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Dichtl K, Osterman A, Forster J, Jakob L, Suerbaum S, Flaig MJ, Schubert S, Wagener J. A retrospective evaluation of the Euroarray STI-11 multiplex system for the detection of eight STI causing agents. Sci Rep 2023; 13:11382. [PMID: 37452127 PMCID: PMC10349140 DOI: 10.1038/s41598-023-38121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Abstract
With an incidence of more than > 1,000,000/day, sexually transmitted diseases remain a major challenge for health care systems worldwide. To reduce disease burden, complications, and spread, rapid diagnosis permitting early therapy is pivotal. The range of pathogens is wide and co-infections are common. This complicates pre-analytics, which are based on different laboratory techniques with potentially long turnaround times, e.g., cultivation and multistep serologies. Multiplex PCR provides the opportunity to overcome these limitations. In this study, we evaluated a novel assay, the Euroarray STI-11 microarray (EA; Euroimmun Medizinische Labordiagnostika), for the detection of eight obligate or facultative pathogens. Three-hundred-thirteen clinical specimens, which had been tested and pre-characterized for STI causing agents as part of routine diagnostics, were used as cases and controls in this retrospective study. The EA detected 34/44 Chlamydia trachomatis, 48/50 HSV-1, 50/50 HSV-2, 48/48 Mycoplasma hominis, 45/47 Neisseria gonorrhoeae, 9/11 Treponema pallidum, 46/46 Ureaplasma parvum, and 49/49 Ureaplasma urealyticum infections, respectively. 293 samples were EA positive, with polymicrobial infections (positive for two to six microbial or viral agents) detected in 130/293 cases. Specificities were 100% in the respective control groups (n = 18-48 depending on targeted pathogen) except for N. gonorrhoeae (25/26) and U. urealyticum (44/45). The broad spectrum of obligate and facultative pathogens targeted by the EA makes it a valuable tool in the setting of STI diagnostics and surveillance. The test has the potential to diagnose diseases neglected or overlooked in routine clinical practice. Besides a low sensitivity for C. trachomatis, the EA demonstrated high performance for all analyzed parameters. Further studies are warranted in order to capture a larger variety of the tested pathogens.
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Affiliation(s)
- Karl Dichtl
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Osterman
- Lehrstuhl für Virologie, Max von Pettenkofer-Institut, LMU München, Medizinische Fakultät, Munich, Germany
| | - Johannes Forster
- Institut für Hygiene und Mikrobiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lena Jakob
- Klinik und Poliklinik für Dermatologie und Allergologie, Klinikum der Universität München, LMU München, Munich, Germany
| | - Sebastian Suerbaum
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
| | - Michael J Flaig
- Klinik und Poliklinik für Dermatologie und Allergologie, Klinikum der Universität München, LMU München, Munich, Germany
| | - Sören Schubert
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany
| | - Johannes Wagener
- Lehrstuhl für Medizinische Mikrobiologie und Krankenhaushygiene, Max von Pettenkofer-Institut, Medizinische Fakultät, LMU München, Munich, Germany.
- Institut für Hygiene und Mikrobiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Department of Clinical Microbiology, School of Medicine, Trinity College Dublin, the University of Dublin, St. James's Hospital Campus, Dublin, Ireland.
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2
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Puolakkainen M, Mannonen L, Unemo M. The diagnostic-escape Finnish new variant of Chlamydia trachomatis first described in 2019 remains present in Finland three years after the introduction of an updated Aptima Combo 2 assay. Clin Microbiol Infect 2023; 29:658-659. [PMID: 36804908 DOI: 10.1016/j.cmi.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Affiliation(s)
- Mirja Puolakkainen
- Department of Virology, University of Helsinki, Helsinki, Finland; Helsinki University Hospital Laboratory, Clinical Microbiology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Laura Mannonen
- Helsinki University Hospital Laboratory, Clinical Microbiology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Institute for Global Health, University College London, London, United Kingdom
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3
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Cole MJ, Davis GS, Fifer H, Saunders JM, Unemo M, Hadad R, Roberts DJ, Fazal M, Day MJ, Minshull J, Muir P, Horner PJ, Gill NO, Folkard K. No widespread dissemination of Chlamydia trachomatis diagnostic-escape variants and the impact of Neisseria gonorrhoeae positivity on the Aptima Combo 2 assay. Sex Transm Infect 2021; 98:366-370. [PMID: 34510008 DOI: 10.1136/sextrans-2021-054988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/04/2021] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES A Finnish Chlamydia trachomatis (CT) new variant was detected in 2019 that escaped detection in the Hologic Aptima Combo 2 (AC2) assay due to a C1515T mutation in the CT 23S rRNA target region. Reflex testing of CT-negative/CT-equivocal specimens as well as those positive for Neisseria gonorrhoeae (NG) with the Hologic Aptima CT (ACT) assay was recommended to identify any CT variants. METHODS From June to October 2019, specimens with discrepant AC2/ACT CT results were submitted to Public Health England and screened for detectable CT DNA using an inhouse real-time (RT)-PCR. When enough DNA was present, partial CT 23S rRNA gene sequencing was performed. Analysis of available relative light units and interpretative data was performed. RESULTS A total of 317 discordant AC2/ACT specimens were collected from 315 patients. Three hundred were tested on the RT-PCR; 53.3% (n=160) were negative and 46.7% (n=140) were positive. Due to low DNA load in most specimens, sequencing was successful for only 36 specimens. The CT 23S rRNA wild-type sequence was present in 32 specimens, and two variants with C1514T or G1523A mutation were detected in four specimens from three patients. Of the discordant specimens with NG interpretation, 36.6% of NG-negative/CT-negative AC2 specimens had detectable CT DNA on the inhouse RT-PCR vs 53.3% of NG-positive/CT-negative specimens. CONCLUSIONS No widespread dissemination of AC2 diagnostic-escape CT variants has occurred in England. We however identified the impact of NG positivity on the discordant AC2/ACT specimens; a proportion appeared due to NG positivity and the associated NG signal, rather than any diagnostic-escape variants or low DNA load. Several patients with gonorrhoea may therefore receive false-negative AC2 CT results. Single diagnostic targets and multiplex diagnostic assays have their limitations such as providing selection pressure for escape mutants and potentially reduced sensitivity, respectively. These limitations must be considered when establishing diagnostic pathways.
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Affiliation(s)
| | - Grahame S Davis
- National Infection Service, Public Health England, London, UK
| | - Helen Fifer
- National Infection Service, Public Health England, London, UK
| | - John Michael Saunders
- National Infection Service, Public Health England, London, UK.,Research Department of Infection and Population Health, University College London, London, UK
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Orebro, Sweden
| | - Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for Pathogenic Neisseria, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Orebro, Sweden
| | - David J Roberts
- National Infection Service, Public Health England, London, UK
| | - Mohammed Fazal
- National Infection Service, Public Health England, London, UK
| | | | - Jack Minshull
- National Infection Service, Public Health England, London, UK
| | - Peter Muir
- Bristol Public Health Laboratory, Public Health England, Bristol, UK
| | - Paddy J Horner
- School of Social and Community Medicine, University of Bristol, Bristol, UK.,Bristol Sexual Health Centre, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Noel O Gill
- National Infection Service, Public Health England, London, UK
| | - Kate Folkard
- National Infection Service, Public Health England, London, UK
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4
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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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5
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Weinbaum B, Williams A, Hadad R, Vinluan B, Puolakkainen M, Unemo M, Getman D. Validation of an Aptima-format Finnish new variant of Chlamydia trachomatis (FI-nvCT) surveillance assay, 2019. ACTA ACUST UNITED AC 2020; 25. [PMID: 32046818 PMCID: PMC7014671 DOI: 10.2807/1560-7917.es.2020.25.5.2000038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Finnish new variant of Chlamydia trachomatis (FI-nvCT) is escaping diagnostics in Finland, Norway and Sweden. We have developed and validated an Aptima-format nucleic acid amplification test (NAAT) designed specifically to detect the FI-nvCT. This NAAT has high sensitivity (100%) and specificity (100%) for the FI-nvCT strain, enabling further investigation of the geographic distribution, prevalence and transmission of this diagnostic-escape mutant in screening populations in Europe.
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Affiliation(s)
- Barbara Weinbaum
- Research and Development, Hologic Inc., San Diego, United States
| | - Analee Williams
- Research and Development, Hologic Inc., San Diego, United States
| | - Ronza Hadad
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bryan Vinluan
- Research and Development, Hologic Inc., San Diego, United States
| | - Mirja Puolakkainen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Damon Getman
- Research and Development, Hologic Inc., San Diego, United States
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6
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Roberts DJ, Davis GS, Cole MJ, Naik D, Maru H, Woodford N, Muir P, Horner P, Simms I, Thickett G, Crook P, Foster K, Andrews N, Saunders J, Fifer H, Folkard K, Gill ON, On Behalf Of The Incident Management Team. Prevalence of new variants of Chlamydia trachomatis escaping detection by the Aptima Combo 2 assay, England, June to August 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31552817 PMCID: PMC6761577 DOI: 10.2807/1560-7917.es.2019.24.38.1900557] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We identified two new Chlamydia trachomatis (CT) variants escaping Aptima Combo 2 (AC2) assay detection, in clinical specimens of two patients. One had a C1514T mutation the other a G1523A mutation, both within the AC2 23S rRNA target region. The prevalence of such variants among persons tested for CT in England was estimated to be fewer than 0.003%.
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Affiliation(s)
- David J Roberts
- National Infection Service, Public Health England, London, United Kingdom
| | - Grahame S Davis
- National Infection Service, Public Health England, London, United Kingdom
| | - Michelle J Cole
- National Infection Service, Public Health England, London, United Kingdom
| | - Dixita Naik
- National Infection Service, Public Health England, London, United Kingdom
| | - Hitiksha Maru
- National Infection Service, Public Health England, London, United Kingdom
| | - Neil Woodford
- National Infection Service, Public Health England, London, United Kingdom
| | - Peter Muir
- South West Regional Public Health Laboratory, Public Health England, Bristol, United Kingdom
| | - Paddy Horner
- Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Ian Simms
- National Infection Service, Public Health England, London, United Kingdom
| | - George Thickett
- National Infection Service, Public Health England, London, United Kingdom
| | - Paul Crook
- Field Service South East and London, Public Health England, London, United Kingdom
| | - Kirsty Foster
- Public Health England North East Centre, Newcastle-upon-Tyne, United Kingdom
| | - Nick Andrews
- Statistics, Modelling and Economics Department, Public Health England, London, United Kingdom
| | - John Saunders
- National Infection Service, Public Health England, London, United Kingdom
| | - Helen Fifer
- National Infection Service, Public Health England, London, United Kingdom
| | - Kate Folkard
- National Infection Service, Public Health England, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom
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7
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Unemo M, Hansen M, Hadad R, Lindroth Y, Fredlund H, Puolakkainen M, Sundqvist M. Finnish new variant of Chlamydia trachomatis escaping detection in the Aptima Combo 2 assay also present in Örebro County, Sweden, May 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31266590 PMCID: PMC6607738 DOI: 10.2807/1560-7917.es.2019.24.26.1900370] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We identified the first two cases of the Finnish new variant of Chlamydia trachomatis (F-nvCT) beyond Finland in two clinical urogenital specimens in Örebro County, Sweden. These Aptima Combo 2 assay-negative specimens were Aptima Chlamydia trachomatis (CT) assay positive and had the characteristic C1515T mutation in the 23S rRNA gene. From 22 March to 31 May 2019, 1.3% (2/158) of the CT-positive cases in Örebro County were missed because of the F-nvCT. International awareness, investigations and actions are essential.
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Affiliation(s)
- Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marit Hansen
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Ronza Hadad
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Ylva Lindroth
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Skåne Laboratory Medicine, Lund, Sweden
| | - Hans Fredlund
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mirja Puolakkainen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Martin Sundqvist
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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8
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Johansen TB, Kløvstad H, Rykkvin R, Herrfurth-Erichsen EB, Sorthe J, Njølstad G, Ebbesen MH, Nygaard RM, Sandmoen EK, Thilesen C, Onken A, Liljedal I, Hadad R, Unemo M. The 'Finnish new variant of Chlamydia trachomatis' escaping detection in the Aptima Combo 2 assay is widespread across Norway, June to August 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31640843 PMCID: PMC6807255 DOI: 10.2807/1560-7917.es.2019.24.42.1900592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ‘Finnish new variant of Chlamydia trachomatis’ (FI-nvCT), escaping detection in the Aptima Combo 2 assay (AC2), is widespread across Norway. From June to August 2019, 84% (81/97) of available AC2/Aptima CT discordant samples from five laboratories were confirmed as FI-nvCT. Two additional CT variants (CT 23S rRNA C1514T and G1523A) also escaped AC2 detection. The high FI-nvCT proportion might indicate a long-term national spread and it cannot be excluded that FI-nvCT emerged in Norway.
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Affiliation(s)
- Tone Bjordal Johansen
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden.,Norwegian Institute of Public Health, Oslo, Norway
| | | | | | | | | | | | | | | | | | - Carina Thilesen
- Unilabs Laboratory Medicine, Department of Medical Microbiology, Skien, Norway
| | - Annette Onken
- Vestre Viken Hospital Trust, Department of Microbiology, Drammen, Norway
| | - Inger Liljedal
- Levanger Hospital, Department for Laboratory Medicine, Levanger, Norway
| | - Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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9
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Unemo M, Hansen M, Hadad R, Puolakkainen M, Westh H, Rantakokko-Jalava K, Thilesen C, Cole MJ, Boiko I, Lan PT, Golparian D, Ito S, Sundqvist M. Sensitivity, specificity, inclusivity and exclusivity of the updated Aptima Combo 2 assay, which provides detection coverage of the new diagnostic-escape Chlamydia trachomatis variants. BMC Infect Dis 2020; 20:419. [PMID: 32546213 PMCID: PMC7298785 DOI: 10.1186/s12879-020-05148-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 06/11/2020] [Indexed: 01/30/2023] Open
Abstract
Background Four new variants of Chlamydia trachomatis (nvCTs), detected in several countries, cause false-negative or equivocal results using the Aptima Combo 2 assay (AC2; Hologic). We evaluated the clinical sensitivity and specificity, as well as the analytical inclusivity and exclusivity of the updated AC2 for the detection of CT and Neisseria gonorrhoeae (NG) on the automated Panther system (Hologic). Methods We examined 1004 clinical AC2 samples and 225 analytical samples spiked with phenotypically and/or genetically diverse NG and CT strains, and other potentially cross-reacting microbial species. The clinical AC2 samples included CT wild type (WT)-positive (n = 488), all four described AC2 diagnostic-escape nvCTs (n = 170), NG-positive (n = 214), and CT/NG-negative (n = 202) specimens. Results All nvCT-positive samples (100%) and 486 (99.6%) of the CT WT-positive samples were positive in the updated AC2. All NG-positive, CT/NG-negative, Trichomonas vaginalis (TV)-positive, bacterial vaginosis-positive, and Candida-positive AC2 specimens gave correct results. The clinical sensitivity and specificity of the updated AC2 for CT detection was 99.7 and 100%, respectively, and for NG detection was 100% for both. Examining spiked samples, the analytical inclusivity and exclusivity were 100%, i.e., in clinically relevant concentrations of spiked microbe. Conclusions The updated AC2, including two CT targets and one NG target, showed a high sensitivity, specificity, inclusivity and exclusivity for the detection of CT WT, nvCTs, and NG. The updated AC2 on the fully automated Panther system offers a simple, rapid, high-throughput, sensitive, and specific diagnosis of CT and NG, which can easily be combined with detection of Mycoplasma genitalium and TV.
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Affiliation(s)
- Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden.
| | - Marit Hansen
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Ronza Hadad
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Mirja Puolakkainen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Henrik Westh
- Department of Clinical Medicine, Faculty of Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | | | - Carina Thilesen
- Department of Microbiology, Unilabs Laboratory Medicine, Skien, Norway
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Iryna Boiko
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden.,Department of Functional and Laboratory Diagnostics, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Pham T Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | | | - Martin Sundqvist
- World Health Organization Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
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10
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Casañ López C, Rivaya Sánchez B, Fernández Rivas G, Hernández Rodríguez Á, Antuori Torres A, Linares Llamas G, Matas Andreu L. Evaluation of VIASURE Sexually Transmitted Diseases Real Time PCR Detection kit (CerTest Biotec) for the diagnostic of sexually transmitted infections. Enferm Infecc Microbiol Clin 2020; 39:229-233. [PMID: 32498967 DOI: 10.1016/j.eimc.2020.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 11/17/2022]
Abstract
INTRODUCTION Sexually transmitted infections (STIs) are common in our environment, and trends have been increasing in the last few years. Different methods for STIs diagnosis have been applied by microbiology laboratories over years, but real-time PCR has improved this process. Our objective was to evaluate VIASURE Sexually Transmitted Diseases Real-Time PCR Detection kit (CerTestBiotec, S.L.) comparing with the real-time PCR technique used in our laboratory (Allplex™ STI7 Essential Assay, Seegene) which was considered as reference assay. METHODS A total of 948 samples from different sites (vaginal, endocervical, urethral, rectal, pharyngeal swabs and urine samples) were analyzed from July to September 2018. RESULTS A discordant result was obtained in 4.5% (43 samples). These discrepancies were mainly observed in threshold cycle (Ct) value next to the limit of detection. The k coefficient obtained shows a very high agreement between both methods with k values from 0.92 to 0.99. CONCLUSIONS VIASURE Sexually Transmitted Diseases Real-Time PCR Detection kit provides a very good correlation with Allplex STI7 and therefore, it's a good tool for the diagnostic of STIs. Positive results with Ct value obtained from 35 and low amplification signal should be applied with caution and should be interpreted based on the patient's clinical data.
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Affiliation(s)
- Cristina Casañ López
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.
| | - Belén Rivaya Sánchez
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Gema Fernández Rivas
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Badalona, Spain
| | - Águeda Hernández Rodríguez
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Badalona, Spain
| | - Adrián Antuori Torres
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Georgina Linares Llamas
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Lurdes Matas Andreu
- Servicio de Microbiología, Laboratorio Clínico Metropolitana Norte, Hospital Universitari Germans Trias i Pujol, Badalona, Spain; Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Badalona, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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11
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Smit PW, Cornelissen AR, Bruisten SM. Reduction of non-typeable results using a plasmid oriented Lymfogranuloma venereum PCR for typing of Chlamydia trachomatis positive samples. PLoS One 2020; 15:e0233990. [PMID: 32497069 PMCID: PMC7271987 DOI: 10.1371/journal.pone.0233990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/16/2020] [Indexed: 11/18/2022] Open
Abstract
Objectives Typing of Chlamydia trachomatis (CT) is traditionally performed by characterising the ompA gene, resulting in more than a dozen different genovars, A to L. Type L is associated with Lymphogranuloma venereum (LGV) and commonly screened for using PCR, targeting the chromosomal pmpH gene. We aimed to develop and validate a new CT/LGV plasmid-based typing assay targeting the pgp3 gene, to increase sensitivity and thus reduce the number of non-typeable results. Methods The new pgp3 PCR assay using LNA probes to detect point mutations was analytically and prospectively validated in a routine diagnostic laboratory setting. For the analytical tests, quantified nucleotide constructs (gBlocks) were used to perform limit of detection analyses. Quality control panel samples from 2018 and 2019 for CT were also tested. For the clinical study patient samples which were collected in two months in 2018 were tested simultaneously using the pmpH PCR and the pgp3 PCR. Results Analytically, the assay proved to be 100% specific relative to the previously used LGV typing assay targeting the single copy pmpH gene but it was much more sensitive to detect non-LGV CT. In the quality control panel 2 nonLGV samples and 7 LGV samples were solely positive with the pgp3 PCR and not with the pmpH PCR. None of the samples from analytical specificity panels were positive, indicating 100% specificity. In a prospective panel of 152 clinical samples, 142 (93%) were successfully typed with the pgp3 PCR compared to 78% with the pmpH PCR. The pgp3 PCR was fully concordant with the pmpH PCR to identify all LGV subtypes and detected an increased number of clinical samples of non-LGV subtype. Conclusion We developed and validated a sensitive and specific plasmid-based typing assay to discriminate LGV from non-LGV CT subtypes. This is useful in a clinical setting to quickly determine the optimal treatment for Chlamydia trachomatis infections.
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Affiliation(s)
- Pieter Willem Smit
- Public Health Laboratory (GGD) Amsterdam, Department of infectious diseases, Amsterdam, The Netherlands
- Medical Microbiology Laboratory, Maasstad ziekenhuis, Rotterdam, The Netherlands
| | - Akke Rosanne Cornelissen
- Public Health Laboratory (GGD) Amsterdam, Department of infectious diseases, Amsterdam, The Netherlands
| | - Sylvia Maria Bruisten
- Public Health Laboratory (GGD) Amsterdam, Department of infectious diseases, Amsterdam, The Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam, The Netherlands
- * E-mail:
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12
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Unemo M, Getman D, Hadad R, Cole M, Thomson N, Puolakkainen M, Spiteri G. Letter to the editor: Chlamydia trachomatis samples testing falsely negative in the Aptima Combo 2 test in Finland, 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31213219 PMCID: PMC6582517 DOI: 10.2807/1560-7917.es.2019.24.24.1900354] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michelle Cole
- National Infection Service, Public Health England, London, United Kingdom
| | - Nicholas Thomson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Mirja Puolakkainen
- Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Huslab, Helsinki, Finland
| | - Gianfranco Spiteri
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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13
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Hadad R, Jensen JS, Westh H, Grønbaek I, Schwartz LJ, Nielsen L, Vang TM, Nielsen R, Weinreich LS, Skov MN, Olsen M, Møller JK, Kolmos B, Unemo M, Hoffmann S. A Chlamydia trachomatis 23S rRNA G1523A variant escaping detection in the Aptima Combo 2 assay (Hologic) was widespread across Denmark in July-September 2019. APMIS 2020; 128:440-444. [PMID: 32202687 DOI: 10.1111/apm.13043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/16/2020] [Indexed: 01/20/2023]
Abstract
Chlamydia trachomatis infection is the most common bacterial sexually transmitted infection globally, and nucleic acid amplification tests (NAATs) are recommended for highly sensitive and specific diagnosis. In early 2019, the Finnish new variant of Chlamydia trachomatis (FI-nvCT) was identified. The FI-nvCT has a C1515T mutation in the 23S rRNA gene, making it escaping detection in the Aptima Combo 2 (AC2; Hologic) NAAT, and the FI-nvCT has been subsequently reported in Sweden and Norway. In the present study, we investigated the presence of the FI-nvCT and other AC2 diagnostic-escape CT mutants in July-September 2019 in Denmark. The FI-nvCT was present but rare in Denmark. However, another AC2 diagnostic-escape CT mutant (with a 23S rRNA G1523A mutation) was found to be widespread across Denmark, accounting for 95% (76/80) of AC2 diagnostic-escape nvCT samples from five Danish CT-diagnostic laboratories. This nvCT-G1523A has previously only been detected in one single sample in the United Kingdom and Norway, respectively. It is vital to monitor the continued stability of the NAAT targets in local, national and international settings and monitor as well as appropriately analyse incidence, unexplained shifts in diagnostics rates and/or annual collections of samples diagnosed as negative/equivocal using NAATs with different target(s). Furthermore, diagnostic CT NAATs with dual target sequences are crucial, and fortunately, an updated Hologic AC2 assay including one additional target sequence is in advanced development.
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Affiliation(s)
- Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jørgen Skov Jensen
- Department for Bacteria, Parasites and Fungi, Infectious Diseases Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Ida Grønbaek
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Lasse Jessen Schwartz
- Department for Bacteria, Parasites and Fungi, Infectious Diseases Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev, Denmark
| | - Tobias Müller Vang
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev, Denmark
| | - Rikke Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Marianne N Skov
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Marlene Olsen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | | | - Birte Kolmos
- Department of Clinical Microbiology, Vejle University Hospital, Vejle, Denmark
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Steen Hoffmann
- Department for Bacteria, Parasites and Fungi, Infectious Diseases Preparedness, Statens Serum Institut, Copenhagen, Denmark
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14
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Borges V, Cordeiro D, Salas AI, Lodhia Z, Correia C, Isidro J, Fernandes C, Rodrigues AM, Azevedo J, Alves J, Roxo J, Rocha M, Côrte-Real R, Vieira L, Borrego MJ, Gomes JP. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microb Genom 2020; 5. [PMID: 31697227 PMCID: PMC6927300 DOI: 10.1099/mgen.0.000313] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
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Affiliation(s)
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Dora Cordeiro
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Ana Isabel Salas
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Zohra Lodhia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Cristina Correia
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Cândida Fernandes
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Ana Maria Rodrigues
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Jacinta Azevedo
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Alves
- Sexually Transmitted Diseases Clinic, Lapa Health Centre, Lisbon, Portugal
| | - João Roxo
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Miguel Rocha
- CheckpointLX, Grupo de Ativistas em Tratamentos, Lisboa, Portugal
| | - Rita Côrte-Real
- Sexually Transmitted Diseases Clinic, Dermatovenereology Department, Central Lisbon University Hospital Centre (CHULC), Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Maria José Borrego
- National Reference Laboratory (NRL) for Curable Sexually Transmitted Infections (STIs), National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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15
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Desai M, Fernández-Huerta M, Daskalopoulou M. Research news in clinical context. Sex Transm Infect 2020; 96:157-158. [PMID: 31969380 DOI: 10.1136/sextrans-2019-054270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Monica Desai
- National Institute for Health and Care Excellence, Manchester, UK
| | - Miguel Fernández-Huerta
- Microbiology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
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16
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Note from the editors: Don't stop thinking about tomorrow. Euro Surveill 2020; 25:2001091. [PMID: 31937393 PMCID: PMC6961261 DOI: 10.2807/1560-7917.es.2020.25.1.2001091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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17
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Smid JH, Althaus CL, Low N, Unemo M, Herrmann B. Rise and fall of the new variant of Chlamydia trachomatis in Sweden: mathematical modelling study. Sex Transm Infect 2019; 96:375-379. [PMID: 31586947 PMCID: PMC7402554 DOI: 10.1136/sextrans-2019-054057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/13/2019] [Accepted: 09/23/2019] [Indexed: 02/04/2023] Open
Abstract
Objectives A new variant of Chlamydia trachomatis (nvCT) was discovered in Sweden in 2006. The nvCT has a plasmid deletion, which escaped detection by two nucleic acid amplification tests (Abbott-Roche, AR), which were used in 14 of 21 Swedish counties. The objectives of this study were to assess when and where nvCT emerged in Sweden, the proportion of nvCT in each county and the role of a potential fitness difference between nvCT and co-circulating wild-type strains (wtCT). Methods We used a compartmental mathematical model describing the spatial and temporal spread of nvCT and wtCT. We parameterised the model using sexual behaviour data and Swedish spatial and demographic data. We used Bayesian inference to fit the model to surveillance data about reported diagnoses of chlamydia infection in each county and data from four counties that assessed the proportion of nvCT in multiple years. Results Model results indicated that nvCT emerged in central Sweden (Dalarna, Gävleborg, Västernorrland), reaching a proportion of 1% of prevalent CT infections in late 2002 or early 2003. The diagnostic selective advantage enabled rapid spread of nvCT in the presence of high treatment rates. After detection, the proportion of nvCT decreased from 30%–70% in AR counties and 5%–20% in counties that Becton Dickinson tests, to around 5% in 2015 in all counties. The decrease in nvCT was consistent with an estimated fitness cost of around 5% in transmissibility or 17% reduction in infectious duration. Conclusions We reconstructed the course of a natural experiment in which a mutant strain of C. trachomatis spread across Sweden. Our modelling study provides support, for the first time, of a reduced transmissibility or infectious duration of nvCT. This mathematical model improved our understanding of the first nvCT epidemic in Sweden and can be adapted to investigate the impact of future diagnostic escape mutants.
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Affiliation(s)
- Joost H Smid
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christian L Althaus
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Bjőrn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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18
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de Salazar A, Espadafor B, Fuentes-López A, Barrientos-Durán A, Salvador L, Álvarez M, García F. Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections. PLoS One 2019; 14:e0222439. [PMID: 31513653 PMCID: PMC6742210 DOI: 10.1371/journal.pone.0222439] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/29/2019] [Indexed: 11/26/2022] Open
Abstract
Sexually transmitted infections (STIs) remain a worldwide problem and a severe threat to public health. The purpose of this study was to compare Aptima® Assays (Hologic®) and the Allplex™ STI Essential Assay (Seegene®) for the simultaneous detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis and Mycoplasma genitalium in clinical practice. The Aptima® assays (Hologic®) are based on a transcription-mediated amplification (TMA) method. The Allplex™ STI Essential assay (Seegene®) is based on a multiplex Real-Time PCR (RT-PCR) method. A total of 622 clinical samples from different anatomical sites were tested using both methods. A total of 88 (14.1%) and 66 (10.6%) positive samples were found for any of the TMA assays used and for the RT-PCR assay, respectively. Aptima® assays showed a slightly higher rate of positive results for all pathogens except for T. vaginalis, the results of which were similar to those obtained with Allplex™. The most commonly detected pathogen was C. trachomatis (37 samples; 5.9% using TMA assays) and the anatomical site with the highest prevalence of microorganisms was a non-urogenital site, the pharynx (27 positive samples; 4.3%). Using the Aptima® assays as reference method, the comparison showed that the average specificity of multiplex RT-PCR was 100.0% for the four pathogens. However an average sensitivity of 74.5% was observed, showing 95.2% (CI95%; 93.6–96.9) of overall concordance (κ = 0.80). In conclusion, the Aptima® assays show a higher sensitivity on a wide range of sample types compared to the Allplex™ assay.
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Affiliation(s)
- Adolfo de Salazar
- Hospital Universitario San Cecilio, Servicio de Microbiología, Instituto de Investigación Ibs, Granada, Spain
| | - Beatriz Espadafor
- Hospital Universitario Virgen de las Nieves, Servicio de Dermatología, Centro de ETS, Granada, Spain
| | - Ana Fuentes-López
- Hospital Universitario San Cecilio, Servicio de Microbiología, Instituto de Investigación Ibs, Granada, Spain
| | - Antonio Barrientos-Durán
- Hospital Universitario San Cecilio, Servicio de Microbiología, Instituto de Investigación Ibs, Granada, Spain
| | - Luis Salvador
- Hospital Universitario Virgen de las Nieves, Servicio de Dermatología, Centro de ETS, Granada, Spain
| | - Marta Álvarez
- Hospital Universitario San Cecilio, Servicio de Microbiología, Instituto de Investigación Ibs, Granada, Spain
| | - Federico García
- Hospital Universitario San Cecilio, Servicio de Microbiología, Instituto de Investigación Ibs, Granada, Spain
- * E-mail:
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19
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Hokynar K, Rantakokko-Jalava K, Hakanen A, Havana M, Mannonen L, Jokela P, Kurkela S, Lappalainen M, Unemo M, Puolakkainen M. The Finnish New Variant of Chlamydia trachomatis with a Single Nucleotide Polymorphism in the 23S rRNA Target Escapes Detection by the Aptima Combo 2 Test. Microorganisms 2019; 7:microorganisms7080227. [PMID: 31370214 PMCID: PMC6723375 DOI: 10.3390/microorganisms7080227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/28/2019] [Accepted: 07/29/2019] [Indexed: 01/18/2023] Open
Abstract
In 2019, more than 200 cases of Chlamydia trachomatis negative/equivocal by the Aptima Combo 2 assay (AC2, target: 23S rRNA) with slightly elevated relative light units (RLUs), but positive by the Aptima Chlamydia trachomatis assay (ACT, target: 16S rRNA) have been detected in Finland To identify the cause of the AC2 CT false-negative specimens, we sequenced parts of the CT 23S rRNA gene in 40 specimens that were AC2 negative/equivocal but ACT positive. A single nucleotide polymorphism (SNP; C1515T in the C. trachomatis 23S rRNA gene) was revealed in 39 AC2/ACT discordant specimens. No decrease in the number of mandatorily notified C. trachomatis cases was observed nationally in Finland in 2010–2019. When RLUs obtained for AC2 negative specimens were retrospectively evaluated in 2011–2019, a continuous increase in the proportion of samples with RLUs 10–19 was observed since 2014, and a slight increase in the proportion of samples with RLUs 20–84 in 2017–2019, indicating that the Finnish new variant of C. trachomatis might have been spreading nationally for several years. This emphasizes that careful surveillance of epidemiology, positivity rate and test performance are mandatory to detect any changes affecting detection of infections.
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Affiliation(s)
- Kati Hokynar
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Kaisu Rantakokko-Jalava
- Department of Clinical Microbiology, Turku University Hospital, Turku 20500, Finland
- Department of Virology, University of Turku, Turku 20500, Finland
| | - Antti Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku 20500, Finland
- Department of Virology, University of Turku, Turku 20500, Finland
| | | | - Laura Mannonen
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Pia Jokela
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Satu Kurkela
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Maija Lappalainen
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - Magnus Unemo
- World Health Organization (WHO) Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections (STIs), National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, SE-701 85 Örebro, Sweden
| | - Mirja Puolakkainen
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland.
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