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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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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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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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