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Shiluli C, Kamath S, Kanoi BN, Kimani R, Maina M, Waweru H, Kamita M, Ndirangu I, Abkallo HM, Oduor B, Pamme N, Dupaty J, Klapperich CM, Lolabattu SR, Gitaka J. Improving gonorrhoea molecular diagnostics: Genome mining-based identification of identical multi-repeat sequences (IMRS) in Neisseria gonorrhoeae. Heliyon 2024; 10:e27344. [PMID: 38533083 PMCID: PMC10963193 DOI: 10.1016/j.heliyon.2024.e27344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/19/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Background Curable sexually transmitted infections (STIs), such as Neisseria gonorrhoeae (N. gonorrhoeae), are a major cause of poor pregnancy outcomes. The infection is often asymptomatic in pregnant women, and a syndrome-based approach of testing leads to a missed diagnosis. Culture followed by microscopy is inadequate and time-consuming. The gold standard nucleic acid amplification tests require advanced infrastructure settings, whereas point-of-care tests are limited to immunoassays with sensitivities and specificities insufficient to accurately diagnose asymptomatic cases. This necessitates the development and validation of assays that are fit for purpose. Methods We identified new diagnostic target biomarker regions for N. gonorrhoeae using an algorithm for genome mining of identical multi-repeat sequences (IMRS). These were then developed as DNA amplification primers to design better diagnostic assays. To test the primer pair, genomic DNA was 10-fold serially diluted (100 pg/μL to 1 × 10-3 pg/μL) and used as DNA template for PCR reactions. The gold standard PCR using 16S rRNA primers was also run as a comparative test, and both assay products were resolved on 1% agarose gel. Results Our newly developed N. gonorrhoeae IMRS-PCR assay had an analytical sensitivity of 6 fg/μL representing better sensitivity than the 16S rRNA PCR assay with an analytical sensitivity of 4.3096 pg/μL. The assay was also successfully validated using clinical urethral swab samples. We further advanced this technique by developing an isothermal IMRS, which was both reliable and sensitive for detecting cultured N. gonorrhoeae isolates at a concentration of 38 ng/μL. Combining isothermal IMRS with a low-cost lateral flow assay, we were able to detect N. gonorrhoeae amplicons at a starting concentration of 100 pg/μL. Conclusion Therefore, there is a potential to implement this concept within miniaturized, isothermal, microfluidic platforms, and laboratory-on-a-chip diagnostic devices for highly reliable point-of-care testing.
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Affiliation(s)
- Clement Shiluli
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Shwetha Kamath
- Division of Research and Development, Jigsaw Bio Solutions Private Limited, Bangalore, India
| | - Bernard N. Kanoi
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Racheal Kimani
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Michael Maina
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Harrison Waweru
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Moses Kamita
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Ibrahim Ndirangu
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
| | - Hussein M. Abkallo
- Animal and Human Health Program, International Livestock Research Institute, Nairobi, Kenya
| | - Bernard Oduor
- Animal and Human Health Program, International Livestock Research Institute, Nairobi, Kenya
| | - Nicole Pamme
- Department of Materials and Environmental Chemistry, Stockholm University, Sweden
| | - Joshua Dupaty
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | | | - Jesse Gitaka
- Centre for Research in Infectious Diseases, College of Graduate Studies and Research, Mount Kenya University, Thika, Kenya
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Dighe K, Moitra P, Gunaseelan N, Alafeef M, Jensen T, Rafferty C, Pan D. Highly-Specific Single-Stranded Oligonucleotides and Functional Nanoprobes for Clinical Determination of Chlamydia Trachomatis and Neisseria Gonorrhoeae Infections. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304009. [PMID: 37870167 PMCID: PMC10754082 DOI: 10.1002/advs.202304009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/18/2023] [Indexed: 10/24/2023]
Abstract
Early detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) is the key to controlling the spread of these bacterial infections. An important step in developing biosensors involves identifying reliable sensing probes against specific genetic targets for CT and NG. Here, the authors have designed single-stranded oligonucleotides (ssDNAs) targeting mutually conserved genetic regions of cryptic plasmid and chromosomal DNA of both CT and NG. The 5'- and 3'- ends of these ssDNAs are differentially functionalized with thiol groups and coupled with gold nanoparticles (AuNP) to develop absorbance-based assay. The AuNPs agglomerate selectively in the presence of its target DNA sequence and demonstrate a change in their surface plasmon resonance. The optimized assay is then used to detect both CT and NG DNA extracted from 60 anonymized clinical samples with a clinical sensitivity of ∼100%. The limit of detection of the assays are found to be 7 and 5 copies/µL for CT and NG respectively. Furthermore, it can successfully detect the DNA levels of these two bacteria without the need for DNA extraction and via a lateral flow-based platform. These assays thus hold the potential to be employed in clinics for rapid and efficient monitoring of sexually transmitted infections.
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Affiliation(s)
- Ketan Dighe
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Parikshit Moitra
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Nivetha Gunaseelan
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Maha Alafeef
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Tor Jensen
- Cancer Center at IllinoisUniversity of Illinois Urbana‐Champaign405 N. Mathews Ave.UrbanaIL61801‐2325USA
| | - Carla Rafferty
- Department of Family MedicineCarle Health1818 E Windsor Rd.UrbanaIL61802USA
| | - Dipanjan Pan
- Department of PediatricsCentre of Blood Oxygen Transport & HemostasisUniversity of Maryland Baltimore School of MedicineBaltimoreMaryland21201USA
- Department of Chemical & Biochemical EngineeringUniversity of Maryland Baltimore CountyBaltimore CountyMaryland21250USA
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Department of Materials Science and EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Huck Institutes of the Life Sciences101 Huck Life Sciences BuildingUniversity ParkPA16802USA
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Braam JF, van Dam AP, Bruisten SM, van Rooijen MS, de Vries HJ, Schim van der Loeff MF, Vergunst CE. Macrolide-Resistant Mycoplasma genitalium Impairs Clinical Improvement of Male Urethritis After Empirical Treatment. Sex Transm Dis 2022; 49:360-367. [PMID: 34962241 PMCID: PMC8994036 DOI: 10.1097/olq.0000000000001591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/05/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Mycoplasma genitalium (MG) is associated with urethritis in men and could play a role in clinical outcome. We examined clinical improvement of symptoms in men receiving empirical treatment for urethritis and correlated the outcome with Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), MG, and MG macrolide resistance-associated mutations (MRAM) status. METHODS At the sexually transmitted infection clinic in Amsterdam, the Netherlands, empirical treatment for gonococcal urethritis is 1 g ceftriaxone and for nongonococcal urethritis 1 g azithromycin. In 2018 to 2019, we tested urine samples of men with urethritis for CT, NG, and MG using transcription-mediated amplification assays. Mycoplasma genitalium-positive samples were tested for MRAM using quantitative polymerase chain reaction. Two weeks after receiving therapy, men were sent a text message inquiring after clinical improvement. RESULTS We evaluated 2505 cases of urethritis. The positivity rates of NG, CT, and MG were 26% (648 of 2489), 29% (726 of 2489), and 23% (522 of 2288), respectively. In 768 of 2288 of the cases (34%), no causative agent was detected. Most cases were infected with a single pathogen: NG, 417 of 2288 (18%); CT, 486 of 2288 (21%); and MG, 320 of 2288 (14%). The prevalence of MRAM among MG-positives was 74% (327 of 439). For 642 (25.6%) cases, we could evaluate clinical improvement after treatment of whom 127 (20%) indicated no improvement; 9% (15 of 174) in NG cases, 18% (35 of 195) in CT cases, 14% (4 of 28) in MG wild-type cases, and 40% (38 of 94) in MG-MRAM cases. Clinical improvement in MG-MRAM cases was significantly lower compared with all other groups (P < 0.001). CONCLUSIONS Presence of MG-MRAM is associated with lack of clinical improvement in azithromycin-treated nongonococcal urethritis.
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Affiliation(s)
- Joyce F. Braam
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
| | - Alje P. van Dam
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AII)
| | - Sylvia M. Bruisten
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
- Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AII)
| | | | - Henry J.C. de Vries
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
- Department of Dermatology
| | - Maarten F. Schim van der Loeff
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
- Department of Internal Medicine, Amsterdam Institute for Infection and Immunity (AII), Amsterdam University Medical Center (UMC), Amsterdam
| | - Clarissa E. Vergunst
- From the Department of Infectious Diseases, Public Health Service of Amsterdam
- Department of Dermatology, NWZ, Den Helder, the Netherlands
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Chen X, Zhou Q, Wu X, Wang S, Liu R, Dong S, Yuan W. Visual and Rapid Diagnosis of Neisseria gonorrhoeae Using Loop-Mediated Isothermal Amplification Combined With a Polymer Nanoparticle-Based Biosensor in Clinical Application. Front Mol Biosci 2021; 8:702134. [PMID: 34368230 PMCID: PMC8333867 DOI: 10.3389/fmolb.2021.702134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/23/2021] [Indexed: 01/12/2023] Open
Abstract
Neisseria gonorrhoeae is a host-adapted human pathogen that causes sexually transmitted gonorrhea and remains to be a serious global public health challenge, especially in low- and middle-income regions. It is vital to devise a reliable, simple, cost-saving, and easy-to-use assay for detecting the N. gonorrhoeae agent. In the current study, we firstly report a novel approach, loop-mediated isothermal amplification linked with a polymer nanoparticle-based biosensor (LAMP-PNB), that was used for identifying N. gonorrhoeae in clinical samples. The results showed that the LAMP primers based on the orf1 gene were valid for development of the N. gonorrhoeae-LAMP-PNB assay. The detection system with optimal conditions could be performed at a fixed temperature of 64°C for 40 min. The whole process, including genomic DNA preparation (approximately 10 min), LAMP reaction (40 min), and PNB reporting (approximately 2 min), could be accomplished within 60 min. The limit of detection (LoD) of the N. gonorrhoeae-LAMP-PNB assay was 50 copies per test. The specificity of the current assay was 100%, and no cross-reactions to non-N. gonorrhoeae isolates were observed. These results confirmed that the N. gonorrhoeae-LAMP-PNB technique is a reliable, specific, sensitive, rapid, low-cost, and easy-to-use method for detecting gonococci isolates. More importantly, this assay has great potential to develop a point-of-care (POC) testing method in clinical practice, especially in resource-constrained regions.
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Affiliation(s)
- Xu Chen
- The Second Clinical College, Guizhou University of Traditional Chinese Medicine, Guiyang, China
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qingxue Zhou
- Clinical Laboratory, Hangzhou Women’s Hospital, Hangzhou, China
| | - Xueli Wu
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Shuoshi Wang
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Rui Liu
- Central Laboratory of the Second Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Wei Yuan
- Guizhou Provincial Center for Clinical Laboratory, Guiyang, China
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Trick AY, Melendez JH, Chen FE, Chen L, Onzia A, Zawedde A, Nakku-Joloba E, Kyambadde P, Mande E, Matovu J, Atuheirwe M, Kwizera R, Gilliams EA, Hsieh YH, Gaydos CA, Manabe YC, Hamill MM, Wang TH. A portable magnetofluidic platform for detecting sexually transmitted infections and antimicrobial susceptibility. Sci Transl Med 2021; 13:13/593/eabf6356. [PMID: 33980576 DOI: 10.1126/scitranslmed.abf6356] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Effective treatment of sexually transmitted infections (STIs) is limited by diagnostics that cannot deliver results rapidly while the patient is still in the clinic. The gold standard methods for identification of STIs are nucleic acid amplification tests (NAATs), which are too expensive for widespread use and have lengthy turnaround times. To address the need for fast and affordable diagnostics, we have developed a portable, rapid, on-cartridge magnetofluidic purification and testing (PROMPT) polymerase chain reaction (PCR) test. We show that it can detect Neisseria gonorrhoeae, the pathogen causing gonorrhea, with simultaneous genotyping of the pathogen for resistance to the antimicrobial drug ciprofloxacin in <15 min. The duplex test was integrated into a low-cost thermoplastic cartridge with automated processing of penile swab samples from patients using magnetic beads. A compact instrument conducted DNA extraction, PCR, and analysis of results while relaying data to the user via a smartphone app. This platform was tested on penile swab samples from sexual health clinics in Baltimore, MD, USA (n = 66) and Kampala, Uganda (n = 151) with an overall sensitivity and specificity of 97.7% (95% CI, 94.7 to 100%) and 97.6% (95% CI, 94.1 to 100%), respectively, for N. gonorrhoeae detection and 100% concordance with culture results for ciprofloxacin resistance. This study paves the way for delivering accessible PCR diagnostics for rapidly detecting STIs at the point of care, helping to guide treatment decisions and combat the rise of antimicrobial resistant pathogens.
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Affiliation(s)
- Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Johan H Melendez
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Liben Chen
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Annet Onzia
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Aidah Zawedde
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | | | - Peter Kyambadde
- AIDS Control Program, Division of Sexually Transmitted Infections, Ministry of Health, Kampala, Uganda
| | - Emmanuel Mande
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Joshua Matovu
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Maxine Atuheirwe
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Richard Kwizera
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Elizabeth A Gilliams
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sexual Health Clinics, Baltimore City Health Department, Baltimore, MD 21205, USA
| | - Yu-Hsiang Hsieh
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Matthew M Hamill
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sexual Health Clinics, Baltimore City Health Department, Baltimore, MD 21205, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA. .,Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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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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Braam JF, Hetem DJ, Vergunst CE, Kuizenga Wessel S, van Rooijen MS, Nijhuis RHT, Schim van der Loeff MF, van Dam AP, Bruisten SM. Evaluating the prevalence and risk factors for macrolide resistance in Mycoplasma genitalium using a newly developed qPCR assay. PLoS One 2020; 15:e0240836. [PMID: 33079948 PMCID: PMC7575077 DOI: 10.1371/journal.pone.0240836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/02/2020] [Indexed: 11/19/2022] Open
Abstract
Mycoplasma genitalium (MG) is a sexually transmitted bacterium in which macrolide resistance is rapidly increasing, limiting treatment options. We validated a new assay to detect the presence of macrolide resistance-associated mutations in MG (MG-MRAM). In 2018, symptomatic and asymptomatic clients visiting sexually transmitted infections (STI) clinics in Amsterdam or The Hague were tested for MG using transcription mediated amplification (TMA) assays. The sensitivity to detect MG of the newly developed MG-MRAM qPCR was compared to the MgPa qPCR, both in relation to the TMA assay. For the sensitivity and specificity to detect relevant mutations the MG-MRAM qPCR was compared to 23SrRNA sequencing analysis. The qPCR was subsequently used to determine the presence of MG-MRAM at different anatomical locations and to identify risk factors for MG-MRAM. MG-positive clients (402) providing 493 MG-positive samples were included. In total 309/493 (62.7%) samples from 291 (72.4%) clients were successfully typed with the MG-MRAM qPCR. The MG-MRAM qPCR had a sensitivity of 98.6% (95%CI 91.1%-99.9%) and specificity of 94.1% (95%CI 78.9%-99.0%) to detect MG-MRAM compared to sequencing analysis. Infection with MG-MRAM was detected in 193/291 (66.3%) clients: in 129/178 (72.5%) men and 64/113 (56.6%) women (p = 0.005). Prevalence of MG-MRAM was significantly higher in men, clients with a higher education, HIV-positive clients and clients with >10 sexual partners in the previous six months, but in multivariable analysis no factor was significantly associated with MG-MRAM presence. Since MG-MRAM prevalence was very high, testing for MG-MRAM is essential if treatment for MG is considered, and can be performed with this sensitive and specific qPCR test in routine diagnostics.
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Affiliation(s)
- Joyce F. Braam
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| | - David J. Hetem
- Department of Medical Microbiology, Haaglanden Medical Center, The Hague, The Netherlands
| | - Clarissa E. Vergunst
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
- Department of Dermatology, NWZ Den Helder, Den Helder, The Netherlands
| | | | - Martijn S. van Rooijen
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
| | - Roel H. T. Nijhuis
- Department of Medical Microbiology, Haaglanden Medical Center, The Hague, The Netherlands
- Laboratory for Medical microbiology and immunology, Meander Medical Center, Amersfoort, The Netherlands
| | - Maarten F. Schim van der Loeff
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
- Department of Internal Medicine, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam University Medical Center (UMC), Amsterdam, The Netherlands
| | - Alje P. van Dam
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam University Medical Center (UMC), Amsterdam, The Netherlands
| | - Sylvia M. Bruisten
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, The Netherlands
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam University Medical Center (UMC), Amsterdam, The Netherlands
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Prevalence of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis including relevant resistance-associated mutations in a single center in the Netherlands. Eur J Clin Microbiol Infect Dis 2020; 40:591-595. [PMID: 33029766 DOI: 10.1007/s10096-020-04061-w] [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: 07/06/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
Abstract
PURPOSE In this study, we report the prevalence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) amongst clinical specimens of patients suspected for sexually transmitted infections received at our laboratory and in addition report the prevalence of resistance-associated mutations (RAM) for ciprofloxacin in NG and azithromycin and moxifloxacin in MG. METHODS All specimens received from December 2018 to May 2019 were tested for the four pathogens. In addition, the presence of RAM associated with resistance to ciprofloxacin in NG and to azithromycin and moxifloxacin in MG was determined by different real-time PCR assays on all NG- and MG-positive specimens. RESULTS CT was detected most often (267/2613, 10.2%), followed by MG (106/2592, 4.1%), NG (41/2613, 1.6%) and TV (10/2592, 0.4%) amongst all specimens. The prevalence of ciprofloxacin RAM in NG was 21.2%, and the prevalence of RAM in MG was 40.6% for azithromycin and 8.1% for moxifloxacin. Nearly all specimens containing moxifloxacin-resistant MG also contained azithromycin-resistant MG. CONCLUSION CT is found most often in our population followed by MG and NG. By using molecular assays to detect RAM supplementary to pathogen identification of NG and MG, optimal therapy can be advised.
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Priyadarshi K, Prakash P, Rani A, Singh SK. Multiplex nested polymerase chain reaction targeting multiple genes for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in genitourinary specimens. Indian J Sex Transm Dis AIDS 2019; 40:152-158. [PMID: 31922106 PMCID: PMC6896390 DOI: 10.4103/ijstd.ijstd_73_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Objectives: The objective of this study was to design and evaluate a novel multiplex nested polymerase chain reaction (PCR) protocol for simultaneous detection of Neisseria gonorrhoeae and Chlamydia trachomatis in genitourinary specimens obtained from symptomatic patients clinically suspected of sexually transmitted infections (STIs), targeting two different genes each for these pathogens. Materials and Methods: A total of 116 genitourinary specimens were collected from men (n = 12) and women (n = 104). Direct microscopy, culture isolation, and antimicrobial susceptibility testing for N. gonorrhoeae were performed. Multiplex nested PCR was performed on clinical samples using novel designed primers targeting porA pseudogene and opa gene of N. gonorrhoeae and momp gene and cryptic plasmid of C. trachomatis simultaneously. DNA sequence analysis of nested PCR amplicons for each of four gene targets was carried out for the validation of in-house designed primers and PCR protocol. Results: A total of 51.72% (60/116) patients were detected to have either of the two STIs. About 35.35% (41/116) of patients were positive for C. trachomatis and 33.62% (39/116) for N. gonorrhoeae by employing multiplex nested PCR. Coinfection with N. gonorrhoeae and C. trachomatis was detected in 17.24% (20/116) patients. 31.5% endocervical swabs (n = 54), 64.4% speculum-assisted high vaginal swabs (n = 45), and 80% self-collected vaginal swabs (n = 5) were detected positive for either of two STIs. Conclusions: The multiplex nested PCR protocol designed and employed in the present study may be used in the diagnosis and management of both symptomatic as well as asymptomatic cases of N. gonorrhoeae and C. trachomatis, particularly among high-risk groups.
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Affiliation(s)
- Ketan Priyadarshi
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Pradyot Prakash
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Anjali Rani
- Department of Obstetrics and Gynaecology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Satyendra Kumar Singh
- Department of Dermatology and Venerology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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10
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Chen L, Shin DJ, Zheng S, Melendez JH, Gaydos CA, Wang TH. Direct-qPCR Assay for Coupled Identification and Antimicrobial Susceptibility Testing of Neisseria gonorrhoeae. ACS Infect Dis 2018; 4:1377-1384. [PMID: 29999304 DOI: 10.1021/acsinfecdis.8b00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multidrug-resistant gonorrhea has become an urgent issue for global public health. As the causative agent of gonorrhea, Neisseria gonorrhoeae, has been progressively developing resistance to nearly all prescribed antimicrobial drugs, monitoring its antimicrobial resistance on a broader scale has become a crucial agenda for effective antibiotic stewardship. Unfortunately, gold standard antimicrobial susceptibility testing (AST) relies on time and labor-intensive phenotypic assays, which lag behind the current diagnostic workflow for N. gonorrhoeae identification based on nucleic acid amplification tests (NAAT). Newer assay technologies based on NAAT can rapidly identify N. gonorrhoeae from clinical specimen but fundamentally lack the capacity to provide phenotypic AST information. Herein, we propose a direct-quantitative PCR (direct-qPCR) assay that enables pathogen-specific identification and phenotypic AST via quantitative measurement of N. gonorrhoeae growth directly from a liquid medium without any sample preprocessing. The assay has an analytical sensitivity of 102 CFU/mL and is highly specific to N. gonorrhoeae in the presence of urogenital flora and clinical swab eluent. We tested seven N. gonorrhoeae strains against three antibiotic agents, penicillin, tetracycline, and ciprofloxacin, and achieved 95.2% category agreement and 85.7% essential agreement with the FDA-approved E-test. The assay presented in this work has the unique ability to identify N. gonorrhoeae and provide phenotypic AST directly from the liquid medium with cell densities as low as 102 CFU/mL, demonstrating an accelerated, sensitive, and scalable workflow for performing both identification and AST of N. gonorrhoeae.
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Affiliation(s)
| | | | | | - Johan H. Melendez
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Charlotte A. Gaydos
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
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Gonorrhea in Indonesia: High Prevalence of Asymptomatic Urogenital Gonorrhea but No Circulating Extended Spectrum Cephalosporins-Resistant Neisseria gonorrhoeae Strains in Jakarta, Yogyakarta, and Denpasar, Indonesia. Sex Transm Dis 2017; 43:608-16. [PMID: 27626188 DOI: 10.1097/olq.0000000000000510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Little is known about the epidemiology of asymptomatic urogenital gonorrhea and antimicrobial susceptibility of Neisseria gonorrhoeae (NG) strains circulating in Indonesia. We studied these issues in 3 large Indonesian cities. METHODS In 2014, participants were recruited from sexually transmitted infection clinics and through outreach in Jakarta, Yogyakarta, and Denpasar. Neisseria gonorrhoeae detection in genital specimens was performed with NG-qPCR at the Public Health Service in Amsterdam. Antimicrobial susceptibility was investigated using the Etest. RESULTS Among 992 participants, 781 were asymptomatic and included in the risk factors analysis: 439 (56.2%) men, 258 (33.0%) women, and 84 (10.8%) transwomen. They differed significantly in age and were mostly men who have sex with men (35.2%) and female sex workers (29.3%).Overall, 175 (22.4%) asymptomatic participants had a positive NG-qPCR result. Factors positively associated with asymptomatic urogenital gonorrhea were being recruited through outreach (vs clinic-based), inconsistent condom use, and being divorced/widowed (vs single).Among 79 urogenital cultured isolates derived from 27 symptomatic and 52 asymptomatic participants, all isolates were susceptible to ceftriaxone and cefixime, and 98.7% of isolates were susceptible to azithromycin. In contrast, resistance to doxycycline (98.7%) and ciprofloxacin (97.4%) was common. CONCLUSIONS Prevalence of asymptomatic urogenital gonorrhea among Indonesian key populations is very high. Little to no resistance against extended spectrum cephalosporins and azithromycin was observed. However, almost all isolates were resistant to doxycycline and ciprofloxacin. Strengthening outreach sexually transmitted infections services, composing guidelines to screen asymptomatic individuals, and implementing periodical antimicrobial resistance surveillance are recommended.
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Budkaew J, Chumworathayi B, Pientong C, Ekalaksananan T. Conventional culture versus nucleic acid amplification tests for screening of urethral Neisseria gonorrhea infection among asymptomatic men who have sex with men. Pragmat Obs Res 2017; 8:167-173. [PMID: 28919833 PMCID: PMC5590682 DOI: 10.2147/por.s137377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Many methods are used to detect urethral Neisseria gonorrhea (NG) infection among asymptomatic men who have sex with men (MSM). The objective of this study was to define the performance of conventional culture compared to real-time polymerase chain reaction (PCR) for diagnosis of asymptomatic urethral gonorrhea among MSM. METHODS In this cross-sectional study, 147 clinical specimens for NG testing from asymptomatic participants were evaluated. MSM >18 years old who consented to undergo urethral swab and collection of urine samples from two clinics (one was the sexually transmitted diseases (STDs) mobile clinic and the second was the antiretroviral clinic) located in Khon Kaen, Thailand, were recruited. For conventional culture, 147 swab specimens from urethra were analyzed. For real-time PCR, the same samples and collected urine (147 urethral swab and 62 urine) were evaluated. RESULTS Participants were predominately older aged (mean age: 28.79 years, range: 18-54), asymptomatic (99.3%), and engaged in sex with multiple partners (63% had at least two partners and 36% had at least three partners during the previous 3 months). Twenty-five MSM (17%) had history of STD, mainly human immunodeficiency virus infection. Of the 147 specimens, 42 were positive for NG detected by real-time PCR (prevalence: 28.6%, 95% confidence interval [CI]: 24.8%-32.4%), while none of the 147 MSM were positive for NG detected by conventional culture (prevalence: 0.0%, 95% CI: 0.0%-7.3%). These findings indicated that conventional culture had low sensitivity but high specificity (0.0% and 100%, respectively). We could not demonstrate that many of the factors that were identified in other studies were associated to increased (or decreased) risk of urethral gonococcal infection in our population. CONCLUSION In asymptomatic MSM, nucleic acid amplification tests are more appropriate for screening of urethral NG infection than conventional culture. However, the culture method is necessary for monitoring emerging antimicrobial resistance and to inform gonorrhea treatment guidelines.
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Affiliation(s)
- Jiratha Budkaew
- Department of Social Medicine, Khon Kaen Center Hospital, Khon Kaen, Thailand
| | - Bandit Chumworathayi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,HPV and EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand
| | - Chamsai Pientong
- HPV and EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.,Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tipaya Ekalaksananan
- HPV and EBV and Carcinogenesis Research Group, Khon Kaen University, Khon Kaen, Thailand.,Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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13
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Hananta IPY, van Dam AP, Bruisten SM, van der Loeff MFS, Soebono H, Christiaan de Vries HJ. Value of light microscopy to diagnose urogenital gonorrhoea: a diagnostic test study in Indonesian clinic-based and outreach sexually transmitted infections services. BMJ Open 2017; 7:e016202. [PMID: 28801418 PMCID: PMC5629680 DOI: 10.1136/bmjopen-2017-016202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Gonorrhoea is a common sexually transmitted disease caused by Neisseria gonorrhoeae (Ng) infection. Light microscopy of urogenital smears is used as a simple tool to diagnose urogenital gonorrhoea in many resource-limited settings. We aimed to evaluate the accuracy of light microscopy to diagnose urogenital gonorrhoea as compared with a PCR-based test. METHODS In 2014, we examined 632 male urethral and 360 endocervical smears in clinic-based and outreach settings in Jakarta, Yogyakarta and Denpasar, Indonesia. Using the detection of Ng DNA by a validated PCR as reference test, we evaluated the accuracy of two light microscopic criteria to diagnose urogenital gonorrhoea in genital smears: (1) the presence of intracellular Gram-negative diplococci (IGND) and (2) ≥5 polymorphonuclear leucocytes (PMNL)/oil-immersion field (oif) in urethral or ≥20 PMNL/oif in endocervical smears. RESULTS In male urethral smears, IGND testing had a sensitivity (95% CI), specificity (95% CI) and kappa±SE of 59.0% (50.1 to 67.4), 89.4% (86.3 to 91.9) and 0.49±0.04, respectively. For PMNL count, these were 59.0% (50.1 to 67.4), 83.7% (80.2 to 86.9) and 0.40±0.04, respectively. The accuracy of IGND in the clinic-based settings (72.0% (57.5 to 83.3), 95.2% (91.8 to 97.5) and 0.68±0.06, respectively) was better than in the outreach settings (51.2% (40.0 to 62.3), 83.4% (78.2 to 87.8) and 0.35±0.06, respectively). In endocervical smears, light microscopy performed poorly regardless of the setting or symptomatology, with kappas ranging from -0.09 to 0.24. CONCLUSION Light microscopy using IGND and PMNL criteria can be an option with moderate accuracy to diagnose urethral gonorrhoea among males in a clinic-based setting. The poor accuracy in detecting endocervical infections indicates an urgent need to implement advanced methods, such as PCR. Further investigations are needed to identify the poor diagnostic outcome in outreach services.
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Affiliation(s)
- I Putu Yuda Hananta
- Deartment of Dermatology, Academic Medical Center, University of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, Noord Holland, The Netherlands
| | - Alje P van Dam
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Onze Lieve Vrouwe Gasthuis (OLVG) Hospital, Amsterdam, The Netherlands
| | - Sylvia Maria Bruisten
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Center for Infections and Immunology Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten Franciscus Schim van der Loeff
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Amsterdam Infection and Immunity Institute (AI&II), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hardyanto Soebono
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Henry John Christiaan de Vries
- Deartment of Dermatology, Academic Medical Center, University of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Department of Infectious Diseases, Public Health Service (GGD) of Amsterdam, Amsterdam, Noord Holland, The Netherlands
- Amsterdam Infection and Immunity Institute (AI&II), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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14
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Verma R, Mahajan N, Sood S. Gonococcal opa gene as a diagnostic target for nucleic acid amplification tests in Indian Population. Indian J Med Microbiol 2016; 34:560-561. [PMID: 27934846 DOI: 10.4103/0255-0857.195361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- R Verma
- Department of Microbiology, All Institute of Medical Sciences, New Delhi, India
| | - N Mahajan
- Department of Microbiology, All Institute of Medical Sciences, New Delhi, India
| | - S Sood
- Department of Microbiology, All Institute of Medical Sciences, New Delhi, India
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Abstract
In the last 20 years, nucleic acid amplification tests (NAATs) have gradually replaced traditional methods for the detection of sexually transmitted infections. NAAT technology comes with some considerable benefits for diagnosis, including increased sensitivity, rapid result turnaround and suitability for high throughput screening of asymptomatic individuals using more-readily available specimens. However, the transition to NAAT has not come without its problems. False-negative and false-positive results have been reported owing to various technical issues. Furthermore, increased reliance on NAATs for diagnosis have created the need to develop NAAT-based methods to inform treatment, being an area that presents its own set of challenges. In this review article, we explore NAAT-based detection of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium and Trichomonas vaginalis. In doing so, we consider the benefits and limitations of NAAT-based technology and highlight areas where further research and development is in need.
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Serra-Pladevall J, Caballero E, Roig G, Juvé R, Barbera MJ, Andreu A. Comparison between conventional culture and NAATs for the microbiological diagnosis in gonococcal infection. Diagn Microbiol Infect Dis 2015; 83:341-3. [PMID: 26323884 DOI: 10.1016/j.diagmicrobio.2015.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 11/16/2022]
Abstract
Gonorrhea is a public health problem. Fast diagnostics is necessary. The aim of this study was to compare the diagnostic yield of culture with that of polymerase chain reaction (PCR) in gonococcal infection. This is a study comparing the results of Neisseria gonorrhoeae detection by culture versus PCR from July to December 2012. Molecular diagnosis was performed by real-time PCR using the Versant CT/GC DNA 1.0 assay. In the 768 specimens, 96.9% the results were concordant. In 3.1%, the results were discordant, being PCR-positive and culture-negative in 21 cases and PCR-negative and culture-positive in 3. The sensitivity, specificity, positive predictive value, and negative predictive value for culture were 86.2%, 99.8%, 99.2%, and 96.7%, and for PCR, 98.7%, 100%, 100% and 99.7%, respectively. In laboratories where antimicrobial susceptibility is monitored, an effective approach would be to perform culture in addition to PCR in symptomatic patients.
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Affiliation(s)
- J Serra-Pladevall
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Universitat Autonoma de Barcelona, Barcelona, Spain.
| | - E Caballero
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Universitat Autonoma de Barcelona, Barcelona, Spain
| | - G Roig
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - R Juvé
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - M J Barbera
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - A Andreu
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain; Universitat Autonoma de Barcelona, Barcelona, Spain
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17
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Successful Combination of Nucleic Acid Amplification Test Diagnostics and Targeted Deferred Neisseria gonorrhoeae Culture. J Clin Microbiol 2015; 53:1884-90. [PMID: 25832300 DOI: 10.1128/jcm.00369-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/25/2015] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid amplification tests (NAATs) are recommended for the diagnosis of N. gonorrhoeae infections because of their superior sensitivity. Increasing NAAT use causes a decline in crucial antimicrobial resistance (AMR) surveillance data, which rely on culture. We analyzed the suitability of the ESwab system for NAAT diagnostics and deferred targeted N. gonorrhoeae culture to allow selective and efficient culture based on NAAT results. We included patients visiting the STI Clinic Amsterdam, The Netherlands, in 2013. Patient characteristics and urogenital and rectal samples for direct N. gonorrhoeae culture, standard NAAT, and ESwab were collected. Standard NAAT and NAAT on ESwab samples were performed using the Aptima Combo 2 assay for N. gonorrhoeae and C. trachomatis. Two deferred N. gonorrhoeae cultures were performed on NAAT-positive ESwab samples after storage at 4°C for 1 to 3 days. We included 2,452 samples from 1,893 patients. In the standard NAAT, 107 samples were N. gonorrhoeae positive and 284 were C. trachomatis positive. The sensitivities of NAAT on ESwab samples were 83% (95% confidence interval [CI], 75 to 90%) and 87% (95% CI, 82 to 90%), respectively. ESwab samples were available for 98 of the gonorrhea-positive samples. Of these, 82% were positive in direct culture and 69% and 56% were positive in the 1st and 2nd deferred cultures, respectively (median storage times, 27 and 48 h, respectively). Deferred culture was more often successful in urogenital samples or when the patient had symptoms at the sampling site. Deferred N. gonorrhoeae culture of stored ESwab samples is feasible and enables AMR surveillance. To limit the loss in NAAT sensitivity, we recommend obtaining separate samples for NAAT and deferred culture.
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18
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Vahidnia A, Costa S, Veenings S, Tuin H, van Loon L, Bliekendaal H. Comparative evaluation of Roche Aurora FLOW, Becton and Dickinson Viper system, and Dynex DS2 for detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Trichomonas vaginalis in various clinical specimens. Diagn Microbiol Infect Dis 2014; 80:191-2. [PMID: 25172824 DOI: 10.1016/j.diagmicrobio.2014.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 10/24/2022]
Abstract
The purpose of this study is to introduce a high-throughput system, Aurora FLOW, for the simultaneous detection of 3 clinically relevant pathogens of sexually transmitted infections. Comparative evaluation with other systems revealed an overall concordance of 97.9% for Chlamydia trachomatis and comparable performance for Neisseria gonorrhoeae and Trichomonas vaginalis.
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Affiliation(s)
- Ali Vahidnia
- Molecular Diagnostic Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands.
| | - Sandra Costa
- Medical Microbiology Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands
| | - Sanne Veenings
- Molecular Diagnostic Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands
| | - Hellen Tuin
- Medical Microbiology Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands
| | - Linda van Loon
- Molecular Diagnostic Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands
| | - Harry Bliekendaal
- Medical Microbiology Laboratory, Atal-Medial Medical Diagnostic Center, Jan Tooropstraat 138, 1061 AD, Amsterdam, the Netherlands
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Cervical Infection with Herpes simplex Virus, Chlamydia trachomatis, and Neisseria gonorrhoeae among Symptomatic Women, Dubai, UAE: A Molecular Approach. Interdiscip Perspect Infect Dis 2014; 2014:347602. [PMID: 24982675 PMCID: PMC4058512 DOI: 10.1155/2014/347602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 04/24/2014] [Accepted: 05/13/2014] [Indexed: 11/20/2022] Open
Abstract
Tragically, genital tract infections are still a major public health problem in many regions. This study was undertaken to determine the prevalence of cervical infection with Herpes simplex virus (HSV), Chlamydia trachomatis (CT), and Neisseria gonorrhoeae (NG) among married women referring to Iranian Hospital, Dubai, UAE. In a retrospective cross-sectional survey, 201 female patients aged 16–80 years who referred to the Obstetrics and Gynecology Department of Iranian Hospital, Dubai, UAE, in 2010 were enrolled. The patients were categorized into three age groups: 15–30 (group I), 31–40 (group II), and ≥41 years old (group III). A cervical swab sample was collected from each woman and the prevalence of cervical infection with HSV, CT, and NG was determined by PCR method. HSV, CT, and NG were detected in 6.5%, 10.4%, and 5.5% of swab samples, respectively. Regarding age, a significant difference was noticed for prevalence of NG and HSV between groups I and III. Because of public health importance of sexual transmitted diseases (STDs), their long-lasting impact on quality of life, and their economic burden, preventing measures and education of women seem necessary.
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Schmitt M, Depuydt C, Stalpaert M, Pawlita M. Bead-based multiplex sexually transmitted infection profiling. J Infect 2014; 69:123-33. [PMID: 24814157 DOI: 10.1016/j.jinf.2014.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 04/23/2014] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Sexually transmitted infections are a significant cause of genital disease, infertility and hospital admissions. The economic impact is high. An accurate diagnosis is often difficult and time consuming. We report the development and validation of a novel bead-based multiplex sexually transmitted infection profiling (STIP) assay that detects 18 sexually transmitted infections using a multiplex PCR followed by Luminex bead-based hybridisation. METHODS STIP was validated using urogenital samples pretested by commercially available quantitative PCR, microscopy or by culturing methods. RESULTS STIP specifically detects Chlamydia trachomatis, Herpes simplex virus 1 and 2, Treponema pallidum, Trichomonas vaginalis, Neisseria gonorrhoeae, Mycoplasma (M.) genitalium, M. hominis, M. pneumonia, M. spermatophilum, Ureaplasma urealyticum and U. parvum, and quantifies bacterial vaginosis-associated Atopobium vaginae and Gardnerella vaginalis as well as three Candida species and normal genital flora-associated Lactobacillus species. STIP reached an overall concordance of 95-100% with commercially available quantitative PCR tests. Compared to Nugent score, STIP reached a sensitivity of 95% and a specificity of 86% for bacterial vaginosis detection. Candida specimens, pretested by direct culturing, were identified with a sensitivity of 97% and a specificity of 99%. CONCLUSIONS STIP is a powerful high-throughput tool in assessing a broad spectrum of urogenital infections.
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Affiliation(s)
- Markus Schmitt
- German Cancer Research Center (DKFZ), Research Program Infection and Cancer, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
| | - Christophe Depuydt
- Laboratory of Molecular and Clinical Pathology (RIATOL), AML, Sonic Healthcare Benelux, Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Michel Stalpaert
- Laboratory of Molecular and Clinical Pathology (RIATOL), AML, Sonic Healthcare Benelux, Emiel Vloorsstraat 9, 2020 Antwerp, Belgium
| | - Michael Pawlita
- German Cancer Research Center (DKFZ), Research Program Infection and Cancer, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany.
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Perry MD, Jones RN, Corden SA. Is confirmatory testing of Roche cobas 4800 CT/NG test Neisseria gonorrhoeae positive samples required? Comparison of the Roche cobas 4800 CT/NG test with an opa/pap duplex assay for the detection of N gonorrhoeae. Sex Transm Infect 2014; 90:303-8. [PMID: 24653040 DOI: 10.1136/sextrans-2013-051410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES Recently marketed nucleic acid amplification tests (NAAT) for the detection of Neisseria gonorrhoeae (NG) have improved specificity over previous generation assays. A study to assess the necessity for confirmation of Roche cobas 4800 NG positive samples was undertaken by the Public Health Wales Microbiology Molecular Diagnostic Unit in Cardiff. METHODS Classical NG culture identification was compared to cobas 4800 (DR-9), opacity (opa) gene and porA pseudogene (pap) results. Confirmatory NAATs (opa/pap) were performed prospectively for 120 cobas 4800 NG positive urogenital and extragenital samples. Retrospective supplementary NAAT and sequence analysis of additional cobas 4800 NG positive extragenital samples was also carried out. RESULTS Of the 188 classically identified clinical NG isolates, 184 were identified as NG in all 3 molecular targets. Two isolates were only detected by 2 molecular targets. A further 2 isolates were culture false-positives. Combining the results from prospective and retrospective testing, the sensitivity and negative predictive value for cobas 4800 NG detection for urogenital, rectal and oropharyngeal samples was 100%. Specificity for all sample types was greater than 99.7%. Positive predictive value was 96.0% and 96.4% for urogenital and rectal specimens, respectively, and 88.6% for oropharyngeal samples. CONCLUSIONS Molecular tests could be used for culture confirmation where available. Roche cobas 4800 Chlamydia trachomatis/Neisseria gonorrhoeae (CT/NG)CT/NG gonorrhoea diagnosis is superior to culture with urogenital and rectal positives not requiring confirmation. Roche cobas 4800 oropharyngeal NG detection findings warrant further prospective study of routine confirmatory testing accounting for its cost and clinical usefulness.
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Affiliation(s)
- Michael D Perry
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
| | - Rachel N Jones
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
| | - Sally A Corden
- Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
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Loop-mediated isothermal amplification test for detection of Neisseria gonorrhoeae in urine samples and tolerance of the assay to the presence of urea. J Clin Microbiol 2014; 52:2163-5. [PMID: 24622100 DOI: 10.1128/jcm.00314-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A loop-mediated isothermal amplification (LAMP) assay for open reading frame 1 (ORF1) of the glutamine synthetase gene of Neisseria gonorrhoeae was able to tolerate urea concentrations of ≤ 1.8 M, compared with a PCR assay that was functional at concentrations of <100 mM. The LAMP assay was as sensitive as the PCR assay while being faster and simpler to perform.
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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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Coupling electrochemical response of a DNA biosensor with PCR for Neisseria gonorrhoeae detection. Diagn Microbiol Infect Dis 2014; 78:16-23. [DOI: 10.1016/j.diagmicrobio.2013.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/10/2013] [Accepted: 09/15/2013] [Indexed: 12/20/2022]
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Tunsjø HS, Smedsrud E, Holm PC, Rokvam K, Schie C, Rognlien V, Augustin I, Fostervold A. Purification of DNA eluates from the ProbeTec GC Q(x) assay on BD Viper™ XTR allows for further analysis and confirmation of gonorrhea. Eur J Clin Microbiol Infect Dis 2013; 33:49-54. [PMID: 23903665 DOI: 10.1007/s10096-013-1927-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/08/2013] [Indexed: 11/30/2022]
Abstract
Low positive predictive values of Neisseria gonorrhoeae nucleic acid amplification tests in low-prevalence populations are a major challenge for accurate diagnostics. It is therefore necessary to verify all positive N. gonorrhoeae results with a different assay and target gene, preferably using the same sample. The BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens, which is recommended for BD Viper™ XTR, is incompatible with other commercial platforms. Therefore, a confirmatory PCR has not been available for samples received on this transport medium. To be able to verify results from these samples with another assay, our objective was to establish a procedure for using the DNA eluates from BD Viper™ XTR for further analysis. DNA eluates from BD Viper™ XTR were collected and analyzed in two in-house confirmatory real-time PCRs targeting the porA pseudogene and the opa multicopy gene. BD Viper™ XTR DNA eluates were analyzed directly and also after purification with the nucleic acid extraction system NucliSENS® easyMag®. Purification of BD Viper™ XTR DNA eluates with the nucleic acid extraction system NucliSENS® easyMag® provided a sensitivity of the in-house PCR comparable to BD Viper™. With the inclusion of two target genes in the confirmatory PCR, specific and reliable verification of results were obtained. This study presents a simple, inexpensive procedure which allows for rapid verification of gonorrhea from samples received on the BD ProbeTec™ Q(x) Collection Kit for Endocervical or Lesion Specimens.
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Affiliation(s)
- H S Tunsjø
- Unit of Gene Technology and Department of Microbiology, Division of Diagnostics and Technology, Akershus University Hospital, Sykehusveien 27, 1478, Nordbyhagen, Norway,
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Crucitti T, De Deken B, Smet H, Cuylaerts V, Abdellati S, Vuylsteke B. Evaluation of the APTIMA Combo 2 Assay using self-administered vaginal swabs for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae. Diagn Microbiol Infect Dis 2013; 76:385-6. [PMID: 23598167 DOI: 10.1016/j.diagmicrobio.2013.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 10/27/2022]
Abstract
We report on the performance of the APTIMA Combo 2 assay for the detection of chlamydial infection and gonorrhea using self-administered vaginal specimens in specimen transport medium and specimen kept dry. The results are compared with the results using the Amplicor assay and the BD ProbeTec assay™.
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Hassanzadeh P, Mardaneh J, Motamedifar M. Conventional Agar-Based Culture Method, and Nucleic Acid Amplification Test (NAAT) of the cppB Gene for Detection of Neisseria gonorrhea in Pregnant Women Endocervical Swab Specimens. IRANIAN RED CRESCENT MEDICAL JOURNAL 2013; 15:207-11. [PMID: 23983999 PMCID: PMC3745748 DOI: 10.5812/ircmj.3726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 07/07/2012] [Accepted: 07/15/2012] [Indexed: 11/26/2022]
Abstract
Background Neisseria gonorrhea is the etiological agent of the sexually transmitted disease (STD) gonorrhea, and primarily infects the mucous membranes of the urethra, endocervix, pharynx or rectum of females which may result in substantial morbidity. N. gonorrhea also causes disseminated infection, with complications that may result in ectopic pregnancy, tubal infertility, chronic pelvic pain or maternal transmission of gonorrhea, and also increases susceptibility to HIV. Objectives In the present investigation, we used conventional agar-based culture method, and nucleic acid amplification of CCPB gene for detection of Neisseria gonorrhea in endocervical swabs samples collected from pregnant women studied Patients and Methods Endocervical swabs specimens for this study were obtained from 1100 pregnant women who presented to Shiraz (Iran) Hospitals from 2009 to 2011. In the present investigation we used conventional agar-based culture method, and nucleic acid amplification test (NAAT) of CCPB gene for detection of Neisseria gonorrhea in endocervical swabs samples collected from pregnant women studied. From each pregnant woman two endocervical swabs were taken: one swab placed in tubes containing phosphate buffered saline for Polymerase Chain Reaction, and the other to inoculate on culture media. Results Among 1100 endocervical swabs examined, 13 (1.18%) samples had positive results by polymerase chain reaction (PCR) on Neisseria gonorrhea CCPB gene. All endocervical swabs culture had negative results for Neisseria gonorrhea. 84 (7%) of the women had vaginal discharge, in whom PCR on endocervical swabs of these individuals had negative findings. Conclusions Nucleic acid amplification tests (NAATs) are very appropriate in detection of infected individuals. Detection techniques such as NAATs are independent of bacterial viability, and have a potential to limit false negative samples, therefore, in our country, the application of different laboratory diagnosis methods including NAATs with culture as gold standard for determination antimicrobial susceptibility is essential.
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Affiliation(s)
- Parvin Hassanzadeh
- Department of Biology, School of Sciences, Shiraz University, Shiraz, IR Iran
- Corresponding author: Parvin Hassanzadeh, Department of Biology, School of Sciences, Shiraz University, Shiraz, IR Iran. Tel/Fax: +98-7112280916, E-mail:
| | - Jalal Mardaneh
- Department of Pathobiology, School of Public Health and Institute of Public Health Research, Tehran University of Medical Sciences, Tehran, IR Iran
- Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Mohammad Motamedifar
- Department of Bacteriology & Virology, Medical School, Shiraz HIV/Aids Research Center
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Protocol for a facile multiplex PCR for multi-antimicrobial resistance and Gonococcus detection. Methods Mol Biol 2012. [PMID: 22782830 DOI: 10.1007/978-1-61779-937-2_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Gonorrhea is a continuing problem worldwide particularly in terms of the spread of multiple drug resistance. We have successfully developed an efficient PCR method for the simultaneous identification of gonococci and detection of the antimicrobial-resistant profile. By this method, penicillinase-producing Neisseria gonorrhoeae (PPNG), high-level tetracycline-resistant N. gonorrhoeae (TRNG), and ciprofloxacin-resistant N. gonorrhoeae (CRNG) can be clearly identified. Moreover, the plasmid-types of penicillin and tetracycline resistance are also characterized. The method has 100 % sensitivity and specificity. It is also time- and labor-saving compared to the conventional method. Thus, the procedure is suitable for epidemiological surveillance.
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HRM confirmation of Neisseria gonorrhoeae in clinical specimens by G→A (position 857) mutation detection in the 16S rRNA gene before sequencing and after porA confirmation. J Microbiol Methods 2012; 89:148-52. [DOI: 10.1016/j.mimet.2012.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/25/2012] [Accepted: 03/02/2012] [Indexed: 11/23/2022]
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Evaluation of an opa gene-based nucleic acid amplification test for detection of Neisseria gonorrhoeae in urogenital samples in North India. Epidemiol Infect 2012; 140:2110-6. [PMID: 22244259 DOI: 10.1017/s0950268811002883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Due to the poor positive predictive value of nucleic acid amplification tests (NAATs) for gonorrhoea when applied to a low-prevalence setting, current guidelines recommend the use of supplementary polymerase chain reaction (PCR) targeting a different gene for confirmation of true positives in urogenital specimens. This study sought to standardize and evaluate performance of an in-house opa gene-based PCR assay for gonorrhoea compared to assays targeting the porA pseudogene and 16S rRNA gene. Four hundred samples (300 endocervical, 100 urethral swabs) from patients attending STD clinics in New Delhi, India were used. The sensitivity, specificity, positive predictive value and negative predictive value of the opa-based PCR were 100%, 97·9%, 89·5% and 100%, respectively. In females, the use of NAATs provided enhanced diagnosis of gonorrhoea.
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Bongaerts M, van de Bovenkamp JH, Morré SA, Manders ME, Heddema ER. Evaluation of the Siemens VERSANT® CT/GC DNA 1.0 Assay (kPCR) for detection of Chlamydia trachomatis and Neisseria gonorrhoeae. J Microbiol Methods 2011; 87:139-42. [DOI: 10.1016/j.mimet.2011.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Revised: 09/01/2011] [Accepted: 09/02/2011] [Indexed: 10/17/2022]
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Muvunyi CM, Dhont N, Verhelst R, Crucitti T, Reijans M, Mulders B, Simons G, Temmerman M, Claeys G, Padalko E. Evaluation of a new multiplex polymerase chain reaction assay STDFinder for the simultaneous detection of 7 sexually transmitted disease pathogens. Diagn Microbiol Infect Dis 2011; 71:29-37. [DOI: 10.1016/j.diagmicrobio.2011.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/28/2011] [Accepted: 06/08/2011] [Indexed: 10/17/2022]
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Walsh A, Rourke FO, Crowley B. Molecular detection and confirmation of Neisseria gonorrhoeae in urogenital and extragenital specimens using the Abbott CT/NG RealTime assay and an in-house assay targeting the porA pseudogene. Eur J Clin Microbiol Infect Dis 2010; 30:561-7. [DOI: 10.1007/s10096-010-1120-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 11/13/2010] [Indexed: 11/25/2022]
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Shahcheraghi F, Shafiei M, Valadkhani Z. Detection of Neisseria gonorrhoeae from vaginal swabs of Ewin, Rajaii shahr, Karaj and Varamin female prisoners by PCR and culture methods. Pak J Biol Sci 2010; 13:198-200. [PMID: 20437689 DOI: 10.3923/pjbs.2010.198.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Isolation of N. gonorrhoeae by culture method is currently the gold standard for the definitive diagnosis of gonorrhoea. However, PCR techniques are being used more frequently as sensitivity and specificity of the newer tests are improved. In this study, 500 vaginal swabs from Ewin, Rajaii shahr, Karaj and Varamin female prisoners were used for detection of N. gonorrhoae by culture and PCR techniques. Five hundred vaginal swabs from Ewin, Rajaii shahr, Karaj and Varamin female prisoners were cultured in modified Thayer Martin in 37 degrees C with 5% CO2 for 72 h. Oxidase, catalase tests, biochemical tests such as maltose and glucose oxidation and gram staining, were used to confirm the isolated species. Amplification by PCR using 2 targets which are specific for N. gonorrhoeae, Ngu1 and Ngu2, were used to detect the presence of gonococcal specific DNA. Despite of finding some questionable samples as N. gonorrhoeae by using biochemical tests, PCR method confirmed that none of them were positive for N. gonorrhoeae. This study deals with detection of N. gonorrhoeae among woman prisoners in three main prisons in Tehran, Iran. The high specificity and sensitivity coupled with low cost and rapidity of the method (PCR) provided a substantial advantages over the time consuming culture methods currently used in hospitals and laboratories.
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Affiliation(s)
- F Shahcheraghi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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35
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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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36
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Walsh A, Rourke FO, Laoi BN, Crowley B. Evaluation of the Abbott RealTime™ CT assay with the BD ProbeTec™ ET assay for the detection of Chlamydia trachomatis in a clinical microbiology laboratory. Diagn Microbiol Infect Dis 2009; 64:13-9. [DOI: 10.1016/j.diagmicrobio.2009.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 01/20/2009] [Accepted: 01/23/2009] [Indexed: 11/26/2022]
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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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Whiley DM, Lambert SB, Bialasiewicz S, Goire N, Nissen MD, Sloots TP. False-negative results in nucleic acid amplification tests-do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation? Crit Rev Microbiol 2008; 34:71-6. [PMID: 18568861 DOI: 10.1080/10408410801960913] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Nucleic acid amplification tests (NAATs) have numerous advantages over traditional diagnostic techniques and so are now widely used by diagnostic laboratories for routine detection of infectious agents. However, there is some concern over the increasing numbers of reports of NAAT false-negative results caused by sequence variation. Highly conserved NAAT target sequences have been reported for many organisms, yet sequence-related problems continue to be observed in commercial and in-house assays targeting a broad range of microbial pathogens. In light of these ongoing problems, it may be time to consider the use of two genetic targets in NAAT methods to reduce the potential for sequence-related false-negative results.
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Affiliation(s)
- D M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Sir Albert Sakzewski Virus Research Centre, Royal Children's Hospital and Health Service Distric, Queensland, Australia.
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Clinical Validation of a Real-Time Polymerase Chain Reaction Detection of Neisseria gonorrheae porA Pseudogene Versus Culture Techniques. Sex Transm Dis 2008; 35:517-20. [DOI: 10.1097/olq.0b013e3181644bc9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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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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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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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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Hjelmevoll SO, Olsen ME, Sollid JUE, Haaheim H, Unemo M, Skogen V. A fast real-time polymerase chain reaction method for sensitive and specific detection of the Neisseria gonorrhoeae porA pseudogene. J Mol Diagn 2007; 8:574-81. [PMID: 17065426 PMCID: PMC1876173 DOI: 10.2353/jmoldx.2006.060024] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ever since the advent of molecular methods, the diagnostics of Neisseria gonorrhoeae has been troubled by false negative and false positive results compared with culture. Commensal Neisseria species and Neisseria meningitidis are closely related to N. gonorrhoeae and may cross-react when using molecular tests comprising too-low specificity. We have devised a real-time polymerase chain reaction (PCR), including an internal amplification control, that targets the N. gonorrhoeae porA pseudogene. DNA was automatically isolated on a BioRobot M48. Our subsequent PCR method amplified all of the different N. gonorrhoeae international reference strains (n = 34) and N. gonorrhoeae clinical isolates (n = 176) but not isolates of the 13 different nongonococcal Neisseria species (n = 68) that we tested. Furthermore, a panel of gram-negative bacterial (n = 18), gram-positive bacterial (n = 23), fungal (n = 1), and viral (n = 4) as well as human DNA did not amplify. The limit of detection was determined to be less than 7.5 genome equivalents/PCR reaction. In conclusion, the N. gonorrhoeae porA pseudogene real-time PCR developed in the present study is highly sensitive, specific, robust, rapid and reproducible, making it suitable for diagnosis of N. gonorrhoeae infection.
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Affiliation(s)
- Stig Ove Hjelmevoll
- Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway.
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46
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Elston DM. Laboratory results that should be ignored. MEDGENMED : MEDSCAPE GENERAL MEDICINE 2006; 8:9. [PMID: 17415291 PMCID: PMC1868335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Dirk M Elston
- Department of Dermatology, Geisinger Medical Center, Danville, Pennsylvania, USA.
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