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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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The Prevalence of Neisseria gonoroheae among Iranian Women by Phenotyping and Genotyping Methods. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2016. [DOI: 10.22207/jpam.10.4.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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3
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Meyer T, Püschel K, Seifert D. Diagnostik sexuell übertragbarer Infektionen. Rechtsmedizin (Berl) 2014. [DOI: 10.1007/s00194-014-0992-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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4
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Ndowa FJ, Ison CA, Cole MJ, Lusti-Narasimhan M. Gonococcal antimicrobial resistance: challenges for public health control. Sex Transm Infect 2014; 89 Suppl 4:iv3-4. [PMID: 24243877 DOI: 10.1136/sextrans-2013-051395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Francis J Ndowa
- Department of Reproductive Health and Research, World Health Organization, , Geneva, Switzerland
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5
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Trembizki E, Lahra M, Stevens K, Freeman K, Hogan T, Hogg G, Lawrence A, Limnios A, Pearson J, Smith H, Nissen M, Sloots T, Whiley D. A national quality assurance survey of Neisseria gonorrhoeae testing. J Med Microbiol 2014; 63:45-49. [DOI: 10.1099/jmm.0.065094-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aims of this study were to (1) conduct a national survey of Neisseria gonorrhoeae identification by National Neisseria Network (NNN) reference laboratories contributing data to the Australian Gonococcal Surveillance Programme and (2) determine the prevalence in Australia of strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays for confirmation of gonococcal nucleic acid amplification tests. Gonococcal clinical isolates referred to NNN laboratories for the first half of 2012 were screened using in-house real-time PCR assays targeting multicopy opa, porA pseudogene and cppB genes. There were 2455 clinical gonococcal isolates received in the study period; 98.6 % (2420/2455) of isolates harboured all three gene targets, 0.12 % (3/2455) were porA-negative, 0.04 % (1/2455) opa-negative and 1.14 % (28/2455) cppB-negative by PCR. Notably, no isolates were simultaneously negative for two targets. However, three isolates failed to be amplified by all three PCR methods, one isolate of which was shown to be a commensal Neisseria strain by 16S rRNA sequencing. Using PCR as the reference standard the results showed that (1) identification of N. gonorrhoeae isolates by NNN laboratories was highly specific (99.96 %) and (2) strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays are present but not widespread throughout Australia at this point in time.
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Affiliation(s)
- Ella Trembizki
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - Monica Lahra
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Kevin Freeman
- Microbiology Laboratory, Pathology Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Tiffany Hogan
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Lawrence
- Microbiology and Infectious Diseases Department, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Athena Limnios
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Julie Pearson
- PathWest Laboratory Medicine-WA, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Helen Smith
- Public Health Microbiology, Communicable Disease, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Michael Nissen
- Microbiology Division, Pathology Queensland Central, Royal Brisbane and Women’s Hospital Campus, Queensland, Australia
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - Theo Sloots
- Microbiology Division, Pathology Queensland Central, Royal Brisbane and Women’s Hospital Campus, Queensland, Australia
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - David Whiley
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
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Wang H, Kong F, Wang B, Mckechnie ML, Gilbert GL. Multiplex polymerase chain reaction-based reverse line blot hybridization assay to detect common genital pathogens. Int J STD AIDS 2010; 21:320-5. [PMID: 20498099 DOI: 10.1258/ijsa.2009.008481] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The objective of the present paper is to develop and apply a multiplex polymerase chain reaction (mPCR) based reverse line blot (RLB) hybridization assay to facilitate the diagnosis of genital infections by detection of seven recognized or putative genital pathogens (Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma genitalium, Mycoplasma hominis and Trichomonas vaginalis). Species-specific biotin-labelled primer pairs were used in a single mPCR to amplify target regions in each of seven pathogens. The amplified biotin-labelled PCR products were hybridized with membrane-bound-specific oligonucleotide probes and were detected by chemiluminescence. Two hundred and eleven specimens (104 male urethral and 107 female vaginal swabs), collected from patients with suspected genital infections attending the Wuhan First Hospital Sexually Transmitted Diseases (STD) clinic, were tested by mPCR/RLB and results were confirmed by single PCR using different species-specific targets. The sensitivity of the assay was assessed using dilutions of positive DNA controls with known copy numbers, for each target. The assay correctly identified all reference strains and detected potential pathogens in a high proportion of clinical specimens. There was no cross-reaction between the seven pathogens. The mPCR/RLB can detect <or= 10(2) copies of the target gene fragments. Comparison of mPCR/RLB and single PCR assays showed discrepant results in six of 211 (2.8%) clinical specimens, which were positive by mPCR/RLB assay, but negative by the corresponding single PCR. Nested PCR on the six discrepant specimens gave results consistent with those of mPCR/RLB. In conclusion, the mPCR/RLB hybridization assay is sensitive and specific, and able to rapidly detect genital pathogens in clinical specimens.
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Affiliation(s)
- H Wang
- Research Laboratory for Infectious Skin Diseases, Department of Dermatology, Wuhan First Hospital, Wuhan 430022, P R China
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7
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High Performance and Acceptability of Self-Collected Rectal Swabs for Diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae in Men Who Have Sex With Men and Women. Sex Transm Dis 2009; 36:493-7. [DOI: 10.1097/olq.0b013e3181a44b8c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Koressaar T, Jõers K, Remm M. Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms. Bioinformatics 2009; 25:1349-55. [PMID: 19357101 PMCID: PMC2682524 DOI: 10.1093/bioinformatics/btp241] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/16/2009] [Accepted: 04/03/2009] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor. RESULTS We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from five medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests. AVAILABILITY AND IMPLEMENTATION A web version of the method called MultiMPrimer3 was implemented and is freely available at (http://bioinfo.ut.ee/multimprimer3/).
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Affiliation(s)
- Triinu Koressaar
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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9
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Lee SH, Vigliotti VS, Pappu S. Molecular tests for human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cytology specimen. BMC Womens Health 2009; 9:8. [PMID: 19358733 PMCID: PMC2672071 DOI: 10.1186/1472-6874-9-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 04/09/2009] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Laboratory detection of Human papillomavirus (HPV), Chlamydia trachomatis and Neisseria gonorrhoeae in liquid-based cervicovaginal cytology specimens is now based on identification of the DNA sequences unique to these infectious agents. However, current commercial test kits rely on nucleotide probe hybridization to determine DNA sequences, which may lead to diagnostic errors due to cross-reactivity. The aim of this study was to find a practical approach to perform automated Sanger DNA sequencing in clinical laboratories for validation of the DNA tests for these three infectious agents. METHODS A crude proteinase K digest of 5% of the cells collected in a liquid-based cervicovaginal cytology specimen was used for the detection of DNA molecules specific for HPV, C trachomatis and N gonorrhoeae, and for preparation of materials suitable for direct automated DNA sequencing. Several sets of commercially available polymerase chain reaction (PCR) primers were used to prepare nested PCR amplicons for direct DNA sequencing. RESULTS Some variants of HPV-16 and HPV-31 were found to share an at least 34-base long sequence homology downstream of the GP5+ binding site, and all HPV-6 and HPV-11 variants shared an upstream 34-base sequence including part of the GP5+ primer. Accurate HPV genotyping frequently required more than 34-bases for sequence alignments to distinguish some of the HPV genotype variants with closely related sequences in this L1 gene hypervariable region. Using the automated Sanger DNA sequencing method for parallel comparative studies on split samples and to retest the residues of samples previously tested positive for C trachomatis and/or for N gonorrhoeae, we also found false-negative and false-positive results as reported by two commercial nucleic acid test kits. CONCLUSION Identification of a signature DNA sequence by the automated Sanger method is useful for validation of HPV genotyping and for molecular testing of C trachomatis and N gonorrhoeae in liquid-based cervicovaginal Papanicolaou (Pap) cytology specimens for clinical laboratories with experience in molecular biology to increase the specificity of these DNA-based tests. However, even a highly specific test for high-risk HPV genotyping may have unacceptably low positive predictive values for precancer lesion in populations with a low cervical cancer prevalence rate.
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Affiliation(s)
- Sin Hang Lee
- Department of Pathology, Milford Hospital, Milford, Connecticut, USA
| | | | - Suri Pappu
- Department of Pathology, Milford Hospital, Milford, Connecticut, USA
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Kimmitt PT, Kirby A, Perera N, Nicholson KG, Schober PC, Rajakumar K, Chapman CA. Identification of Neisseria gonorrhoeae as the causative agent in a case of culture-negative dermatitis-arthritis syndrome using real-time PCR. J Travel Med 2008; 15:369-71. [PMID: 19006515 DOI: 10.1111/j.1708-8305.2008.00240.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sexually transmitted infections (STIs) are an increasingly common and important cause of a fever in a returning traveler. Systemic complications of STIs, human immunodeficiency virus seroconversion illness, and secondary syphilis are diagnoses that can easily be missed. We present a case of culture-negative disseminated gonococcal infection presenting with fever, malaise, polyarthralgia, arthritis, and a rash that developed following orogenital contact and was diagnosed using real-time polymerase chain reaction. This technology has major potential to improve the speed and sensitivity of diagnosis and consequent management of patients with this syndrome.
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11
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Koek AG, Bruisten SM, Dierdorp M, van Dam AP, Templeton K. Specific and sensitive diagnosis of syphilis using a real-time PCR for Treponema pallidum. Clin Microbiol Infect 2008; 12:1233-6. [PMID: 17121633 DOI: 10.1111/j.1469-0691.2006.01566.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A real-time PCR assay with a Taqman probe was developed that targeted the polA gene of Treponema pallidum. The test was validated using an analytical panel (n = 140) and a clinical panel of genital samples (n = 112) from patients attending a sexually transmitted infections clinic. High sensitivities and specificities of 94-100% were achieved using two real-time PCR platforms, the Rotor-Gene and the iCycler. The assay can be completed within 2 h, enabling reporting in <8 h. This fast and robust assay is suitable for implementation in routine laboratories for diagnosing primary syphilis.
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Affiliation(s)
- A G Koek
- Amsterdam Municipal Health Laboratory and Department of Infectious Diseases, Amsterdam, The Netherlands
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12
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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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13
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Chui L, Chiu T, Kakulphimp J, Tyrrell G. A comparison of three real-time PCR assays for the confirmation of Neisseria gonorrhoeae following detection of N. gonorrhoeae using Roche COBAS AMPLICOR. Clin Microbiol Infect 2008; 14:473-9. [DOI: 10.1111/j.1469-0691.2008.01950.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Whiley DM, Garland SM, Harnett G, Lum G, Smith DW, Tabrizi SN, Sloots TP, Tapsall JW. Exploring 'best practice' for nucleic acid detection of Neisseria gonorrhoeae. Sex Health 2008; 5:17-23. [PMID: 18361850 DOI: 10.1071/sh07050] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 12/12/2007] [Indexed: 11/23/2022]
Abstract
Nucleic acid detection tests (NADT) have considerable benefits for the detection of Neisseria gonorrhoeae (GC), including high sensitivity across a range of specimen types and use under widely differing settings and conditions. However, sexual health practitioners and others who use data generated by NADT for GC should be aware of some important limitations of these tests. False-positive results caused by cross reaction with commensal Neisseria species have been observed in many assays, and have lead to unacceptably low positive-predictive values in some patient populations. Further, false-negative results can be caused by GC sequence variation, with some gonococci lacking certain NADT target sequences. This review examines the issues associated with gonococcal NADT and considers best practice for use of these assays based on current knowledge. We emphasise the need for supplementary testing and extensive assay validation, and suggest appropriate strategies for these requirements irrespective of the setting in which they are used. Further, we highlight the need to maintain culture-based testing for certain specimen sites as well as for antimicrobial resistance surveillance.
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Affiliation(s)
- David M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service District, Brisbane, Qld 4029, Australia
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A duplex Neisseria gonorrhoeae real-time polymerase chain reaction assay targeting the gonococcal porA pseudogene and multicopy opa genes. Diagn Microbiol Infect Dis 2008; 61:6-12. [PMID: 18248938 DOI: 10.1016/j.diagmicrobio.2007.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 12/03/2007] [Accepted: 12/05/2007] [Indexed: 11/23/2022]
Abstract
Cross-reactions of gonococcal nucleic acid amplification tests (NAATs) with commensal Neisseria strains are well documented. Recent data now indicate that sequence-related false-negative results can occur in gonococcal NAATs, whereby target sequences either are absent or contain several mutations. In this study, a duplex Neisseria gonorrhoeae real-time polymerase chain reaction (PCR) (NGduplex) assay targeting the gonococcal porA pseudogene and multicopy opa genes was developed. The NGduplex was evaluated by testing 596 clinical specimens, including 292 urogenital specimens and 304 throat swab specimens. The results were compared with those obtained using a consensus reference standard comprising 3 monoplex real-time PCR assays. The results show that the NGduplex assay is highly suitable for routine screening for gonorrhea, providing an overall clinical sensitivity and specificity of 100% and 99.3%, respectively, for both urogenital and throat swab specimens. In addition, the 2-target system of the NGduplex assay decreases the potential for sequence-related false-negative results and can provide simultaneous confirmation of positive results.
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Diagnostic value of molecular confirmation assays for Neisseria gonorrhoeae. J Clin Microbiol 2007; 45:3856; author reply 3856-8. [PMID: 17984285 DOI: 10.1128/jcm.01008-07] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tapsall J, Whiley D, Sloots T. Applications of molecular testing in clinical laboratories for the diagnosis and control of gonorrhea. Future Microbiol 2007; 1:317-24. [PMID: 17661644 DOI: 10.2217/17460913.1.3.317] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The potential for enhanced diagnosis and control of gonococcal infection through the application of advances in molecular medicine is now being realized. However, the introduction of diagnostic nucleic acid amplification assays (NAATs) revealed some significant limitations of these applications. Resolution of some, but not all, of these problems has led to recommendations for refined testing algorithms and a better recognition and acceptance of the limitations of NAATs. Resource restriction has limited the use of diagnostic NAATs, especially in less-developed countries where disease rates are highest. However, NAATs have also proved useful in public health approaches to gonorrhea control in all settings. Additional applications including molecular typing of gonococci to identify and interrupt gonococcal transmission chains and definition of antimicrobial resistance patterns in the gonococcus have been proposed. These approaches, especially those for antimicrobial resistance determination, have been less successful for a number of reasons, including their cost and other unresolved issues.
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Affiliation(s)
- John Tapsall
- The Prince of Wales Hospital, WHO Collaborating Centre for STD & HIV, Microbiology Department, South Eastern Area Laboratory Services, Randwick, Sydney, Australia.
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Van der Bij AK, Geskus RB, Fennema HSA, Adams K, Coutinho RA, Dukers NHTM. No evidence for a sustained increase in sexually transmitted diseases among heterosexuals in Amsterdam, the Netherlands: a 12-year trend analysis at the sexually transmitted disease outpatient clinic, Amsterdam. Sex Transm Dis 2007; 34:461-7. [PMID: 17195773 DOI: 10.1097/01.olq.0000251230.62493.f3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Sexually transmitted diseases (STDs) are on the rise, mainly among men having sex with men (MSM). GOAL The goal of this study was to evaluate whether STD increases as seen in MSM are also visible among heterosexuals. STUDY DESIGN Attendees of the STD clinic in Amsterdam, The Netherlands, are routinely tested for chlamydia, gonorrhea, and syphilis. Additionally, all women are tested for trichomoniasis. STD time trends of heterosexual attendees between 1994 and 2005 were analyzed by logistic regression and generalized linear models with a negative binomial distribution. RESULTS The number of consultations doubled since 1994. However, no long-term increase was seen in the number of syphilis and gonorrhea infections. Additionally, the trichomonas prevalence declined. However, the number of chlamydia infections increased over time. CONCLUSIONS Although the number of attendees increased, no evidence for increasing STD incidence was found among heterosexuals. The increase in chlamydia infections can probably be explained by increased screening resulting from increased numbers of attendees.
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Affiliation(s)
- Akke K Van der Bij
- Department of Research, Cluster Infectious Diseases, Health Service of Amsterdam, Amsterdam, The Netherlands
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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: 23] [Impact Index Per Article: 1.4] [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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Lum G, Garland SM, Tabrizi S, Harnett G, Smith DW, Sloots TP, Whiley DM, Tapsall JW. Supplemental testing is still required in australia for samples positive for Neisseria gonorrhoeae by nucleic acid detection tests. J Clin Microbiol 2006; 44:4292-4; author reply 4293-4. [PMID: 17088373 PMCID: PMC1698317 DOI: 10.1128/jcm.01577-06] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Whiley DM, Anderson TP, Barratt K, Beaman MH, Buda PJ, Carter M, Freeman K, Hallsworth P, Limnios EA, Lum G, Merien F, Vernel-Pauillac F, Tapsall JW, Witt MJ, Nissen MD, Sloots TP. Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target. Pathology 2006; 38:445-8. [PMID: 17008285 DOI: 10.1080/00313020600928253] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AIMS The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR. METHODS A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states. RESULTS All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia. CONCLUSIONS The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.
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Affiliation(s)
- David M Whiley
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand.
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22
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Lowe P, O'Loughlin P, Evans K, White M, Bartley PB, Vohra R. Comparison of the Gen-Probe APTIMA Combo 2 assay to the AMPLICOR CT/NG assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine samples from Australian men and women. J Clin Microbiol 2006; 44:2619-21. [PMID: 16825397 PMCID: PMC1489522 DOI: 10.1128/jcm.00476-06] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of the APTIMA Combo 2 assay (AC2) for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections in urine samples was compared to that of the AMPLICOR CT/NG assay (AMP). The AC2 performance was superior to that of AMP for both organisms in this study.
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Affiliation(s)
- Peter Lowe
- Infectious Diseases and Immunology, QML Pathology, 60 Ferry Road, West End 4101, Brisbane, Australia.
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23
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van Bergen JEAM, Spaargaren J, Götz HM, Veldhuijzen IK, Bindels PJE, Coenen TJ, Broer J, de Groot F, Hoebe CJPA, Richardus JH, van Schaik D, Verhooren M. Population prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae in the Netherlands. Should asymptomatic persons be tested during population-based Chlamydia screening also for gonorrhoea or only if chlamydial infection is found? BMC Infect Dis 2006; 6:42. [PMID: 16522201 PMCID: PMC1450285 DOI: 10.1186/1471-2334-6-42] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 03/07/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Screening and active case finding for Chlamydia trachomatis (CT) is recommended to prevent reproductive morbidity. However insight in community prevalence of gonococcal infections and co-infections with Neisseria gonorrhoea (NG) is lacking. METHODS Nested study within a large population-based Chlamydia Screening Pilot among 21.000 persons 15-29 year. All CT-positive (166) and a random sample of 605 CT-negative specimens were as well tested for gonococcal infection. RESULTS Overall Chlamydia prevalence in the Pilot was 2.0% (95% CI: 1.7-2.3), highest in very urban settings (3.2%; 95% CI: 2.4-4.0) and dependent of several risk factors. Four gonococcal infections were found among 166 participants with CT infection (4/166 = 2.4%; 95% CI: 0.1%-4.7%). All four had several risk factors and reported symptoms. Among 605 CT-negative persons, no infection with NG could be confirmed. CONCLUSION A low rate of co-infections and a very low community prevalence of gonococcal infections were found in this population based screening programme among young adults in the Netherlands. Population screening for asymptomatic gonococcal infections is not indicated in the Netherlands. Although co-infection with gonorrhoea among CT-positives is dependent on symptoms and well-known algorithms for elevated risks, we advise to test all CT-positives also for NG, whether symptomatic or asymptomatic.
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Affiliation(s)
- Jan EAM van Bergen
- STI AIDS Netherlands (Soa Aids Nederland), Amsterdam, The Netherlands
- Department of General Practice, Academic Medical Centre-University of Amsterdam, The Netherlands
| | - Joke Spaargaren
- Municipal Public Health Laboratory GGD Amsterdam, The Netherlands
| | | | | | - Patrick JE Bindels
- Department of General Practice, Academic Medical Centre-University of Amsterdam, The Netherlands
| | - Ton J Coenen
- STI AIDS Netherlands (Soa Aids Nederland), Amsterdam, The Netherlands
| | - Jan Broer
- Municipal Public Health Service Groningen, The Netherlands
| | | | | | - Jan-Hendrik Richardus
- Municipal Public Health Service Rotterdam, The Netherlands
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Daniel van Schaik
- STI AIDS Netherlands (Soa Aids Nederland), Amsterdam, The Netherlands
| | - Marije Verhooren
- Municipal Public Health Service "Hart van Brabant", The Netherlands
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24
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Whiley DM, Tapsall JW, Sloots TP. Nucleic acid amplification testing for Neisseria gonorrhoeae: an ongoing challenge. J Mol Diagn 2006; 8:3-15. [PMID: 16436629 PMCID: PMC1871692 DOI: 10.2353/jmoldx.2006.050045] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2005] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review.
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Affiliation(s)
- David M Whiley
- Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital & Health Service District, Herston Road, Herston, Queensland, Australia 4029.
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25
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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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26
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Lum G, Freeman K, Nguyen NL, Limnios EA, Tabrizi SN, Carter I, Chambers IW, Whiley DM, Sloots TP, Garland SM, Tapsall JW. A cluster of culture positive gonococcal infections but with false negative cppB gene based PCR. Sex Transm Infect 2005; 81:400-2. [PMID: 16199739 PMCID: PMC1745040 DOI: 10.1136/sti.2004.013805] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES To describe the prevalence and characteristics of isolates of Neisseria gonorrhoeae grown from urine samples that produced negative results with nucleic acid amplification assays (NAA) targeting the cppB gene. METHODS An initial cluster of culture positive, but cppB gene based NAA negative, gonococcal infections was recognised. Urine samples and suspensions of gonococci isolated over 9 months in the Northern Territory of Australia were examined using cppB gene based and other non-cppB gene based NAA. The gonococcal isolates were phenotyped by determining the auxotype/serovar (A/S) class and genotyped by pulsed field gel electrophoresis (PFGE). RESULTS 14 (9.8%) of 143 gonococci isolated were of A/S class Pro(-/)Brpyut, indistinguishable on PFGE and negative in cppB gene based, but not other, NAA. CONCLUSIONS This cluster represents a temporal and geographic expansion of a gonococcal subtype lacking the cppB gene with consequent loss of sensitivity of NAA dependent on amplification of this target. Gonococci lacking the cppB gene have in the past been more commonly associated with the PAU-/PCU- auxotype, a gonococcal subtype hitherto infrequently encountered in Australia. NAA based on the cppB gene as a target may produce false positive as well as false negative NAA. This suggests that unless there is continuing comparison with culture to show their utility, cppB gene based NAA should be regarded as suboptimal for use either as a diagnostic or supplemental assay for diagnosis of gonorrhoea, and NAA with alternative amplification targets should be substituted.
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Affiliation(s)
- G Lum
- Department of Microbiology, Royal Darwin Hospital, Casuarina, Northern Territory, Australia
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27
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Tapsall JW, Limnios EA, Nguyen NL, Carter I, Lum G, Freeman K, Tabrizi SN, Garland SM, Whiley DM, Sloots TP, Chambers IW. Cryptic-plasmid-free gonococci may contribute to failure of cppB gene-based assays to confirm results of BD ProbeTEC PCR for identification of Neisseria gonorrhoeae. J Clin Microbiol 2005; 43:2036-7. [PMID: 15815057 PMCID: PMC1081405 DOI: 10.1128/jcm.43.4.2036-2037.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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28
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Boel CHE, van Herk CMC, Berretty PJM, Onland GHW, van den Brule AJC. Evaluation of conventional and real-time PCR assays using two targets for confirmation of results of the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae test for detection of Neisseria gonorrhoeae in clinical samples. J Clin Microbiol 2005; 43:2231-5. [PMID: 15872247 PMCID: PMC1153731 DOI: 10.1128/jcm.43.5.2231-2235.2005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2004] [Revised: 11/04/2004] [Accepted: 01/17/2005] [Indexed: 11/20/2022] Open
Abstract
Two conventional PCR-enzyme immunoassays (PCR-EIAs) and two real-time PCR assays (LightCycler system; Roche Diagnostics) were evaluated as confirmation assays with cppB and 16S rRNA genes as targets. Of 765 male and female genitourinary and nasopharyngeal specimens positive for Neisseria gonorrhoeae in the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae PCR test (Roche Diagnostics), 229 (30%) were confirmed positive; 13 of these (5.7%) were lacking the cppB gene. Of the 534 samples (70%) that could not be confirmed, 81 (15%) showed a positive crossing point. However, melting curve analysis revealed an aberrant melting temperature in the LightCycler 16S rRNA assay; therefore, these samples were considered non-N. gonorrhoeae Neisseria species. Both of the 16S rRNA assays performed well, with positive predictive values of 99.1% and 100% for the PCR-EIAs and the real-time assays, respectively, and a negative predictive value of 99.8% for both. The cppB assays were compromised by the absence of the cppB gene in 5.7% of the N. gonorrhoeae-positive samples, resulting in negative predictive values of 96.8% and 97.6% for the PCR-EIAs and the real-time assays, respectively. Therefore, the 16S rRNA gene is preferable to the cppB gene as a target for confirmation assays. The melting curve analysis of the real-time assays provides useful additional information.
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Affiliation(s)
- C H E Boel
- Laboratory for Medical Microbiology, PAMM Laboratories, P.O. Box 2, NL-5500 AA Veldhoven, The Netherlands.
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