to screen for nvCT. We developed a screening assay based on high‐resolution melting (HRM), targeting the 23S rRNA gene and cryptic plasmid. To evaluate the performance of the assay, 404 archived C. trachomatis DNA specimens and 570 extracted clinical specimens were analysed. Our HRM assay not only identified C. trachomatis in clinical specimens, but also correctly differentiated nvCT carrying C1514T, C1515T and G1523A mutations from the wild‐type. We observed no cross‐reactions with other clinically related agents, and the limit of detection was 11.26 (95% CI; 7.61–31.82) copies per reaction. Implementation of this screening assay could reduce detection times and costs for C. trachomatis diagnoses, and facilitate increased research on the presence and monitoring of nvCT.
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Affiliation(s)
- Leshan Xiu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yamei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yizhun Li
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yaling Zeng
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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2
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Dahlberg J, Hadad R, Elfving K, Larsson I, Isaksson J, Magnuson A, Fredlund H, Unemo M, Herrmann B. Ten years transmission of the new variant of Chlamydia trachomatis in Sweden: prevalence of infections and associated complications. Sex Transm Infect 2017; 94:100-104. [PMID: 28724744 PMCID: PMC5870454 DOI: 10.1136/sextrans-2016-052992] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES In 2006, a new variant of Chlamydia trachomatis (nvCT) was discovered in Sweden. It has a deletion in the plasmid resulting in failed detection by the single target systems from Abbott and Roche used at that time, whereas the third system used, from Becton Dickinson (BD), detects nvCT. The proportion of nvCT was initially up to 65% in counties using Abbott/Roche systems. This study analysed the proportion of nvCT from 2007 to 2015 in four selected counties and its impact on chlamydia-associated complications. METHODS C. trachomatis-positive specimens collected from 2007 to 2015 were analysed by a specific PCR to identify nvCT cases. Genotyping was performed by multilocus sequence typing (MLST) and ompA sequencing. Ectopic pregnancy and pelvic inflammatory disease records were extracted from the national registers. RESULTS In total, 5101 C. trachomatis-positive samples were analysed. The nvCT proportion significantly decreased in the two counties using Roche systems, from 56% in 2007 to 6.5% in 2015 (p<0.001). In the two counties using BD systems, a decrease was also seen, from 19% in 2007 to 5.2% in 2015 (p<0.001). Fifteen nvCT cases from 2015 and 102 cases from 2006 to 2009 had identical MLST profiles. Counties using Roche/Abbott systems showed higher mean rates of ectopic pregnancy and pelvic inflammatory disease compared with counties using BD systems. CONCLUSIONS The nvCT proportion has decreased in all counties and converged to a low prevalence irrespective of previous rates. Genotyping showed that nvCT is clonal and genetically stable. Failing detection only marginally affected complication rates.
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Affiliation(s)
- Jenny Dahlberg
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University, Örebro, Sweden
| | - Karin Elfving
- Department of Clinical Microbiology, Falu Lasarett, Falun, Sweden
| | - Inger Larsson
- Department of Clinical Microbiology, Sunderby Hospital, Luleå, Sweden
| | - Jenny Isaksson
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Anders Magnuson
- Department of Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Hans Fredlund
- WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, Örebro University, Örebro, Sweden
| | - Bjőrn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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Turingan RS, Kaplun L, Krautz-Peterson G, Norsworthy S, Zolotova A, Joseph SJ, Read TD, Dean D, Tan E, Selden RF. Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay. PLoS One 2017; 12:e0178653. [PMID: 28562672 PMCID: PMC5451082 DOI: 10.1371/journal.pone.0178653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/16/2017] [Indexed: 11/19/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) are recommended by the CDC for detection of Chlamydia trachomatis (Ct) urogenital infections. Current commercial NAATs require technical expertise and sophisticated laboratory infrastructure, are time-consuming and expensive, and do not differentiate the lymphogranuloma venereum (LGV) strains that require a longer duration of treatment than non-LGV strains. The multiplexed microfluidic PCR-based assay presented in this work simultaneously interrogates 13 loci to detect Ct and identify LGV and non-LGV strain-types. Based on amplified fragment length polymorphisms, the assay differentiates LGV, ocular, urogenital, and proctocolitis clades, and also serovars L1, L2, and L3 within the LGV group. The assay was evaluated in a blinded fashion using 95 clinical swabs, with 76 previously reported as urogenital Ct-positive samples and typed by ompA genotyping and/or Multi-Locus Sequence Typing. Results of the 13-plex assay showed that 51 samples fell within urogenital clade 2 or 4, 24 samples showed both clade 2 and 4 signatures, indicating possible mixed infection, gene rearrangement, or inter-clade recombination, and one sample was a noninvasive trachoma biovar (either a clade 3 or 4). The remaining 19 blinded samples were correctly identified as LGV clade 1 (3), ocular clade 3 (4), or as negatives (12). To date, no NAAT assay can provide a point-of-care applicable turnaround time for Ct detection while identifying clinically significant Ct strain types to inform appropriate treatment. Coupled with rapid DNA processing of clinical swabs (approximately 60 minutes from swab-in to result-out), the assay has significant potential as a rapid POC diagnostic for Ct infections.
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Affiliation(s)
| | - Ludmila Kaplun
- NetBio, Waltham, Massachusetts, United States of America
| | | | | | - Anna Zolotova
- NetBio, Waltham, Massachusetts, United States of America
| | - Sandeep J. Joseph
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Timothy D. Read
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deborah Dean
- Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- University of California at San Francisco School of Medicine, San Francisco, California, United States of America
- University of California at Berkeley and University of California at San Francisco Joint Graduate Program in Bioengineering, Berkeley, California, United States of America
| | - Eugene Tan
- NetBio, Waltham, Massachusetts, United States of America
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Abstract
Sex-specific endocrine and immune responses are widely recognized to account for differential disease outcomes between females and males. Surprisingly, sex-specific risk assessments for influenza, a viral pathogen that affects human populations worldwide through seasonal epidemics and irregular occurring pandemics, are sparse and-if available-ambiguous. To date, this precludes proposing an unequivocal sex-dependent susceptibility to influenza. However, one undisputable observation recurrently confirmed during influenza seasons of the last decades is the significantly increased risk for pregnant women. This increased risk is likely attributable to the contradictory demands for the maternal immune system to adapt to pregnancy and to simultaneously mount an immune response to clear the influenza virus infection. Here, we review published evidence on the potential association between sex on influenza risk and propose that future epidemiologic studies should carefully dissect surveillance data for sex-specific effects. Moreover, we propose potential mechanisms involved in enhanced risk for severe influenza during pregnancy that could be studied to identify causal pathways.
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Affiliation(s)
- Gülsah Gabriel
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology
| | - Petra Clara Arck
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Germany
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Won H, Ramachandran P, Steece R, Van Der Pol B, Moncada J, Schachter J, Gaydos C. Is there evidence of the new variant Chlamydia trachomatis in the United States? Sex Transm Dis 2013; 40:352-3. [PMID: 23588122 DOI: 10.1097/olq.0b013e3182841786] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A specific real-time polymerase chain reaction followed by melt curve analysis was developed for the detection of the Swedish variant (nvCT) strain of Chlamydia trachomatis (CT). Surveillance was performed on 476 CT-positive clinical specimens obtained from 15 laboratories around the United States using nucleic acid amplification test assays, which would not miss the nvCT. All were negative for nvCT; thus, there is no evidence of the nvCT in the United States.
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Affiliation(s)
- Helen Won
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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6
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Jurstrand M, Fredlund H, Unemo M. The new variant ofChlamydia trachomatiswas present as early as 2003 in Örebro County, Sweden, but remained undetected until 2006. Sex Transm Infect 2013; 89:607-8. [DOI: 10.1136/sextrans-2013-051018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Dean D, Turingan RS, Thomann HU, Zolotova A, Rothschild J, Joseph SJ, Read TD, Tan E, Selden RF. A multiplexed microfluidic PCR assay for sensitive and specific point-of-care detection of Chlamydia trachomatis. PLoS One 2012; 7:e51685. [PMID: 23272140 PMCID: PMC3522697 DOI: 10.1371/journal.pone.0051685] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 11/05/2012] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Chlamydia trachomatis (Ct) is the most common cause of bacterial sexually transmitted diseases (STD) worldwide. While commercial nucleic acid amplification tests (NAAT) are available for Ct, none are rapid or inexpensive enough to be used at the point-of-care (POC). Towards the first Ct POC NAAT, we developed a microfluidic assay that simultaneously interrogates nine Ct loci in 20 minutes. METHODOLOGY AND PRINCIPAL FINDINGS Endocervical samples were selected from 263 women at high risk for Ct STDs (∼35% prevalence). A head-to-head comparison was performed with the Roche-Amplicor NAAT. 129 (49.0%) and 88 (33.5%) samples were positive by multiplex and Amplicor assays, respectively. Sequencing resolved 71 discrepant samples, confirming 53 of 53 positive multiplex samples and 12 of 18 positive Amplicor samples. The sensitivity and specificity were 91.5% and 100%, and 62.4% and 95.9%, respectively, for multiplex and Amplicor assays. Positive and negative predictive values were 100% and 91%, and 94.1% and 68.6%, respectively. CONCLUSIONS This is the first rapid multiplex approach to Ct detection, and the assay was also found to be superior to a commercial NAAT. In effect, nine simultaneous reactions significantly increased sensitivity and specificity. Our assay can potentially increase Ct detection in globally diverse clinical settings at the POC.
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Affiliation(s)
- Deborah Dean
- Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- University of California at Berkeley and University of California at San Francisco Joint Graduate Program in Bioengineering, Berkeley, California, United States of America
| | | | | | - Anna Zolotova
- NetBio, Waltham, Massachusetts, United States of America
| | - James Rothschild
- Center for Immunobiology and Vaccine Development, Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- University of California at Berkeley and University of California at San Francisco Joint Graduate Program in Bioengineering, Berkeley, California, United States of America
| | - Sandeep J. Joseph
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Timothy D. Read
- Department of Medicine, Division of Infectious Diseases and Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eugene Tan
- NetBio, Waltham, Massachusetts, United States of America
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Parra-Sánchez M, Palomares JC, Bernal S, González MT, Sivianes N, Pérez L, Pueyo I, Martín-Mazuelos E. Evaluation of the cobas 4800 CT/NG Test for detecting Chlamydia trachomatis and Neisseria gonorrhoeae DNA in urogenital swabs and urine specimens. Diagn Microbiol Infect Dis 2012; 74:338-42. [PMID: 22995365 DOI: 10.1016/j.diagmicrobio.2012.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/06/2012] [Accepted: 08/06/2012] [Indexed: 01/25/2023]
Abstract
We have evaluated 696 samples (488 swabs and 208 urine specimens) with the cobas 4800 (c4800) CT/NG Test for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae DNA in swab and urine specimens. c4800 results were compared with those obtained from COBAS AMPLICOR (CAM) CT/NG Test. Discordant results were reanalyzed with the MultiNA system and compared with clinical data. For C. trachomatis detection by both methods, we obtained 93.8%, 100%, 100%, and 99.1% for sensitivity, specificity, and positive and negative predictive values, respectively. For urine specimens analyzed in c4800, our results were 96.6%, 100%, 100%, and 99.4%, respectively. For N. gonorrhoeae detection, swab results were:88.0%, 100%, 100%, and 99.4%. For urine specimen, results obtained were 100%, 100%, 100%, and 100%. Reanalyses were all concordant between both methods. c4800 results were comparable with those obtained with the CAM system. We had an excellent correlation between swab and urine specimens analyzed by c4800.
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Affiliation(s)
- Manuel Parra-Sánchez
- Unidad de Enfermedades Infecciosas y Microbiología Clínica, Instituto de Biomedicina de Sevilla, University Hospital of Valme. Av. Bellavista, 41014 Seville, Spain.
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9
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Parra M, Palomares JC, Bernal S, Sivianes N, Pérez L, Pueyo I, Almeida C, Martín-Mazuelos E. [Evaluation of the cobas 4800 CT/NG test for detecting Chlamydia trachomatis]. Enferm Infecc Microbiol Clin 2011; 29:421-4. [PMID: 21546129 DOI: 10.1016/j.eimc.2011.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/23/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
Abstract
INTRODUCTION To evaluate the new automated system cobas 4800 CT/NG test for detection of Chlamydia trachomatis in urogenital specimens. MATERIAL AND METHODS We analyzed 696 specimens (488 swabs from urethral or cervical specimens, and 208 urines) to detect C. trachomatis. The results of the cobas 4800 CT/NG test (c4800) were compared to those obtained with Cobas AMPLICOR CT/NG test (CAM). Discordant results were analyzed with a conventional PCR assay and microchip electrophoresis system in agarose gel, MultiNA. RESULTS We made two simultaneous analyses. In the first one, we compared the results obtained with swab specimens using the c4800 system and CAM. In this case, the sensitivity, the specificity, the positive and negative predictive values (PPV and NPV) were: 77.9%, 100%, 100% and 96% respectively. In the second one, we compared the results obtained for urine and its corresponding swab specimens on the c4800. The values obtained were: 100%, 98.9%, 92.9% and 100% respectively. The kappa values of these comparisons were: 0.857 for swab specimens on the c4800 and CAM, and 0.957 for urine versus swab specimens on the c4800. CONCLUSIONS The results obtained with c4800 system were completely comparable with those obtained with CAM. We also noted an excellent correlation with these results when we compared swab specimens with their urine samples in the c4800 system. Therefore this sample type could be used routinely to diagnose infections in men and women.
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Affiliation(s)
- Manuel Parra
- Laboratorio de Microbiología Molecular, Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Valme, Sevilla, Spain.
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Abstract
PURPOSE OF REVIEW This review focuses on the anatomy of the Swedish new variant of Chlamydia trachomatis (nvCT). This information provides an interesting insight into the emergence of new strains (how, where, and when), and the important lessons learned are discussed. RECENT FINDINGS In late 2006, the nvCT was first reported in Sweden; it carries a 377 bp deletion within its plasmid which covers the single targets originally used by Roche and Abbott diagnostic systems. The nvCT spread rapidly with thousands of falsely negative diagnoses. Genome sequencing and phenotypic characterization showed that the biological fitness of nvCT when compared with wild-type CT in vitro is unaltered. Therefore, the rapid transmission of nvCT was due to the selective advantage gained from failed diagnosis and the introduction of nvCT into a high-frequency transmitting population. The proportions of nvCT cases are now converging toward equilibrium with the wild-type CT strains. Interestingly, the nvCT remains rarely reported beyond the Nordic countries. SUMMARY The spread of nvCT had a substantial impact on C. trachomatis identification, epidemiology, and public health in Sweden. Lessons learned from this experience include the importance of investigating the incidence and epidemiology of infection in detail, the frequent participation in appropriate quality assurance schemes, and the careful design of diagnostic assays. The nvCT presents a unique opportunity to study the spread of a single C. trachomatis strain within both the human and bacterial populations; this may substantially increase our knowledge of epidemiology and transmission of chlamydial infections, and other sexually transmitted infections.
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Falk L, Coble BI, Mjörnberg PA, Fredlund H. Sampling for Chlamydia trachomatis infection - a comparison of vaginal, first-catch urine, combined vaginal and first-catch urine and endocervical sampling. Int J STD AIDS 2010; 21:283-7. [PMID: 20378903 DOI: 10.1258/ijsa.2009.009440] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The aim of the study was to evaluate the sensitivity of patients' self-sampled vaginal specimens, first-catch urine (FCU), combined vaginal/FCU specimens and endocervical specimens for detecting chlamydial infection in women. Women attending sexually transmitted disease clinics, youth clinics and a women's health clinic were enrolled. They self-collected a vaginal specimen with two swabs, which were placed into a sterile tube and into a tube containing a buffer medium, respectively. An FCU sample was collected and aliquoted into both an empty tube and the tube containing the vaginal swab. A clinician collected an endocervical swab. The samples were sent to laboratories for analysis using polymerase chain reaction testing and strand displacement amplification testing, respectively. The sensitivities calculated in all 171 Chlamydia trachomatis-infected women were equal for endocervical specimens (97.1%), vaginal specimens (96.5%) and combined vaginal/FCU specimens (95.3%), whereas the sensitivity for FCU was significantly lower (87.7%). The sensitivity of vaginal specimens for the detection of C. trachomatis is as high as that of combined vaginal/FCU specimens.
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Affiliation(s)
- L Falk
- Department of Local Health Care, County of Ostergötland, Linköping University, Linköping.
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12
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Unemo M, Seth-Smith HMB, Cutcliffe LT, Skilton RJ, Barlow D, Goulding D, Persson K, Harris SR, Kelly A, Bjartling C, Fredlund H, Olcén P, Thomson NR, Clarke IN. The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization. MICROBIOLOGY-SGM 2010; 156:1394-1404. [PMID: 20093289 DOI: 10.1099/mic.0.036830-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chlamydia trachomatis is a major cause of bacterial sexually transmitted infections worldwide. In 2006, a new variant of C. trachomatis (nvCT), carrying a 377 bp deletion within the plasmid, was reported in Sweden. This deletion included the targets used by the commercial diagnostic systems from Roche and Abbott. The nvCT is clonal (serovar/genovar E) and it spread rapidly in Sweden, undiagnosed by these systems. The degree of spread may also indicate an increased biological fitness of nvCT. The aims of this study were to describe the genome of nvCT, to compare the nvCT genome to all available C. trachomatis genome sequences and to investigate the biological properties of nvCT. An early nvCT isolate (Sweden2) was analysed by genome sequencing, growth kinetics, microscopy, cell tropism assay and antimicrobial susceptibility testing. It was compared with relevant C. trachomatis isolates, including a similar serovar E C. trachomatis wild-type strain that circulated in Sweden prior to the initially undetected expansion of nvCT. The nvCT genome does not contain any major genetic polymorphisms - the genes for central metabolism, development cycle and virulence are conserved - or phenotypic characteristics that indicate any altered biological fitness. This is supported by the observations that the nvCT and wild-type C. trachomatis infections are very similar in terms of epidemiological distribution, and that differences in clinical signs are only described, in one study, in women. In conclusion, the nvCT does not appear to have any altered biological fitness. Therefore, the rapid transmission of nvCT in Sweden was due to the strong diagnostic selective advantage and its introduction into a high-frequency transmitting population.
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Affiliation(s)
- Magnus Unemo
- National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, örebro University Hospital, örebro, Sweden
| | | | - Lesley T Cutcliffe
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, UK
| | - Rachel J Skilton
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, UK
| | - David Barlow
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, UK
| | - David Goulding
- Microbial Pathogenesis Electron Microscope Facility, The Wellcome Trust Sanger Institute, Cambridge, UK
| | - Kenneth Persson
- Department of Clinical Microbiology, Malmö University Hospital, Malmö, Sweden
| | - Simon R Harris
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | - Anne Kelly
- National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, örebro University Hospital, örebro, Sweden
| | - Carina Bjartling
- Department of Obstetrics and Gynaecology, Malmö University Hospital, Malmö, Sweden
| | - Hans Fredlund
- National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, örebro University Hospital, örebro, Sweden
| | - Per Olcén
- National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Clinical Microbiology, örebro University Hospital, örebro, Sweden
| | - Nicholas R Thomson
- Pathogen Genomics, The Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | - Ian N Clarke
- Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, UK
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Clinical Manifestations and Epidemiology of the New Genetic Variant of Chlamydia trachomatis. Sex Transm Dis 2009; 36:529-35. [DOI: 10.1097/olq.0b013e3181a8cef1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Domeika M, Savicheva A, Sokolovskiy E, Frigo N, Brilene T, Hallén A, Unemo M, Ballard RC, Ward M. Guidelines for the laboratory diagnosis of Chlamydia trachomatis infections in East European countries. J Eur Acad Dermatol Venereol 2009; 23:1353-63. [PMID: 19522706 DOI: 10.1111/j.1468-3083.2009.03328.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present guidelines aim to provide comprehensive information regarding the laboratory diagnosis of infections caused by Chlamydia trachomatis in East European countries. These recommendations contain important information for laboratory staff working with sexually transmitted infections (STIs) and/or STI-related issues. Individual East European countries may be required to make minor national adjustments to these guidelines as a result of lack of accessibility to some reagents or equipment, or laws in a specific country.
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Affiliation(s)
- M Domeika
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
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Shipitsyna E, Zolotoverkhaya E, Agné-Stadling I, Krysanova A, Savicheva A, Sokolovsky E, Domeika M, Unemo M. First evaluation of six nucleic acid amplification tests widely used in the diagnosis ofChlamydia trachomatisin Russia. J Eur Acad Dermatol Venereol 2009; 23:268-76. [DOI: 10.1111/j.1468-3083.2008.03038.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Whiley DM, Lambert SB, Bialasiewicz S, Goire N, Nissen MD, Sloots TP. False-negative results in nucleic acid amplification tests-do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation? Crit Rev Microbiol 2008; 34:71-6. [PMID: 18568861 DOI: 10.1080/10408410801960913] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleic acid amplification tests (NAATs) have numerous advantages over traditional diagnostic techniques and so are now widely used by diagnostic laboratories for routine detection of infectious agents. However, there is some concern over the increasing numbers of reports of NAAT false-negative results caused by sequence variation. Highly conserved NAAT target sequences have been reported for many organisms, yet sequence-related problems continue to be observed in commercial and in-house assays targeting a broad range of microbial pathogens. In light of these ongoing problems, it may be time to consider the use of two genetic targets in NAAT methods to reduce the potential for sequence-related false-negative results.
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Affiliation(s)
- D M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service Distric, Queensland, Australia.
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A duplex Neisseria gonorrhoeae real-time polymerase chain reaction assay targeting the gonococcal porA pseudogene and multicopy opa genes. Diagn Microbiol Infect Dis 2008; 61:6-12. [PMID: 18248938 DOI: 10.1016/j.diagmicrobio.2007.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 12/03/2007] [Accepted: 12/05/2007] [Indexed: 11/23/2022]
Abstract
Cross-reactions of gonococcal nucleic acid amplification tests (NAATs) with commensal Neisseria strains are well documented. Recent data now indicate that sequence-related false-negative results can occur in gonococcal NAATs, whereby target sequences either are absent or contain several mutations. In this study, a duplex Neisseria gonorrhoeae real-time polymerase chain reaction (PCR) (NGduplex) assay targeting the gonococcal porA pseudogene and multicopy opa genes was developed. The NGduplex was evaluated by testing 596 clinical specimens, including 292 urogenital specimens and 304 throat swab specimens. The results were compared with those obtained using a consensus reference standard comprising 3 monoplex real-time PCR assays. The results show that the NGduplex assay is highly suitable for routine screening for gonorrhea, providing an overall clinical sensitivity and specificity of 100% and 99.3%, respectively, for both urogenital and throat swab specimens. In addition, the 2-target system of the NGduplex assay decreases the potential for sequence-related false-negative results and can provide simultaneous confirmation of positive results.
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