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Ma A, Ferrato C, Martin I, Smyczek P, Gratrix J, Dingle TC. Use of genome sequencing to resolve differences in gradient diffusion and agar dilution antimicrobial susceptibility testing performance of Neisseria gonorrhoeae isolates in Alberta, Canada. J Clin Microbiol 2023; 61:e0060623. [PMID: 37882549 PMCID: PMC10662343 DOI: 10.1128/jcm.00606-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/15/2023] [Indexed: 10/27/2023] Open
Abstract
Agar dilution is the gold standard method for phenotypic antimicrobial susceptibility testing (AST) for Neisseria gonorrhoeae. However, this method is laborious and requires expertise, so laboratories that perform N. gonorrhoeae AST may choose alternative methods such as disk diffusion and gradient diffusion. In this study, we retrospectively compare the performance of gradient diffusion to agar dilution for 2,394 unique N. gonorrhoeae isolates identified in Alberta from 2017 to 2020 against azithromycin, cefixime, ceftriaxone, ciprofloxacin, penicillin, and tetracycline. Genome sequencing was utilized to resolve discrepancies between AST methods, detect antimicrobial resistance markers, and identify trends between error rates and sequence types (STs) of isolates. Over 90% of N. gonorrhoeae isolates were susceptible to azithromycin, cefixime, and ceftriaxone, whereas decreased susceptibility was observed for ciprofloxacin, penicillin, and tetracycline. Categorical (CA) and essential agreement (EA) was poorest between the two methods for penicillin (CA: 86.02%; EA: 77.69%) and tetracycline (CA: 47.22%; EA: 55.96%); however, the low CA was primarily attributed to minor errors. Antimicrobial agents with errors outside of acceptable limits included azithromycin (very major error: 18.42%; major error: 7.73%) and tetracycline (very major error: 6.17%). Genome sequencing on a subset of isolates resolved 30.3% of the azithromycin major errors and confirmed the azithromycin or tetracycline very major errors. Significant associations between certain STs and error types for azithromycin and tetracycline were also identified. Overall, gradient diffusion compared well to agar dilution for cefixime, ceftriaxone, and ciprofloxacin, and genome sequencing was identified as a useful tool to arbitrate discrepant susceptibility testing results between gradient diffusion and agar dilution for N. gonorrhoeae.
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Affiliation(s)
- Angela Ma
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Christina Ferrato
- Alberta Precision Laboratories—Provincial Laboratory for Public Health, Edmonton, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Petra Smyczek
- Department of Medicine, University of Alberta, Edmonton, Canada
- Alberta Health Services, STI Services, Edmonton, Canada
| | | | - Tanis C. Dingle
- Alberta Precision Laboratories—Provincial Laboratory for Public Health, Edmonton, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
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Barbee LA, St Cyr SB. Management of Neisseria gonorrhoeae in the United States: Summary of Evidence From the Development of the 2020 Gonorrhea Treatment Recommendations and the 2021 Centers for Disease Control and Prevention Sexually Transmitted Infection Treatment Guidelines. Clin Infect Dis 2022; 74:S95-S111. [PMID: 35416971 DOI: 10.1093/cid/ciac043] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Neisseria gonorrhoeae has developed resistance to all first-line recommended therapies, making gonococcal antimicrobial resistance a major public health concern given limited antibiotic options currently and an even smaller antimicrobial development pipeline. Since the release of the Centers for Disease Control and Prevention (CDC) 2015 STD Treatment Guidelines, azithromycin, part of the 2015 dual-drug treatment regimen, has had a rapid rise in resistance. The 2020 CDC Gonorrhea Treatment Recommendations and the 2021 Sexually Transmitted Infections (STI) Treatment Guidelines were developed weighing the priorities of treating the individual, protecting the population, and preventing antimicrobial resistance. METHODS Gonorrhea subject matter experts (SME) generated 8 key questions and conducted a literature review of updated data from 2013 to 2019 on gonorrhea antimicrobial resistance, treatment failures, clinical trials, and other key topics. More than 2200 abstracts were assessed, and 248 clinically relevant articles were thoroughly reviewed. SMEs also evaluated N gonorrhoeae antimicrobial resistance data from the Gonococcal Isolate Surveillance Project (GISP). EVIDENCE Although there have been reports of ceftriaxone treatment failures internationally, GISP data suggest that ceftriaxone minimal inhibitory concentrations (MICs) have remained stable in the United States, with < 0.1% exhibiting an "alert value" MIC (> 0.25 mcg/mL). However, GISP documented a rapid rise in the proportion of isolates with an elevated MIC (≥ 2.0 mcg/mL) to azithromycin-nearly 5% in 2018. At the same time, new pharmacokinetic/pharmacodynamic data are available, and there is greater recognition of the need for antimicrobial stewardship. SUMMARY The 2021 CDC STI Treatment Guidelines now recommend 500mg ceftriaxone intramuscularly once for the treatment of uncomplicated gonorrhea at all anatomic sites. If coinfection with chlamydia has not been excluded, cotreatment with doxycycline 100mg twice daily for 7 days should be added. Few alternative therapies exist for persons with cephalosporin allergies; there are no recommended alternative therapies for N gonorrhoeae infection of the throat.
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Affiliation(s)
- Lindley A Barbee
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,University of Washington, Seattle, Washington, USA.,Public Health - Seattle & King County HIV/STD Program, Seattle, Washington, USA
| | - Sancta B St Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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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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Hadad R, Cole MJ, Ebeyan S, Jacobsson S, Tan LY, Golparian D, Erskine S, Day M, Whiley D, Unemo M. Evaluation of the SpeeDx ResistancePlus® GC and SpeeDx GC 23S 2611 (beta) molecular assays for prediction of antimicrobial resistance/susceptibility to ciprofloxacin and azithromycin in Neisseria gonorrhoeae. J Antimicrob Chemother 2021; 76:84-90. [PMID: 32929456 DOI: 10.1093/jac/dkaa381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Accurate molecular assays for prediction of antimicrobial resistance (AMR)/susceptibility in Neisseria gonorrhoeae (Ng) can offer individualized treatment of gonorrhoea and enhanced AMR surveillance. OBJECTIVES We evaluated the new ResistancePlus® GC assay and the GC 23S 2611 (beta) assay (SpeeDx), for prediction of resistance/susceptibility to ciprofloxacin and azithromycin, respectively. METHODS Nine hundred and sixty-seven whole-genome-sequenced Ng isolates from 20 European countries, 143 Ng-positive (37 with paired Ng isolates) and 167 Ng-negative clinical Aptima Combo 2 (AC2) samples, and 143 non-gonococcal Neisseria isolates and closely related species were examined with both SpeeDx assays. RESULTS The sensitivity and specificity of the ResistancePlus® GC assay to detect Ng in AC2 samples were 98.6% and 100%, respectively. ResistancePlus® GC showed 100% sensitivity and specificity for GyrA S91 WT/S91F detection and 99.8% sensitivity and specificity in predicting phenotypic ciprofloxacin resistance. The sensitivity and specificity of the GC 23S 2611 (beta) assay for Ng detection in AC2 samples were 95.8% and 100%, respectively. GC 23S 2611 (beta) showed 100% sensitivity and 99.9% specificity for 23S rRNA C2611 WT/C2611T detection and 64.3% sensitivity and 99.9% specificity for predicting phenotypic azithromycin resistance. Cross-reactions with non-gonococcal Neisseria species were observed with both assays, but the analysis software solved most cross-reactions. CONCLUSIONS The new SpeeDx ResistancePlus® GC assay performed well in the detection of Ng and AMR determinants, especially in urogenital samples. The GC 23S 2611 (beta) assay performed relatively well, but its sensitivity, especially for predicting phenotypic azithromycin resistance, was suboptimal and further optimizations are required, including detection of additional macrolide resistance determinant(s).
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Affiliation(s)
- Ronza Hadad
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Lit Yeen Tan
- SpeeDx Pty Ltd, Sydney, New South Wales, Australia
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Michaela Day
- National Infection Service, Public Health England, London, UK
| | - David Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, National Reference Laboratory for Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Peterson SW, Martin I, Demczuk W, Barairo N, Naidu P, Lefebvre B, Allen V, Hoang L, Hatchette TF, Alexander D, Tomas K, Trubnikov M, Wong T, Mulvey MR. Multiplex real-time PCR assays for the prediction of cephalosporin, ciprofloxacin and azithromycin antimicrobial susceptibility of positive Neisseria gonorrhoeae nucleic acid amplification test samples. J Antimicrob Chemother 2020; 75:3485-3490. [PMID: 32830242 DOI: 10.1093/jac/dkaa360] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 07/23/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The incidence of antimicrobial-resistant Neisseria gonorrhoeae (GC) is rising in Canada; however, antimicrobial resistance (AMR) surveillance data are unavailable for infections diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs), representing over 80% of diagnoses. We developed a set of 10 improved molecular assays for surveillance of GC-AMR and prediction of susceptibilities in NAAT specimens. METHODS Multiplex real-time PCR (RT-PCR) assays were developed to detect SNPs associated with cephalosporin (ponA, porB, mtrR -35delA, penA A311V, penA A501, N513Y, G545S), ciprofloxacin (gyrA S91, parC D86/S87/S88) and azithromycin [23S (A2059G, C2611T), mtrR meningitidis-like promoter] resistance. The assays were validated on 127 gonococcal isolates, 51 non-gonococcal isolates and 50 NAATs with matched culture isolates. SNPs determined from the assay were compared with SNPs determined from in silico analysis of WGS data. MICs were determined for culture isolates using the agar dilution method. RESULTS SNP analysis of the 50 NAAT specimens had 96% agreement with the matched culture RT-PCR analysis. When compared with MICs, presence of penA A311V or penA A501 and two or more other SNPs correlated with decreased susceptibility and presence of three or more other SNPs correlated with intermediate susceptibility to cephalosporins; presence of any associated SNP correlated with ciprofloxacin or azithromycin resistance. NAAT-AMR predictions correlated with matched-culture cephalosporin, ciprofloxacin and azithromycin MICs at 94%, 100% and 98%, respectively. CONCLUSIONS We expanded molecular tests for N. gonorrhoeae AMR prediction by adding new loci and multiplexing reactions to improve surveillance where culture isolates are unavailable.
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Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - N Barairo
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - P Naidu
- Provincial Laboratory for Public Health, Edmonton, Alberta, Canada
| | - B Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - V Allen
- Public Health Ontario Laboratories, Toronto, Ontario, Canada
| | - L Hoang
- British Columbia Centres for Disease Control Public Health Microbiology & Reference Laboratory, Vancouver, British Columbia, Canada
| | - T F Hatchette
- Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - D Alexander
- Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada
| | - K Tomas
- Surveillance and Epidemiology Division, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - M Trubnikov
- First Nations and Inuit Health Branch, Indigenous Services Canada, Ottawa, Ontario, Canada
| | - T Wong
- First Nations and Inuit Health Branch, Indigenous Services Canada, Ottawa, Ontario, Canada
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Cotton S, McHugh MP, Etherson M, Shepherd J, Templeton KE. Evaluation of the molecular detection of ciprofloxacin resistance in Neisseria gonorrhoeae by the ResistancePlus GC assay (SpeeDx). Diagn Microbiol Infect Dis 2020; 99:115262. [PMID: 33388573 DOI: 10.1016/j.diagmicrobio.2020.115262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/02/2020] [Accepted: 11/08/2020] [Indexed: 12/26/2022]
Abstract
There is growing concern due to the emergence of multidrug resistance in Neisseria gonorrhoeae. A rapid molecular test which guides and provides antimicrobial susceptibility knowledge prior to start of treatment is needed. This study evaluated the clinical performance of the ResistancePlus GC assay compared to in-house PCR and antimicrobial susceptibility results for ciprofloxacin resistance. Samples were selected from a range of sites with corresponding cultures isolated from the same patient episode. The ResistancePlus GC assay displayed high sensitivity for N. gonorrhoeae detection (98.5%) and gyrA detection (97.1%). There was high agreement (98.9%) between the ResistancePlus GC assay and culture phenotype. Mixed population testing showed that the assay was able to detect resistance in a sample containing a minority variant of 27% resistant. The ResistancePlus GC assay performed well and could be used to provide a clinically relevant indication of ciprofloxacin susceptibility for the treatment of gonorrhoea.
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Affiliation(s)
- Seb Cotton
- Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Martin P McHugh
- Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom; School of Medicine, University of St Andrews, United Kingdom
| | - Michelle Etherson
- Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Jill Shepherd
- Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | - Kate E Templeton
- Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom.
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7
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Xiu L, Li Y, Wang F, Zhang C, Li Y, Zeng Y, Yin Y, Peng J. Multiplex High-Resolution Melting Assay for Simultaneous Identification of Molecular Markers Associated with Extended-Spectrum Cephalosporins and Azithromycin Resistance in Neisseria gonorrhoeae. J Mol Diagn 2020; 22:1344-1355. [DOI: 10.1016/j.jmoldx.2020.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/16/2020] [Accepted: 08/05/2020] [Indexed: 12/13/2022] Open
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Exploration of the Neisseria Resistome Reveals Resistance Mechanisms in Commensals That May Be Acquired by N. gonorrhoeae through Horizontal Gene Transfer. Antibiotics (Basel) 2020; 9:antibiotics9100656. [PMID: 33007823 PMCID: PMC7650674 DOI: 10.3390/antibiotics9100656] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
Nonpathogenic Neisseria transfer mutations encoding antibiotic resistance to their pathogenic relative Neisseria gonorrhoeae. However, the resistance genotypes and subsequent phenotypes of nonpathogens within the genus have been described infrequently. Here, we characterize the minimum inhibitory concentrations (MICs) of a panel of Neisseria (n = 26)—including several commensal species—to a suite of diverse antibiotics. We furthermore use whole genome sequencing and the Comprehensive Antibiotic Resistance Database Resistance Gene Identifier (RGI) platform to predict putative resistance-encoding mutations. Resistant isolates to all tested antimicrobials including penicillin (n = 5/26), ceftriaxone (n = 2/26), cefixime (n = 3/26), tetracycline (n = 10/26), azithromycin (n = 11/26), and ciprofloxacin (n = 4/26) were found. In total, 63 distinct mutations were predicted by RGI to be involved in resistance. The presence of several mutations had clear associations with increased MIC such as DNA gyrase subunit A (gyrA) (S91F) and ciprofloxacin, tetracycline resistance protein (tetM) and 30S ribosomal protein S10 (rpsJ) (V57M) and tetracycline, and TEM-type β-lactamases and penicillin. However, mutations with strong associations to macrolide and cephalosporin resistance were not conclusive. This work serves as an initial exploration into the resistance-encoding mutations harbored by nonpathogenic Neisseria, which will ultimately aid in prospective surveillance for novel resistance mechanisms that may be rapidly acquired by N. gonorrhoeae.
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Ebeyan S, Windsor M, Bordin A, Mhango L, Erskine S, Trembizki E, Mokany E, Tan LY, Whiley D. Evaluation of the ResistancePlus GC (beta) assay: a commercial diagnostic test for the direct detection of ciprofloxacin susceptibility or resistance in Neisseria gonorrhoeae. J Antimicrob Chemother 2020; 74:1820-1824. [PMID: 30897201 DOI: 10.1093/jac/dkz108] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES To evaluate the performance of the ResistancePlus GC (beta) assay for the simultaneous detection of Neisseria gonorrhoeae and gyrA S91 markers of resistance (S91F) and susceptibility (WT) to ciprofloxacin, from both clinical specimens and isolates. METHODS Performance was assessed on several sample banks, including N. gonorrhoeae isolates (n = 822), non-gonococcal isolates (n = 110), N. gonorrhoeae-positive clinical specimens (n = 402) and N. gonorrhoeae-negative specimens (n = 290). Results were compared with previous testing data, including S91 genotyping and phenotypic resistance profiles. RESULTS Overall, the assay demonstrated 100% sensitivity for N. gonorrhoeae detection in clinical isolates. For gyrA S91 mutation detection in clinical isolates, the assay showed 100% sensitivity/specificity compared with the genotype, and >99%/>97% sensitivity/specificity when compared with phenotype. For positive clinical specimens, the assay demonstrated >96% sensitivity for N. gonorrhoeae detection and 100% sensitivity/specificity for gyrA S91 mutation detection. The assay demonstrated >99% specificity for N. gonorrhoeae detection against non-gonococcal isolates and 100% specificity for negative clinical specimens. CONCLUSIONS The ResistancePlus GC (beta) assay is suitable for the detection of N. gonorrhoeae and gyrA markers associated with resistance/susceptibility to ciprofloxacin directly in clinical samples. This assay could be implemented for the individualized treatment of gonorrhoea infections as well as to enhance current antimicrobial resistance surveillance methods.
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Affiliation(s)
| | | | - Amanda Bordin
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Lebogang Mhango
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | | | - Ella Trembizki
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Elisa Mokany
- SpeeDx Pty Ltd, Sydney, New South Wales, Australia
| | - Lit Yeen Tan
- SpeeDx Pty Ltd, Sydney, New South Wales, Australia
| | - David Whiley
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia.,Pathology Queensland Central Laboratory, Brisbane, Queensland, Australia
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Equations To Predict Antimicrobial MICs in Neisseria gonorrhoeae Using Molecular Antimicrobial Resistance Determinants. Antimicrob Agents Chemother 2020; 64:AAC.02005-19. [PMID: 31871081 DOI: 10.1128/aac.02005-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/22/2023] Open
Abstract
The emergence of Neisseria gonorrhoeae strains that are resistant to azithromycin and extended-spectrum cephalosporins represents a public health threat, that of untreatable gonorrhea infections. Multivariate regression modeling was used to determine the contributions of molecular antimicrobial resistance determinants to the overall antimicrobial MICs for ceftriaxone, cefixime, azithromycin, tetracycline, ciprofloxacin, and penicillin. A training data set consisting of 1,280 N. gonorrhoeae strains was used to generate regression equations which were then applied to validation data sets of Canadian (n = 1,095) and international (n = 431) strains. The predicted MICs for extended-spectrum cephalosporins (ceftriaxone and cefixime) were fully explained by 5 amino acid substitutions in PenA, A311V, A501P/T/V, N513Y, A517G, and G543S; the presence of a disrupted mtrR promoter; and the PorB G120 and PonA L421P mutations. The correlation of predicted MICs within one doubling dilution to phenotypically determined MICs of the Canadian validation data set was 95.0% for ceftriaxone, 95.6% for cefixime, 91.4% for azithromycin, 98.2% for tetracycline, 90.4% for ciprofloxacin, and 92.3% for penicillin, with an overall sensitivity of 99.9% and specificity of 97.1%. The correlations of predicted MIC values to the phenotypically determined MICs were similar to those from phenotype MIC-only comparison studies. The ability to acquire detailed antimicrobial resistance information directly from molecular data will facilitate the transition to whole-genome sequencing analysis from phenotypic testing and can fill the surveillance gap in an era of increased reliance on nucleic acid assay testing (NAAT) diagnostics to better monitor the dynamics of N. gonorrhoeae.
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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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12
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Allan-Blitz LT, Klausner JD. Codon 91 Gyrase A Testing Is Necessary and Sufficient to Predict Ciprofloxacin Susceptibility in Neisseria gonorrhoeae. J Infect Dis 2019; 215:491. [PMID: 28003354 DOI: 10.1093/infdis/jiw551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 11/09/2016] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Jeffrey D Klausner
- Division of Infectious Diseases, Department of Medicine and Fielding School of Public Health, University of California, Los Angeles
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13
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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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Molecular Characterization of Markers Associated With Antimicrobial Resistance in Neisseria gonorrhoeae Identified From Residual Clinical Samples. Sex Transm Dis 2019; 45:312-315. [PMID: 29465687 DOI: 10.1097/olq.0000000000000755] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND The emergence and spread of antimicrobial-resistant (AMR) Neisseria gonorrhoeae (NG) is a major public health concern. In the era of nucleic acid amplifications tests, rapid and accurate molecular approaches are needed to help increase surveillance, guide antimicrobial stewardship, and prevent outbreaks. METHODS Residual urethral swabs, collected prospectively in the Baltimore City Health Department during a 6-month period, were analyzed by real-time polymerase chain reaction assays for NG DNA and AMR determinants to fluoroquinolones, penicillin, and extended-spectrum cephalosporins. RESULTS N. gonorrhoeae DNA was detected in 34.8% (73/210) of samples, including 67.3% (68/101) of the swabs that had been previously identified as NG positive by culture. Markers associated with decreased susceptibility to fluoroquinolones were detected in 22.4% of the polymerase chain reaction NG-positive samples. The rate of penicillinase-producing NG was very low (1.6%), and no markers associated with decreased susceptibility to extended-spectrum cephalosporins were detected in this cohort of men using the AMR assays herein described. CONCLUSIONS Detection of molecular markers associated with AMR in NG can be performed directly from residual clinical samples, although the recovery rate of adequate DNA for molecular testing from these samples can be suboptimal. A high number of samples with mutations associated with decreased susceptibility to fluoroquinolones were identified.
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Martin I, Sawatzky P, Allen V, Lefebvre B, Hoang LMN, Naidu P, Minion J, Van Caeseele P, Haldane D, Gad RR, Zahariadis G, Corriveau A, German G, Tomas K, Mulvey MR. Multidrug-resistant and extensively drug-resistant Neisseria gonorrhoeae in Canada, 2012-2016. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2019; 45:45-53. [PMID: 31015818 PMCID: PMC6461123 DOI: 10.14745/ccdr.v45i23a01] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
BACKGROUND Neisseria gonorrhoeae have acquired resistance to many antimicrobials, including third generation cephalosporins and azithromycin, which are the current gonococcal combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections. OBJECTIVE To describe antimicrobial susceptibilities for N. gonorrhoeae circulating in Canada between 2012 and 2016. METHODS Antimicrobial resistance profiles were determined using agar dilution of N. gonorrhoeae isolated in Canada 2012-2016 (n=10,167) following Clinical Laboratory Standards Institute guidelines. Data were analyzed by applying multidrug-resistant gonococci (MDR-GC) and extensively drug-resistant gonococci (XDR-GC) definitions. RESULTS Between 2012 and 2016, the proportion of MDR-GC increased from 6.2% to 8.9% and a total of 19 cases of XDR-GC were identified in Canada (0.1%, 19/18,768). The proportion of isolates with decreased susceptibility to cephalosporins declined between 2012 and 2016 from 5.9% to 2.0% while azithromycin resistance increased from 0.8% to 7.2% in the same period. CONCLUSION While XDR-GC are currently rare in Canada, MDR-GC have increased over the last five years. Azithromycin resistance in N. gonorrhoeae is established and spreading in Canada, exceeding the 5% level at which the World Health Organization states an antimicrobial should be reviewed as an appropriate treatment. Continued surveillance of antimicrobial susceptibilities of N. gonorrhoeae is necessary to inform treatment guidelines and mitigate the impact of resistant gonorrhea.
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Affiliation(s)
- I Martin
- Bacterial Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - P Sawatzky
- Bacterial Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - V Allen
- Public Health Ontario Laboratories, Toronto, ON
| | - B Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, QC
| | - LMN Hoang
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, BC
| | - P Naidu
- Provincial Laboratory for Public Health, Edmonton, AB
| | - J Minion
- Roy Romanow Provincial Laboratory, Regina, SK
| | | | - D Haldane
- Queen Elizabeth II Health Sciences Centre, Halifax, NS
| | - RR Gad
- New Brunswick Department of Health, Fredericton, NB
| | - G Zahariadis
- Newfoundland and Labrador Public Health Laboratory, St. John’s, NL
| | - A Corriveau
- Department of Health and Social Services, Government of the Northwest Territories, Yellowknife, NT
| | | | - K Tomas
- Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, ON
| | - MR Mulvey
- Bacterial Pathogens Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
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Addressing the rising rates of gonorrhea and drug-resistant gonorrhea: There is no time like the present. ACTA ACUST UNITED AC 2019; 45:54-62. [PMID: 31015819 PMCID: PMC6461120 DOI: 10.14745/ccdr.v45i23a02] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Increasing rates of gonococcal (GC) infection and antimicrobial resistant (AMR) GC, are a serious public health concern for Canada and around the world. Previously recommended treatments are ineffective against many of the gonorrhea strains circulating today. The current recommendation for combination therapy is now being threatened by globally emerging and increasingly resistant strains. It is important that coordinated efforts be made now to ensure these new global strains do not become established in Canada. Otherwise, we will be faced with the possibility of persistent GC infection which can lead to pelvic inflammatory disease, infertility and chronic pelvic pain in women; and epididymitis in men. The presence of GC can also increase the risk of HIV acquisition and transmission. There are a number of reasons why we are facing this public health threat. GC infection is often asymptomatic and it is highly transmissible. People may hesitate to seek testing (or to offer testing). Treatment is complex: recommendations vary by site of infection and risk of resistance. Sexual contact during travel is an important source of imported emerging resistant global strains. The new screening and diagnostic Nucleic Acid Amplification Test (NAAT) is excellent but has decreased the number of cultures being done and therefore our capacity to track AMR-GC. There are four key actions that clinicians and front-line public health professionals can take to stem the increase in rates of GC and drug resistant GC. First, normalize and increase GC screening based on risk factors and emphasize the need for safer sex practices. NAAT is useful for screening, but culture is still needed for extra-genital sites. Second, conduct pretravel counselling and include a travel history as part of the risk assessment. Third, use culture along with NAAT to establish the diagnosis and follow up for test-of-cure. Finally, refer to the most current Canadian Guidelines on Sexually Transmitted Infections or provincial/territorial recommendations on combination therapies for patients and their contacts as recommendations may have changed in response to evolving AMR-GC trends.
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A Comparison of Real-Time Polymerase Chain Reaction Assays for the Detection of Antimicrobial Resistance Markers and Sequence Typing From Clinical Nucleic Acid Amplification Test Samples and Matched Neisseria gonorrhoeae Culture. Sex Transm Dis 2019; 45:92-95. [PMID: 29329177 DOI: 10.1097/olq.0000000000000707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Real-time polymerase chain reaction (PCR) assays to detect antimicrobial resistance-associated mutations were tested on Neisseria gonorrhoeae-positive clinical samples with matched isolates. Of the nucleic acid amplification tests/cultures, 87.7% (64/73), 98.6% (72/73), and 98.4% (62/63) predicted cephalosporin, ciprofloxacin, and azithromycin susceptibilities, respectively. N. gonorrhoeae multiantigen sequence type was correctly predicted for 98.7% (79/80), and 13 of 58 N. gonorrhoeae-negative specimens showed false-positive results.
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18
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Utilization of Nucleic Acid Amplification Testing Samples for Antimicrobial Resistance Surveillance in Remote Canadian Communities. Sex Transm Dis 2018; 45:e61. [DOI: 10.1097/olq.0000000000000860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Pham TSH, Mahon PJ, Lai G, Yu A. Reduced Graphene Oxide Nanocomposite Modified Electrodes for Sensitive Detection of Ciprofloxacin. ELECTROANAL 2018. [DOI: 10.1002/elan.201700738] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Tien Song Hiep Pham
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology; Swinburne University of Technology; VIC 3122 Australia
| | - Peter J. Mahon
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology; Swinburne University of Technology; VIC 3122 Australia
| | - Guosong Lai
- Department of Chemistry; Hubei Normal University; Huangshi 435002 PR China
| | - Aimin Yu
- Department of Chemistry and Biotechnology, Faculty of Science, Engineering and Technology; Swinburne University of Technology; VIC 3122 Australia
- Department of Chemistry; Hubei Normal University; Huangshi 435002 PR China
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Perera SR, Khan NH, Martin I, Taheri A, Parti RP, Levett PN, Horsman GB, Kusalik A, Dillon JAR. Multiplex Real-Time PCR Assay for Simultaneous Identification of Neisseria gonorrhoeae and Its Ciprofloxacin Susceptibility Status. J Clin Microbiol 2017; 55:3201-3209. [PMID: 28814585 PMCID: PMC5654903 DOI: 10.1128/jcm.00855-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/06/2017] [Indexed: 01/18/2023] Open
Abstract
A real-time PCR (RT-PCR) assay was designed for the simultaneous identification of Neisseria gonorrhoeae and its ciprofloxacin susceptibility status. A SYBR green-based multiplex RT-PCR format was used; it comprised two different forward primers and a common reverse primer to detect single nucleotide polymorphisms (SNPs) in gyrA of N. gonorrhoeae The primer pairs were evaluated for their sensitivity and specificity using genomic DNA from 254 N. gonorrhoeae isolates (82 were ciprofloxacin susceptible and 172 were ciprofloxacin resistant) and 23 non-N. gonorrhoeae species isolates. The performance of the primers was validated using genomic DNA from 100 different N. gonorrhoeae isolates (46 were ciprofloxacin susceptible and 54 were ciprofloxacin resistant) and 52 non-N. gonorrhoeae isolates. The latter panel was revalidated by testing 99 (46 isolates were ciprofloxacin susceptible and 53 isolates were ciprofloxacin resistant) of the N. gonorrhoeae isolates and 23 non-N. gonorrhoeae isolates. These primers detected N. gonorrhoeae and its ciprofloxacin susceptibility status with over 99% sensitivity and specificity for all panels tested. This assay has the potential to be an inexpensive and rapid test for the simultaneous identification of N. gonorrhoeae and its ciprofloxacin susceptibility status.
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Affiliation(s)
- Sumudu R Perera
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nurul H Khan
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Irene Martin
- National Microbiology Laboratory, Streptococcus and STI Unit, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ali Taheri
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Rajinder P Parti
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul N Levett
- Government of Saskatchewan, Saskatchewan Disease Control Laboratory, Regina, SK, Canada
| | - Greg B Horsman
- Government of Saskatchewan, Saskatchewan Disease Control Laboratory, Regina, SK, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jo-Anne R Dillon
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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Donà V, Low N, Golparian D, Unemo M. Recent advances in the development and use of molecular tests to predict antimicrobial resistance in Neisseria gonorrhoeae. Expert Rev Mol Diagn 2017; 17:845-859. [PMID: 28741392 DOI: 10.1080/14737159.2017.1360137] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION The number of genetic tests, mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae is increasing. Several of these assays are promising, but there are important shortcomings and few assays have been adequately validated and quality assured. Areas covered: Recent advances, focusing on publications since 2012, in the development and use of molecular tests to predict gonococcal AMR for surveillance and for clinical use, advantages and disadvantages of these tests and of molecular AMR prediction compared with phenotypic AMR testing, and future perspectives for effective use of molecular AMR tests for different purposes. Expert commentary: Several challenges for direct testing of clinical, especially extra-genital, specimens remain. The choice of molecular assay needs to consider the assay target, quality controls, sample types, limitations intrinsic to molecular technologies, and specific to the chosen methodology, and the intended use of the test. Improved molecular- and particularly genome-sequencing-based methods will supplement AMR testing for surveillance purposes, and translate into point-of-care tests that will lead to personalized treatments, while sparing the last available empiric treatment option (ceftriaxone). However, genetic AMR prediction will never completely replace phenotypic AMR testing, which detects also AMR due to unknown AMR determinants.
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Affiliation(s)
- Valentina Donà
- a Institute for Infectious Diseases, University of Bern , Bern , Switzerland
| | - Nicola Low
- b Institute of Social and Preventive Medicine, University of Bern , Bern , Switzerland
| | - Daniel Golparian
- c WHO Collaborating Centre for Gonorrhoea , Örebro University , Örebro , Sweden
| | - Magnus Unemo
- c WHO Collaborating Centre for Gonorrhoea , Örebro University , Örebro , Sweden
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22
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Molecular tests for the detection of antimicrobial resistant Neisseria gonorrhoeae: when, where, and how to use? Curr Opin Infect Dis 2016; 29:45-51. [PMID: 26658656 DOI: 10.1097/qco.0000000000000230] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Molecular methods for the diagnosis of Neisseria gonorrhoeae are replacing bacterial culture in many settings. This review focuses on recent progress in the development of molecular tests to detect resistant N. gonorrhoeae both to enhance surveillance and to guide decisions about individual patient management. RECENT FINDINGS Assays to enhance surveillance have been developed to detect determinants of resistance for all antibiotics used as first-line gonorrhoea treatment, or to detect specific 'superbug' strains, but few have been applied in clinical practice. The most advanced strategy relevant to individual case management is to identify ciprofloxacin-sensitive strains so that unnecessary use of ceftriaxone can be avoided. Cross-reactivity with pharyngeal commensal Neisseria species reduces specificity and is a challenge for many assays. SUMMARY Progress with laboratory-based molecular tests to detect gonococcal resistance is being made but substantial challenges remain. No laboratory-based assay has been subjected to a field evaluation and no assay so far can be used as a point-of-care test. Given the threat of antimicrobial resistance, now is the time to exploit the molecular technologies used for diagnosis and to invest in the development of molecular gonococcal resistance tests that can be implemented for public health good.
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Buckley C, Trembizki E, Donovan B, Chen M, Freeman K, Guy R, Lahra MM, Kundu RL, Regan DG, Smith HV, Whiley DM. Real-time PCR detection of Neisseria gonorrhoeae susceptibility to penicillin. J Antimicrob Chemother 2016; 71:3090-3095. [PMID: 27494921 DOI: 10.1093/jac/dkw291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVES The objective of this study was to develop a real-time PCR assay targeting the gonococcal porB gene (PorB-PCR) for predicting susceptibility of Neisseria gonorrhoeae to penicillin. This complements a previously described PCR assay for detecting penicillinase-producing N. gonorrhoeae (PPNG) developed by our laboratory (PPNG-PCR). METHODS The PorB-PCR assay was designed using six probes to characterize various combinations of amino acids at positions 101 and 102 of the PorB1b class protein, including the WT G101/A102 and mutant G101K/A102D, G101K/A102N and G101K/A102G sequences, as well as the PorB1a sequence. The ability of these sequences to predict penicillin susceptibility was initially assessed using 2307 N. gonorrhoeae isolates from throughout Australia for which phenotypic susceptibility data were available. The assay was then applied to N. gonorrhoeae-positive clinical specimens (n = 70). Specificity was assessed by testing commensal Neisseria strains (n = 75) and N. gonorrhoeae-negative clinical specimens (n = 171). RESULTS Testing of the 2307 N. gonorrhoeae isolates using PorB-PCR to detect G101/A102 and PorB1a sequences identified a total of 78.4% (61.2% and 17.2%, respectively) of penicillin-susceptible isolates with specificities of 97.4% and 99.3% and positive predictive values of 98.8% and 98.9%, where PPNG strains were simultaneously identified and excluded. Similar performance data were obtained when the PorB-PCR assay was applied to the N. gonorrhoeae-positive clinical specimens. No false-positive results were observed for the N. gonorrhoeae-negative samples and no cross-reactions were observed with the non-gonococcal species. CONCLUSIONS When used in parallel with the previously described PPNG-PCR, the PorB-PCR approach has the potential to facilitate individualized treatment of gonorrhoea using penicillin.
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Affiliation(s)
- Cameron Buckley
- The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
| | - Ella Trembizki
- The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
| | - Basil Donovan
- Kirby Institute, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Marcus Chen
- Melbourne Sexual Health Centre, Alfred Health, Carlton, 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
| | - 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
| | - Ratan L Kundu
- 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 V Smith
- Public Health Microbiology, Communicable Disease, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - David M Whiley
- The University of Queensland, UQ Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia.,Pathology Queensland, Microbiology Department, Herston, Queensland, Australia
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Graham RMA, Doyle CJ, Jennison AV. Epidemiological typing of Neisseria gonorrhoeae and detection of markers associated with antimicrobial resistance directly from urine samples using next generation sequencing. Sex Transm Infect 2016; 93:65-67. [PMID: 26968786 DOI: 10.1136/sextrans-2015-052422] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 02/16/2016] [Accepted: 02/20/2016] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES To investigate the potential for next generation sequencing (NGS) to be used directly on clinical specimens that have tested positive for Neisseria gonorrhoeae by nucleic acid amplification testing (NAAT), to generate information on epidemiological genotyping and antimicrobial resistance (AMR) markers. METHODS DNA was extracted from 13 N. gonorrhoeae NAAT-positive urine specimens, enriched for microbial DNA and sequenced using the Ion Torrent PGM workflow. Sequences that aligned to the human genome were filtered out and the remaining sequences were de novo assembled. The resulting contigs were searched for regions of interest using Ridom SeqSphere. MLST and NG-MAST alleles were assigned according to the schemes at PubMLST.org and NG-MAST.net, respectively. RESULTS In total, 11 of the 13 samples tested generated a sufficient number of N. gonorrhoeae sequence reads to provide full coverage of the genome at a depth of 6-130×. Complete MLST and NG-MAST sequence types could be generated for each of these samples. The presence of 10 different AMR markers was investigated, and both previously reported and novel mutations were identified in genes associated with reduced susceptibility to several antimicrobials. CONCLUSIONS We found that sequencing the entire genome of N. gonorrhoeae directly from clinical samples is possible using NGS, and that multiple levels of N. gonorrhoeae typing information can be generated. As NAAT only testing becomes more common, this method could be used to detect both known and novel mutations associated with AMR and to generate genotyping information, supporting AMR and epidemiological surveillance in the absence of culturing.
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Affiliation(s)
- R M A Graham
- Public Health Microbiology, Public and Environmental Health, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Queensland, Australia
| | - C J Doyle
- Public Health Microbiology, Public and Environmental Health, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Queensland, Australia
| | - A V Jennison
- Public Health Microbiology, Public and Environmental Health, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Queensland, Australia
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