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Oree G, Naicker M, Maise HC, Tinarwo P, Ramsuran V, Abbai NS. Comparison of methods for the detection of Neisseria gonorrhoeae from South African women attending antenatal care. Int J STD AIDS 2021; 32:396-402. [PMID: 33570465 DOI: 10.1177/0956462420971439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The detection of Neisseria gonorrhoeae using culture assays is challenging. This study aims to compare different assays for the detection of N. gonorrhoeae. This cross-sectional study was conducted at King Edward VIII Hospital and included 307 antenatal attendees, each willing to provide two endocervical swabs. The first swab was used for culture identification of N. gonorrhoeae, and the second swab was processed for the detection of the pathogen by the TaqMan quantitative polymerase chain reaction (qPCR) assay, an in-house 16S ribosomal RNA (rRNA) PCR and PCR detection of the opa gene. Culture and the nucleic acid amplification assays were each used as comparator tests in the analysis. Sensitivity and specificity were calculated using RS Studio. The prevalence of N. gonorrhoeae was 7.8%. When compared to the TaqMan assay, the 16S rRNA PCR exhibited the highest sensitivity of 62%, with a substantial level of agreement (kappa level of agreement: 0.60), followed by the opa PCR (38%) with a moderate level of agreement (0.52) and culture exhibiting the lowest sensitivity of 25% with a fair level of agreement (0.38). The diagnostic accuracy of all the assays was >90%. The TaqMan qPCR assay has the ability to serve as a future diagnostic assay for the detection of N. gonorrhoeae.
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Affiliation(s)
- Glynis Oree
- School of Clinical Medicine Research Laboratory, Nelson R Mandela School of Medicine, 56394University of KwaZulu-Natal, Durban, South Africa
| | - Meleshni Naicker
- School of Clinical Medicine Research Laboratory, Nelson R Mandela School of Medicine, 56394University of KwaZulu-Natal, Durban, South Africa
| | - Hopolang C Maise
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Nelson R Mandela School of Medicine, 56394University of KwaZulu-Natal, Durban, South Africa
| | - Partson Tinarwo
- Department of Biostatistics, Nelson R Mandela School of Medicine, 56394University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, 56394University of KwaZulu-Natal, Durban, South Africa
| | - Nathlee S Abbai
- School of Clinical Medicine Research Laboratory, Nelson R Mandela School of Medicine, 56394University of KwaZulu-Natal, Durban, South Africa
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Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife 2020; 9:e56367. [PMID: 32602459 PMCID: PMC7326491 DOI: 10.7554/elife.56367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/17/2020] [Indexed: 12/14/2022] Open
Abstract
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape.
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Affiliation(s)
- Allison L Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Melinda Ashcroft
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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Evaluation of six commercial nucleic acid amplification tests for detection of Neisseria gonorrhoeae and other Neisseria species. J Clin Microbiol 2011; 49:3610-5. [PMID: 21813721 DOI: 10.1128/jcm.01217-11] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular detection of Neisseria gonorrhoeae in extragenital samples may result in false-positive results due to cross-reaction with commensal Neisseria species or Neisseria meningitidis. This study examined 450 characterized clinical culture isolates, comprising 216 N. gonorrhoeae isolates and 234 isolates of nongonococcal Neisseria species (n = 218) and 16 isolates of other closely related bacteria, with six commercial nucleic acid amplification tests (NAATs). The six NAATs tested were Gen-Probe APTIMA COMBO 2 and APTIMA GC, Roche COBAS Amplicor CT/NG and COBAS 4800 CT/NG tests, BD ProbeTec GC Qx amplified DNA assay, and Abbott RealTime CT/NG test. All assays except COBAS Amplicor CT/NG test where four (1.9%) isolates were not detected showed a positive result with all N. gonorrhoeae isolates (n = 216). Among the 234 nongonococcal isolates examined, initial results from all assays displayed some false-positive results due to cross-reactions. Specifically, the COBAS Amplicor and ProbeTec tests showed the highest number of false-positive results, detecting 33 (14.1%) and 26 (11%) nongonococcal Neisseria isolates, respectively. On the first testing, APTIMA COMBO 2, APTIMA GC, Abbott RealTime, and Roche COBAS 4800 showed lower level of cross-reactions with five (2.1%), four (1.7%), two (1%), and two (1%) of the isolates showing low-level positivity, respectively. Upon retesting of these nine nongonococcal isolates using freshly cultured colonies, none were positive by the APTIMA COMBO 2, Abbott RealTime, or COBAS 4800 test. In conclusion, the COBAS Amplicor and ProbeTec tests displayed high number of false-positive results, while the remaining NAATs showed only sporadic low-level false-positive results. Supplementary testing for confirmation of N. gonorrhoeae NAATs remains recommended with all samples tested, in particular those from extragenital sites.
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Geertsen R, Friderich P, Dobec M, Emler S. Evaluation of an automated extraction method for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Cobas Amplicor PCR from different sample materials. ACTA ACUST UNITED AC 2009; 39:405-8. [PMID: 17464862 DOI: 10.1080/00365540601087582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A commercially available automated device (MagNA Pure LC) was adapted for nucleic acid extraction of urogenital specimen for subsequent PCR detection of Chlamydia trachomatis and Neisseria gonorrhoeae in a clinical laboratory. Results were compared to the standard manual extraction procedure and showed excellent correlation, with even slightly increased sensitivity.
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Affiliation(s)
- Ralf Geertsen
- Institute Virion Ltd., Molecular Biology, Rueschlikon, Switzerland.
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Schabereiter-Gurtner C, Hufnagl P, Sonvilla G, Selitsch B, Rotter M, Makristathis A, Hirschl A. Evaluation of a novel internally controlled real-time PCR assay targeting the 16S rRNA gene for confirmation of Neisseria gonorrhoeae infections. Clin Microbiol Infect 2008; 14:480-6. [DOI: 10.1111/j.1469-0691.2008.01962.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Herring A, Ballard R, Mabey D, Peeling RW. Evaluation of rapid diagnostic tests: chlamydia and gonorrhoea. Nat Rev Microbiol 2007; 4:S41-8. [PMID: 17366686 DOI: 10.1038/nrmicro1562] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alan Herring
- Veterinary School, University of Bristol, Langford House, Langford, North Somerset, |BS40 5DN, UK
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Mangold KA, Regner M, Tajuddin M, Tajuddin AM, Jennings L, Du H, Kaul KL. Neisseria species identification assay for the confirmation of Neisseria gonorrhoeae-positive results of the COBAS Amplicor PCR. J Clin Microbiol 2007; 45:1403-9. [PMID: 17360838 PMCID: PMC1865884 DOI: 10.1128/jcm.00834-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Screening assays for Neisseria gonorrhoeae exhibit low positive predictive values, particularly in low-prevalence populations. A new real-time PCR assay that detects and identifies individual Neisseria spp. using melt curve analysis was compared to two previously published supplementary assays. NsppID, a 16S rRNA real-time PCR/melt curve assay developed to distinguish N. gonorrhoeae from other Neisseria spp., was compared to real-time PCR assays targeting genes reportedly specific for N. gonorrhoeae, the cppB gene and the porA pseudogene. A total of 408 clinical specimens (324 female endocervical swabs and 84 male urine or urogenital swab specimens) were screened using the COBAS Amplicor assay for Chlamydia trachomatis and N. gonorrhoeae (CT/NG) (Roche Diagnostics, Indianapolis, IN) followed by confirmatory testing via real-time PCR. The NsppID assay detected Neisseria spp. in 150/181 COBAS-positive specimens (82%), including six dual infections, and identified N. gonorrhoeae in 102 (56%) specimens. Sixty-nine of 181 (38%) specimens were positive for N. gonorrhoeae by porA pseudogene, and 115/181 (64%) were positive for cppB. However, cppB was also positive in 15% of COBAS-negative specimens, more than either NsppID (4%) or porA pseudogene (2%) assays. The porA pseudogene assay had the highest specificity for both genders but the lowest sensitivity, especially in female specimens. NsppID had a slightly lower specificity but greater sensitivity and overall accuracy. The least desirable confirmatory assay was cppB, due to poor specificity. The NsppID assay is an accurate confirmatory assay for N. gonorrhoeae detection. In addition, the NsppID assay can identify the non-N. gonorrhoeae species responsible for the majority of false-positive results from the COBAS Amplicor CT/NG assay.
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Affiliation(s)
- Kathy A Mangold
- Department of Pathology and Laboratory Medicine, Evanston Northwestern Healthcare, 2650 Ridge Avenue, Evanston, IL 60201, USA
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Peeling RW, Mabey D, Herring A, Hook EW. Why do we need quality-assured diagnostic tests for sexually transmitted infections? Nat Rev Microbiol 2006; 4:909-21. [PMID: 17109030 DOI: 10.1038/nrmicro1555] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The bacterial sexually transmitted infections (STIs) syphilis, gonorrhoea and chlamydia can all be cured with a single dose of antibiotic. Unfortunately, however, these infections often remain undiagnosed as many infected individuals have few if any symptoms. Diagnostic tests with high sensitivity and specificity are available for all three infections but, owing to their expense and the lack of laboratory capacity, most people in developing countries do not have access to these tests. There is a great need for simple, cheap diagnostic tests for STIs that can be performed at the point of care, enabling treatment to be given immediately. It is hoped that recent advances in our understanding of the pathogenesis of these infections, and the availability of the complete genome sequences for each causative organism, will lead to the development of improved point-of-care tests that will reduce the burden of these diseases in developing countries.
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Affiliation(s)
- Rosanna W Peeling
- WHO/TDR Sexually Transmitted Diseases Diagnostics Initiative (SDI), UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), 20 Avenue Appia, CH-1211 Geneva 27, Switzerland.
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Peeling RW, Mabey D, Herring A, Hook EW. Why do we need quality-assured diagnostic tests for sexually transmitted infections? Nat Rev Microbiol 2006; 4:S7-19. [PMID: 17110922 DOI: 10.1038/nrmicro1569] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The bacterial sexually transmitted infections (STIs) syphilis, gonorrhoea and chlamydia can all be cured with a single dose of antibiotic. Unfortunately, however, these infections often remain undiagnosed as many infected individuals have few if any symptoms. Diagnostic tests with high sensitivity and specificity are available for all three infections but, owing to their expense and the lack of laboratory capacity, most people in developing countries do not have access to these tests. There is a great need for simple, cheap diagnostic tests for STIs that can be performed at the point of care, enabling treatment to be given immediately. It is hoped that recent advances in our understanding of the pathogenesis of these infections, and the availability of the complete genome sequences for each causative organism, will lead to the development of improved point-of-care tests that will reduce the burden of these diseases in developing countries.
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Affiliation(s)
- Rosanna W Peeling
- WHO/TDR Sexually Transmitted Diseases Diagnostics Initiative (SDI), UNICEF/UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR), 20 Avenue Appia, CH-1211 Geneva 27, Switzerland.
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Geraats-Peters CWM, Brouwers M, Schneeberger PM, van der Zanden AGM, Bruisten SM, Weers-Pothoff G, Boel CHE, van den Brule AJC, Harmsen HG, Hermans MHA. Specific and sensitive detection of Neisseria gonorrhoeae in clinical specimens by real-time PCR. J Clin Microbiol 2005; 43:5653-9. [PMID: 16272500 PMCID: PMC1287782 DOI: 10.1128/jcm.43.11.5653-5659.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early diagnosis of Neisseria gonorrhoeae infections is important with regard to patients' health and infectivity. We report the development of a specific and sensitive TaqMan assay for the detection of N. gonorrhoeae in clinical samples. The target sequence is a 76-bp fragment of the 5' untranslated region of the opa genes that encode opacity proteins. A panel of 448 well-defined N. gonorrhoeae isolates was used to evaluate and optimize the assay. The method employs two minor-groove binding probes, one of them recognizing a newly identified sequence in the opa genes. Testing a large panel of related and unrelated microorganisms revealed that other Neisseria strains and other microorganisms tested negative in the opa test. With a lower detection limit of one genome per reaction, the opa test appeared more sensitive than both the COBAS AMPLICOR (Roche Diagnostics Nederland BV, Almere, The Netherlands) and a LightCycler 16S rRNA test. Analysis of a panel of 122 COBAS AMPLICOR-positive samples revealed that 68% were negative in both the 16S rRNA test and the opa assay (confirming that the COBAS AMPLICOR test produces false positives), while 30% were positive in both assays. Three samples were opa positive and 16S rRNA negative, which may be due to the higher sensitivity of the opa assay. We conclude that the opa gene-based real-time amplification assay offers a sensitive, specific, semiquantitative, and reliable assay suitable for the detection of N. gonorrhoeae in clinical specimens and/or for confirmation of less specific tests.
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Affiliation(s)
- C W M Geraats-Peters
- Multidisciplinary Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 5200 ME 's-Hertogenbosch, The Netherlands
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Fredlund H, Falk L, Jurstrand M, Unemo M. Molecular genetic methods for diagnosis and characterisation of Chlamydia trachomatis and Neisseria gonorrhoeae: impact on epidemiological surveillance and interventions. APMIS 2005; 112:771-84. [PMID: 15638837 DOI: 10.1111/j.1600-0463.2004.apm11211-1205.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
One of the mainstays in the prevention of Chlamydia trachomatis and Neisseria gonorrhoeae infections is the availability of laboratory diagnostics with high sensitivity and specificity. Assays for diagnosis of C. trachomatis include cell culture and nucleic acid amplification tests (NAATs). The major target sequences for C. trachomatis diagnosis by NAATs are located at the cryptic plasmid and the major target used for characterisation is the omp1 gene. The gold standard for diagnosis of N. gonorrhoeae is culture. However, numerous NAATs for identification of N. gonorrhoeae and a number of molecular genetic methods for characterisation of N. gonorrhoeae have been developed. Probably no routine laboratory can attain as high sensitivity by culturing C. trachomatis or N. gonorrhoeae as by using NAATs. For that reason NAATs can be recommended for diagnosing C. trachomatis, but not as the only diagnostic assay for N. gonorrhoeae, due to lack of antibiotic susceptibility testing and specificity problems, most pronounced for pharyngeal and rectal samples. Genotyping of C. trachomatis or N. gonorrhoeae provides additional information for contact tracing. It is recommended for N. gonorrhoeae, at least in low prevalence geographic areas, but cannot today be recommended for C. trachomatis. This is due to the low genetic variability and hence the limited benefits for partner notification. However, genotyping of C. trachomatis may play an important role under special circumstances.
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Affiliation(s)
- Hans Fredlund
- Department of Clinical Microbiology, Orebro University Hospital, Orebro, Sweden.
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Bruisten SM, Noordhoek GT, van den Brule AJC, Duim B, Boel CHE, El-Faouzi K, du Maine R, Mulder S, Luijt D, Schirm J. Multicenter validation of the cppB gene as a PCR target for detection of Neisseria gonorrhoeae. J Clin Microbiol 2004; 42:4332-4. [PMID: 15365038 PMCID: PMC516305 DOI: 10.1128/jcm.42.9.4332-4334.2004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cppB gene is often used as a target for detection of Neisseria gonorrhoeae by PCR. Using a coded panel of 500 DNA samples, we determined that the cppB gene is missing in 5.8% of N. gonorrhoeae strains, and therefore we consider the cppB gene to be an unsuitable target.
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Affiliation(s)
- S M Bruisten
- GG&GD Municipal Health Service, Public Health Laboratory, Nieuwe Achtergracht 100, 1018 WT Amsterdam, The Netherlands.
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