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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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Golparian D, Unemo M. Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects. Expert Rev Mol Diagn 2021; 22:29-48. [PMID: 34872437 DOI: 10.1080/14737159.2022.2015329] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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The Accuracy of Molecular Detection Targeting the Mutation C2611T for Detecting Moderate-Level Azithromycin Resistance in Neisseria gonorrhoeae: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2021; 10:antibiotics10091027. [PMID: 34572609 PMCID: PMC8471969 DOI: 10.3390/antibiotics10091027] [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: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (N. gonorrhoeae) is now recognized as a commonly reported sexually transmitted pathogen, and the increasing drug resistance of N. gonorrhoeae has become a serious public health problem. The accuracy of molecular detection for detecting moderate-level azithromycin resistance is not well-established. We summarized the data from studies of the N. gonorrhoeae 23S rRNA mutation at position 2611 with azithromycin resistance to determine the relationship between the mutation and resistance. METHODS AND FINDINGS In this systematic review and meta-analysis, two researchers independently searched six databases for studies with data for the azithromycin minimum inhibitory concentrations (MICs) and the 23S rRNA mutation C2611T of each N. gonorrhoeae isolate. Since the breakpoint of moderate-level resistance to azithromycin (ML-AzmR) was not determined, we divided the moderate level into two groups according to the range of MICs (moderate resistance limited to 2-128 mg/L or 4-128 mg/L) for data extraction. A random-effects model was used to calculate the pooled sensitivity rate, the specificity rate, the pooled positive likelihood ratio (PLR), the negative likelihood ratio (NLR), and the diagnostic odds ratio (DOR). Meta-regression analyses by detection method, isolates sampling (a random sample or not), location, and sample size were performed to explore the possible causes of heterogeneity. The potential publication bias of the included studies was conducted by the Deeks' test. We included 20 studies in our study: 20 studies have data of N. gonorrhoeae with MICs between 2 and 128 mg/L with mutation or without mutation at position 2611(4759 samples), and 14 studies have data of N. gonorrhoeae with MICs between 4 and 128 mg/L (3367 samples). In the group with the moderate level of 2-128 mg/L, the pooled sensitivity rate of the molecular assays was determined to be 71.9% (95% CI, 67.6-74%), the pooled specificity rate was 98.7% (95% CI, 98.2-99.0%), and the DOR ranged from 55.0 to 351.3 (mean, 139.1). In the 4-128 mg/L group, the pooled sensitivity rate was 91.9% (95% CI, 88.9-94.2%), the pooled specificity rate was 95.9% (95% CI, 95.1-96.6%), and the DOR ranged from 41.9 to 364.1 (mean, 123.6). CONCLUSION Through this meta-analysis, we found that the C2611T mutation of 23S rRNA is valuable for the molecular diagnostic of moderate-level azithromycin resistance (ML-AzmR) in N. gonorrhoeae, especially when the moderate level is set at 4-128 mg/L. This rapid molecular detection method can be used for the rapid identification of ML-AzmR isolates in the clinic.
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Singh AE, Pawa J, Kulleperuma K, Prasad E, Marchand S, Dionne K, Trubnikov M, Wong T, Mulvey MR, Martin I. Molecular Characterization and Antimicrobial Resistance in Neisseria gonorrhoeae, Nunavut Region of Inuit Nunangat, Canada, 2018-2019. Emerg Infect Dis 2021; 27:1718-1722. [PMID: 34013864 PMCID: PMC8153863 DOI: 10.3201/eid2706.204407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We assessed antimicrobial resistance (AMR) in Neisseria gonorrhoeae in Nunavut, Canada, using remnant gonorrhea nucleic acid amplification test-positive urine specimens. This study confirms the feasibility of conducting N. gonorrhoeae AMR surveillance and highlights the diversity of gonococcal sequence types and geographic variation of AMR patterns in the territory.
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Bordin A, Pandey S, Coulter C, Syrmis M, Pardo C, Hackett H, Bell SC, Wainwright CE, Nimmo GR, Jennison AV, Clark JE, Whiley DM. Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis. J Med Microbiol 2021; 70. [PMID: 33909552 DOI: 10.1099/jmm.0.001349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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Affiliation(s)
- Amanda Bordin
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Melanie Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Carolyn Pardo
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Hazel Hackett
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C Bell
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Department of Thoracic Medicine, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine Department, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Graeme R Nimmo
- Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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Meyer T, Buder S. The Laboratory Diagnosis of Neisseria gonorrhoeae: Current Testing and Future Demands. Pathogens 2020; 9:E91. [PMID: 32024032 PMCID: PMC7169389 DOI: 10.3390/pathogens9020091] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 02/05/2023] Open
Abstract
The ideal laboratory test to detect Neisseria gonorrhoeae (Ng) should be sensitive, specific, easy to use, rapid, and affordable and should provide information about susceptibility to antimicrobial drugs. Currently, such a test is not available and presumably will not be in the near future. Thus, diagnosis of gonococcal infections presently includes application of different techniques to address these requirements. Microscopy may produce rapid results but lacks sensitivity in many cases (except symptomatic urogenital infections in males). Highest sensitivity to detect Ng was shown for nucleic acid amplification technologies (NAATs), which, however, are less specific than culture. In addition, comprehensive analysis of antibiotic resistance is accomplished only by in vitro antimicrobial susceptibility testing of cultured isolates. As a light at the end of the tunnel, new developments of molecular techniques and microfluidic systems represent promising opportunities to design point-of-care tests for rapid detection of Ng with high sensitivity and specificity, and there is reason to hope that such tests may also provide antimicrobial resistance data in the future.
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Affiliation(s)
- Thomas Meyer
- Department of Dermatology, Venerology and Allergology, St. Josef Hospital, Ruhr-University, 44791 Bochum, Germany
| | - Susanne Buder
- German Consiliary Laboratory for Gonococci, Department of Dermatology and Venerology, Vivantes Hospital Berlin, 12351 Berlin, Germany;
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Berenger BM, Demczuk W, Gratrix J, Pabbaraju K, Smyczek P, Martin I. Genetic Characterization and Enhanced Surveillance of Ceftriaxone-Resistant Neisseria gonorrhoeae Strain, Alberta, Canada, 2018. Emerg Infect Dis 2019; 25:1660-1667. [PMID: 31407661 PMCID: PMC6711210 DOI: 10.3201/eid2509.190407] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In July 2018, a case of Neisseria gonorrhoeae associated with ceftriaxone treatment failure was identified in Alberta, Canada. We identified the isolate and nucleic acid amplification testing (NAAT) specimen as the ceftriaxone-resistant strain multilocus sequence type 1903/NG-MAST 3435/NG-STAR 233, originally identified in Japan (FC428), with the same penA 60.001 mosaic allele and genetic resistance determinants. Core single-nucleotide variant (SNV) analysis identified 13 SNVs between this isolate and FC428. Culture-independent surveillance by PCR for the A311V mutation in the penA allele and N. gonorrhoeae multiantigen sequence typing directly from NAAT transport media positive for N. gonorrhoeae by NAAT did not detect spread of the strain. We identified multiple sequence types not previously detected in Alberta by routine surveillance. This case demonstrates the benefit of using culture-independent methods to enhance detection, public health investigations, and surveillance to address this global threat.
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Considering the Potential Application of Whole Genome Sequencing to Gonorrhea Prevention and Control. Sex Transm Dis 2019; 45:e29-e32. [PMID: 29465637 DOI: 10.1097/olq.0000000000000813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Wang F, Liu J, Liu H, Huang J, Chen S, Chen X, Yin Y. Evaluation of the accuracy of molecular assays targeting the mutation A2059G for detecting high-level azithromycin resistance in Neisseria gonorrhoeae: a systematic review and meta-analysis. Infect Drug Resist 2018; 12:95-104. [PMID: 30643437 PMCID: PMC6312691 DOI: 10.2147/idr.s183754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Neisseria gonorrhoeae resistance to azithromycin has become a significant public health concern globally, and high-level azithromycin-resistant (HL-AzmR) isolates have emerged frequently. However, high-level azithromycin resistance is considered to be caused by mutated alleles of 23S rRNA gene at position 2059, and identification of HL-AzmR isolates mainly relies on agar dilution method or E-test method. This study aimed to assess the accuracy of the molecular assays targeting the mutation A2059G for identifying HL-AzmR isolates and thereby determine the association between the mutation and high-level azithromycin resistance. METHODS Two researchers independently searched six databases to identify studies published from the launch of each database to October 15, 2017. The fixed effects model was used to estimate the pooled sensitivity rate, specificity rate, positive predictive value (PPV), and negative predictive value (NPV). Summary receiver operating characteristic curves were generated, and the area under the curve (AUC) was determined to estimate the overall performance of the assays. The Deeks' test was conducted to evaluate potential publication bias. RESULTS Ten relevant studies were included in the meta-analysis to assess the synthetic accuracy of the molecular assays. The molecular assays had the synthetic sensitivity rate of 97.8% and the synthetic specificity rate of 99.1%. And the aggregated PPV and NPV were 96.4% and 99.5%, respectively. AUC was 0.99, suggesting a close relation existing between the mutation A2059G and high-level azithromycin resistance. This indicated that the molecular assays targeting the mutation A2059G have relatively high overall accuracy for identifying HL-AzmR N. gonor-rhoeae isolates. Publication bias was statistically significant. CONCLUSION The mutation A2059G is the critical factor causing high-level azithromycin resistance. Hence, molecular methods are recommended to be put into clinical practice by commercialization, which will assist clinicians to prescribe more precisely.
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Affiliation(s)
- Feng Wang
- Department of STD Control Laboratory, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Jingwei Liu
- Department of Reference STD Lab, National Center for STD Control, Chinese Center for Disease Control and Prevention, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China,
| | - Hongye Liu
- Department of Reference STD Lab, National Center for STD Control, Chinese Center for Disease Control and Prevention, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China,
| | - Jing Huang
- Department of STD Control Laboratory, Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Shaochun Chen
- Department of Reference STD Lab, National Center for STD Control, Chinese Center for Disease Control and Prevention, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China,
| | - Xiangsheng Chen
- Department of Reference STD Lab, National Center for STD Control, Chinese Center for Disease Control and Prevention, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China,
| | - Yueping Yin
- Department of Reference STD Lab, National Center for STD Control, Chinese Center for Disease Control and Prevention, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China,
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van der Veer BMJW, Wolffs PFG, Hoebe CJPA, Dukers-Muijrers NHTM, van Alphen LB. Culture-free genotyping of Neisseria gonorrhoeae revealed distinct strains at different anatomical sites in a quarter of patients, the Netherlands, 2012 to 2016. Euro Surveill 2018; 23:1800253. [PMID: 30563596 PMCID: PMC6299510 DOI: 10.2807/1560-7917.es.2018.23.50.1800253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundGenotyping of Neisseria gonorrhoeae (NG) is essential for surveillance to monitor NG transmission and dissemination of resistant strains. Current genotyping methods rely on bacterial culture which frequently fails.AimOur aim was to develop a culture-free genotyping method that is compatible with the widely used N. gonorrhoeae multi-antigen sequence typing (NG-MAST) database, which facilitates genotyping of NG detected at separate anatomical sites in individual patients.MethodsSpecific primers for both PCR targets porB and tbpB were designed and technically validated by assessing the analytical sensitivity, cross-reactivity with 32 non-gonoccocal Neisseria species, and concordance with NG-MAST. Clinical application was assessed on 205 paired samples from concurrent NG infections at different anatomical sites of 98 patients (81 men who have sex with men and 17 women) visiting our sexually transmitted infections clinic.ResultsTyping could be consistently performed on samples with a PCR quantification cycle (Cq) value <35. Furthermore, the method showed no cross-reactivity and was concordant with NG-MAST. Culture-free NG-MAST improved the typing rate from 62% (59/95) for cultured samples to 94% (89/95) compared with culture-dependent NG-MAST. Paired samples of 80 of 98 patients were genotyped, revealing distinct NG strains in separate anatomical sites in 25% (20/80) of the patients.ConclusionsThis NG-specific genotyping method can improve NG surveillance as it facilitates genotyping of non-culturable and extra-genital samples. Furthermore, 25% of patients were infected with multiple NG strains, which is missed in current culture-dependent surveillance. Including non-culturable and concurrent NG infections in surveillance informs actions on dissemination of multidrug-resistant NG strains.
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Affiliation(s)
- Brian MJW van der Veer
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Petra FG Wolffs
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Christian JPA Hoebe
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands,Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, the Netherlands
| | - Nicole HTM Dukers-Muijrers
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands,Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, the Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
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Mismatch Amplification Mutation Assay-Based Real-Time PCR for Rapid Detection of Neisseria gonorrhoeae and Antimicrobial Resistance Determinants in Clinical Specimens. J Clin Microbiol 2018; 56:JCM.00365-18. [PMID: 29950339 PMCID: PMC6113480 DOI: 10.1128/jcm.00365-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/25/2018] [Indexed: 01/31/2023] Open
Abstract
Molecular methods are often used for Neisseria gonorrhoeae detection, but complete definition of antimicrobial resistance (AMR) patterns still requires phenotypic tests. We developed an assay that both identifies N. gonorrhoeae and detects AMR determinants in clinical specimens. Molecular methods are often used for Neisseria gonorrhoeae detection, but complete definition of antimicrobial resistance (AMR) patterns still requires phenotypic tests. We developed an assay that both identifies N. gonorrhoeae and detects AMR determinants in clinical specimens. We designed a mismatch amplification mutation assay (MAMA)-based SYBR green real-time PCR targeting one N. gonorrhoeae-specific region (opa); mosaic penA alleles (Asp345 deletion [Asp345del], Gly545Ser) associated with decreased susceptibility to cephalosporins; and alterations conferring resistance to ciprofloxacin (GyrA Ser91Phe), azithromycin (23S rRNA A2059G and C2611T), and spectinomycin (16S rRNA C1192T). We applied the real-time PCR to 489 clinical specimens, of which 94 had paired culture isolates, and evaluated its performance by comparison with the performance of commercial diagnostic molecular and phenotypic tests. Our assay exhibited a sensitivity/specificity of 93%/100%, 96%/85%, 90%/91%, 100%/100%, and 100%/90% for the detection of N. gonorrhoeae directly from urethral, rectal, pharyngeal, cervical, and vaginal samples, respectively. The MAMA strategy allowed the detection of AMR mutations by comparing cycle threshold values with the results of the reference opa reaction. The method accurately predicted the phenotype of resistance to four antibiotic classes, as determined by comparison with the MIC values obtained from 94 paired cultures (sensitivity/specificity for cephalosporins, azithromycin, ciprofloxacin, and spectinomycin resistance, 100%/95%, 100%/100%, 100%/100%, and not applicable [NA]/100%, respectively, in genital specimens and NA/72%, NA/98%, 100%/97%, and NA/96%, respectively, in extragenital specimens). False-positive results, particularly for the penA Asp345del reaction, were observed predominantly in pharyngeal specimens. Our real-time PCR assay is a promising rapid method to identify N. gonorrhoeae and predict AMR directly in genital specimens, but further optimization for extragenital specimens is needed.
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Whiley DM, Trembizki E, Buckley C, Freeman K, Baird RW, Beaman M, Chen M, Donovan B, Kundu RL, Fairley CK, Guy R, Hogan T, Kaldor JM, Karimi M, Limnios A, Regan DG, Ryder N, Su JY, Ward J, Lahra MM. Molecular Antimicrobial Resistance Surveillance for Neisseria gonorrhoeae, Northern Territory, Australia. Emerg Infect Dis 2018; 23:1478-1485. [PMID: 28820128 PMCID: PMC5572890 DOI: 10.3201/eid2309.170427] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neisseria gonorrhoeae antimicrobial resistance (AMR) is a globally recognized health threat; new strategies are needed to enhance AMR surveillance. The Northern Territory of Australia is unique in that 2 different first-line therapies, based primarily on geographic location, are used for gonorrhea treatment. We tested 1,629 N. gonorrhoeae nucleic acid amplification test–positive clinical samples, collected from regions where ceftriaxone plus azithromycin or amoxicillin plus azithromycin are recommended first-line treatments, by using 8 N. gonorrhoeae AMR PCR assays. We compared results with those from routine culture-based surveillance data. PCR data confirmed an absence of ceftriaxone resistance and a low level of azithromycin resistance (0.2%), and that penicillin resistance was <5% in amoxicillin plus azithromycin regions. Rates of ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae were lower when molecular methods were used. Molecular methods to detect N. gonorrhoeae AMR can increase the evidence base for treatment guidelines, particularly in settings where culture-based surveillance is limited.
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Tuite AR, Gift TL, Chesson HW, Hsu K, Salomon JA, Grad YH. Impact of Rapid Susceptibility Testing and Antibiotic Selection Strategy on the Emergence and Spread of Antibiotic Resistance in Gonorrhea. J Infect Dis 2017; 216:1141-1149. [PMID: 28968710 PMCID: PMC5853443 DOI: 10.1093/infdis/jix450] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/29/2017] [Indexed: 12/22/2022] Open
Abstract
Background Increasing antibiotic resistance limits treatment options for gonorrhea. We examined the impact of a hypothetical point-of-care (POC) test reporting antibiotic susceptibility profiles on slowing resistance spread. Methods A mathematical model describing gonorrhea transmission incorporated resistance emergence probabilities and fitness costs associated with resistance based on characteristics of ciprofloxacin (A), azithromycin (B), and ceftriaxone (C). We evaluated time to 1% and 5% prevalence of resistant strains among all isolates with the following: (1) empiric treatment (B and C), and treatment guided by POC tests determining susceptibility to (2) A only and (3) all 3 antibiotics. Results Continued empiric treatment without POC testing was projected to result in >5% of isolates being resistant to both B and C within 15 years. Use of either POC test in 10% of identified cases delayed this by 5 years. The 3 antibiotic POC test delayed the time to reach 1% prevalence of triply-resistant strains by 6 years, whereas the A-only test resulted in no delay. Results were less sensitive to assumptions about fitness costs and test characteristics with increasing test uptake. Conclusions Rapid diagnostics reporting antibiotic susceptibility may extend the usefulness of existing antibiotics for gonorrhea treatment, but ongoing monitoring of resistance patterns will be critical.
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Affiliation(s)
- Ashleigh R Tuite
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Thomas L Gift
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Joshua A Salomon
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Yonatan H Grad
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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Papp JR, Rowlinson MC, O'Connor NP, Wholehan J, Razeq JH, Glennen A, Ware D, Iwen PC, Lee LV, Hagan C. Accuracy and reproducibility of the Etest to detect drug-resistant Neisseria gonorrhoeae to contemporary treatment. J Med Microbiol 2017; 67:68-73. [PMID: 29219803 DOI: 10.1099/jmm.0.000651] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Neisseria gonorrhoeae is a sexually transmitted bacterial pathogen that continues to evolve to become resistant to known antibiotics. In preparing for potential emergence, the Centers for Disease Control and Prevention recommends that clinical laboratories maintain or develop protocols to assess antibiotic susceptibly for this organism. This study examines the intra-laboratory variability of using the Etest method to provide consistent MIC values for N. gonorrhoeae and also compared the results of the Etest to known agar dilution MIC values. METHODOLOGY Clinical N. gonorrhoeae isolates, 100 paired duplicates, were tested by eight laboratories for antibiotic susceptibility to ceftriaxone, cefixime and azithromycin using Etest strips.Results/Key findings. Overall, >80 % of the paired Etest MIC values were within one log2 dilution of the replicate. When compared to the agar dilution reference method, the cefixime Etest MIC values were consistently underreported by one dilution (seven laboratories) or two dilutions (one laboratory). The azithromycin Etest MIC values agreed 90.7 % with the agar dilution MIC values while the agreement with ceftriaxone was 90.9 %. CONCLUSION Overall, the Etest method yielded reproducible MIC values within each laboratory with the azithromycin and ceftriaxone MIC results consistent to the reference agar dilution method while the cefixime result tended to provide a lower MIC value.
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Affiliation(s)
- John R Papp
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Norman P O'Connor
- State Laboratory Division, Hawaii Department of Health, Pearl City, HI, USA
| | - Jason Wholehan
- Michigan Department of Community Health, Lansing, MI, USA
| | - Jafar H Razeq
- Maryland Department of Health, Baltimore, MD, USA.,Present address: Department of Public Health, Rocky Hill, CT, USA
| | | | - Dapne Ware
- Mississippi Public Health Laboratories, Jackson, MS, USA
| | - Peter C Iwen
- Nebraska Public Health Laboratory, Omaha, NE, USA
| | - Lillian V Lee
- New York City Department of Health and Mental Hygiene, New York City, NY, USA
| | - Celia Hagan
- Association of Public Health Laboratories, Silver Spring, MD, USA
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15
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Buckley C, Trembizki E, Donovan B, Chen M, Freeman K, Guy R, Kundu R, Lahra MM, Regan DG, Smith H, Whiley DM. A real-time PCR assay for direct characterization of the Neisseria gonorrhoeae GyrA 91 locus associated with ciprofloxacin susceptibility. J Antimicrob Chemother 2015; 71:353-6. [PMID: 26538505 DOI: 10.1093/jac/dkv366] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/08/2015] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES The objective of this study was to develop a real-time PCR method for specific detection of the gonococcal GyrA amino acid 91 locus directly in clinical samples so as to predict Neisseria gonorrhoeae ciprofloxacin susceptibility. METHODS The real-time PCR assay, GyrA91-PCR, was designed using two probes, one for detection of the WT S91 sequence and the other for detection of the S91F alteration. The performance of the assay was initially assessed using characterized N. gonorrhoeae isolates (n = 70), a panel of commensal Neisseria and Moraxella species (n = 55 isolates) and clinical samples providing negative results by a commercial N. gonorrhoeae nucleic acid amplification test (NAAT) method (n = 171). The GyrA91-PCR was then applied directly to N. gonorrhoeae NAAT-positive clinical samples (n = 210) from the year 2014 for which corresponding N. gonorrhoeae isolates with susceptibility results were also available. RESULTS The GyrA91-PCR accurately characterized the GyrA 91 locus of all 70 N. gonorrhoeae isolates (sensitivity = 100%, 95% CI = 94.9%-100%), whereas all non-gonococcal isolates and N. gonorrhoeae NAAT-negative clinical samples gave negative results by the GyrA91-PCR (specificity = 100%, 95% CI = 98.4%-100%). When applied to the 210 N. gonorrhoeae NAAT-positive clinical samples, the GyrA91-PCR successfully characterized 195 samples (92.9%, 95% CI = 88.5%-95.9%). When compared with the corresponding bacterial culture results, positivity by the GyrA91-PCR WT probe correctly predicted N. gonorrhoeae susceptibility to ciprofloxacin in 161 of 162 (99.4%, 95% CI = 96.6%-99.9%) samples. CONCLUSIONS The use of a PCR assay for detection of mutation in gyrA applied directly to clinical samples can predict ciprofloxacin susceptibility in N. gonorrhoeae.
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Affiliation(s)
- Cameron Buckley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Brisbane, Queensland 4029, Australia University of Queensland Child Health Research Centre, Brisbane, Queensland 4029, Australia
| | - Ella Trembizki
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Brisbane, Queensland 4029, Australia University of Queensland Child Health Research Centre, Brisbane, Queensland 4029, Australia
| | - Basil Donovan
- Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Marcus Chen
- Melbourne Sexual Health Centre, Alfred Health, Carlton, Melbourne, Victoria 3053, Australia Central Clinical School, Monash University, Melbourne, Victoria 3181, Australia
| | - Kevin Freeman
- Microbiology Laboratory, Pathology Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Rebecca Guy
- Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Ratan Kundu
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales 2031, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales 2031, Australia
| | - David G Regan
- Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Helen Smith
- Public Health Microbiology, Communicable Disease, Queensland Health Forensic and Scientific Services, Archerfield, Brisbane, Queensland, Australia
| | - David M Whiley
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children's Medical Research Institute, Brisbane, Queensland 4029, Australia University of Queensland Child Health Research Centre, Brisbane, Queensland 4029, Australia UQ Centre for Clinical Research (UQCCR), The University of Queensland, Brisbane, Queensland 4029, Australia
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