1
|
Unemo M, Sánchez-Busó L, Golparian D, Jacobsson S, Shimuta K, Lan PT, Eyre DW, Cole M, Maatouk I, Wi T, Lahra MM. The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization. J Antimicrob Chemother 2024; 79:1885-1899. [PMID: 38889110 PMCID: PMC11290888 DOI: 10.1093/jac/dkae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
OBJECTIVES MDR and XDR Neisseria gonorrhoeae strains remain major public health concerns internationally, and quality-assured global gonococcal antimicrobial resistance (AMR) surveillance is imperative. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) and WHO Enhanced GASP (EGASP), including metadata and WGS, are expanding internationally. We present the phenotypic, genetic and reference genome characteristics of the 2024 WHO gonococcal reference strains (n = 15) for quality assurance worldwide. All superseded WHO gonococcal reference strains (n = 14) were identically characterized. MATERIAL AND METHODS The 2024 WHO reference strains include 11 of the 2016 WHO reference strains, which were further characterized, and four novel strains. The superseded WHO reference strains include 11 WHO reference strains previously unpublished. All strains were characterized phenotypically and genomically (single-molecule PacBio or Oxford Nanopore and Illumina sequencing). RESULTS The 2024 WHO reference strains represent all available susceptible and resistant phenotypes and genotypes for antimicrobials currently and previously used (n = 22), or considered for future use (n = 3) in gonorrhoea treatment. The novel WHO strains include internationally spreading ceftriaxone resistance, ceftriaxone resistance due to new penA mutations, ceftriaxone plus high-level azithromycin resistance and azithromycin resistance due to mosaic MtrRCDE efflux pump. AMR, serogroup, prolyliminopeptidase, genetic AMR determinants, plasmid types, molecular epidemiological types and reference genome characteristics are presented for all strains. CONCLUSIONS The 2024 WHO gonococcal reference strains are recommended for internal and external quality assurance in laboratory examinations, especially in the WHO GASP, EGASP and other GASPs, but also in phenotypic and molecular diagnostics, AMR prediction, pharmacodynamics, epidemiology, research and as complete reference genomes in WGS analysis.
Collapse
Affiliation(s)
- Magnus Unemo
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
| | - Leonor Sánchez-Busó
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Madrid, Spain
| | - Daniel Golparian
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Pham Thi Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - David W Eyre
- Big Data Institute, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Ismael Maatouk
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, New South Wales Health Pathology, Microbiology, Randwick, NSW, Australia
- Faculty of Medicine, The University of New South Wales, Sydney, Australia
| |
Collapse
|
2
|
Golparian D, Bazzo ML, Ahlstrand J, Schörner MA, Gaspar PC, de Melo Machado H, Martins JM, Bigolin A, Ramos MC, Ferreira WA, Pereira GFM, Miranda AE, Unemo M. Recent dynamics in Neisseria gonorrhoeae genomic epidemiology in Brazil: antimicrobial resistance and genomic lineages in 2017-20 compared to 2015-16. J Antimicrob Chemother 2024; 79:1081-1092. [PMID: 38517452 DOI: 10.1093/jac/dkae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
OBJECTIVES Regular quality-assured WGS with antimicrobial resistance (AMR) and epidemiological data of patients is imperative to elucidate the shifting gonorrhoea epidemiology, nationally and internationally. We describe the dynamics of the gonococcal population in 11 cities in Brazil between 2017 and 2020 and elucidate emerging and disappearing gonococcal lineages associated with AMR, compare to Brazilian WGS and AMR data from 2015 to 2016, and explain recent changes in gonococcal AMR and gonorrhoea epidemiology. METHODS WGS was performed using Illumina NextSeq 550 and genomes of 623 gonococcal isolates were used for downstream analysis. Molecular typing and AMR determinants were obtained and links between genomic lineages and AMR (determined by agar dilution/Etest) examined. RESULTS Azithromycin resistance (15.6%, 97/623) had substantially increased and was mainly explained by clonal expansions of strains with 23S rRNA C2611T (mostly NG-STAR CC124) and mtr mosaics (mostly NG-STAR CC63, MLST ST9363). Resistance to ceftriaxone and cefixime remained at the same levels as in 2015-16, i.e. at 0% and 0.2% (1/623), respectively. Regarding novel gonorrhoea treatments, no known zoliflodacin-resistance gyrB mutations or gepotidacin-resistance gyrA mutations were found. Genomic lineages and sublineages showed a phylogenomic shift from sublineage A5 to sublineages A1-A4, while isolates within lineage B remained diverse in Brazil. CONCLUSIONS Azithromycin resistance, mainly caused by 23S rRNA C2611T and mtrD mosaics/semi-mosaics, had substantially increased in Brazil. This mostly low-level azithromycin resistance may threaten the recommended ceftriaxone-azithromycin therapy, but the lack of ceftriaxone resistance is encouraging. Enhanced gonococcal AMR surveillance, including WGS, is imperative in Brazil and other Latin American and Caribbean countries.
Collapse
Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Maria Luiza Bazzo
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Josefine Ahlstrand
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
| | - Marcos André Schörner
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Pamela Cristina Gaspar
- Department of HIV/AIDS, Tuberculosis, and Sexually Transmitted Infection, Secretariat of Health Surveillance and Environment, Ministry of Health of Brazil, Brasília, Brazil
| | - Hanalydia de Melo Machado
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Jéssica Motta Martins
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Alisson Bigolin
- Department of HIV/AIDS, Tuberculosis, and Sexually Transmitted Infection, Secretariat of Health Surveillance and Environment, Ministry of Health of Brazil, Brasília, Brazil
| | | | | | - Gerson Fernando Mendes Pereira
- Department of HIV/AIDS, Tuberculosis, and Sexually Transmitted Infection, Secretariat of Health Surveillance and Environment, Ministry of Health of Brazil, Brasília, Brazil
| | - Angelica Espinosa Miranda
- Department of HIV/AIDS, Tuberculosis, and Sexually Transmitted Infection, Secretariat of Health Surveillance and Environment, Ministry of Health of Brazil, Brasília, Brazil
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 85, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
| |
Collapse
|
3
|
Golparian D, Cole MJ, Sánchez-Busó L, Day M, Jacobsson S, Uthayakumaran T, Abad R, Bercot B, Caugant DA, Heuer D, Jansen K, Pleininger S, Stefanelli P, Aanensen DM, Bluemel B, Unemo M. Antimicrobial-resistant Neisseria gonorrhoeae in Europe in 2020 compared with in 2013 and 2018: a retrospective genomic surveillance study. THE LANCET. MICROBE 2024; 5:e478-e488. [PMID: 38614111 DOI: 10.1016/s2666-5247(23)00370-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/20/2023] [Accepted: 11/09/2023] [Indexed: 04/15/2024]
Abstract
BACKGROUND Regular quality-assured whole-genome sequencing linked to antimicrobial resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea epidemiology, both nationally and internationally. We aimed to examine the gonococcal population in the European Economic Area (EEA) in 2020, elucidate emerging and disappearing gonococcal lineages associated with AMR and patient metadata, compare with 2013 and 2018 whole-genome sequencing data, and explain changes in gonococcal AMR and gonorrhoea epidemiology. METHODS In this retrospective genomic surveillance study, we analysed consecutive gonococcal isolates that were collected in EEA countries through the European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) in 2020, and made comparisons with Euro-GASP data from 2013 and 2018. All isolates had linked AMR data (based on minimum inhibitory concentration determination) and patient metadata. We performed whole-genome sequencing and molecular typing and AMR determinants were derived from quality-checked whole-genome sequencing data. Links between genomic lineages, AMR, and patient metadata were examined. FINDINGS 1932 gonococcal isolates collected in 2020 in 21 EEA countries were included. The majority (81·2%, 147 of 181 isolates) of azithromycin resistance (present in 9·4%, 181 of 1932) was explained by the continued expansion of the Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) clonal complexes (CCs) 63, 168, and 213 (with mtrD/mtrR promoter mosaic 2) and the novel NG-STAR CC1031 (semi-mosaic mtrD variant 13), associated with men who have sex with men and anorectal or oropharyngeal infections. The declining cefixime resistance (0·5%, nine of 1932) and negligible ceftriaxone resistance (0·1%, one of 1932) was largely because of the progressive disappearance of NG-STAR CC90 (with mosaic penA allele), which was predominant in 2013. No known resistance determinants for novel antimicrobials (zoliflodacin, gepotidacin, and lefamulin) were found. INTERPRETATION Azithromycin-resistant clones, mainly with mtrD mosaic or semi-mosaic variants, appear to be stabilising at a relatively high level in the EEA. This mostly low-level azithromycin resistance might threaten the recommended ceftriaxone-azithromycin therapy, but the negligible ceftriaxone resistance is encouraging. The decreased genomic population diversity and increased clonality could be explained in part by the COVID-19 pandemic resulting in lower importation of novel strains into Europe. FUNDING European Centre for Disease Prevention and Control and Örebro University Hospital.
Collapse
Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | | | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Raquel Abad
- Reference Laboratory for Neisseria, National Centre of Microbiology-Instituto de Salud Carlos III, Majadahonda, Spain
| | - Beatrice Bercot
- French National Reference Center for Bacterial STI, Associated Laboratory for Gonococci, APHP, Paris Cité University, IAME 1137, Paris, France
| | | | - Dagmar Heuer
- Unit 18: 'Sexually Transmitted Bacterial Pathogens and HIV', Department of Infectious Disease, Robert Koch Institute, Berlin, Germany
| | - Klaus Jansen
- Unit 34: 'HIV/AIDS, STI and Blood-Borne Infections', Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | | | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benjamin Bluemel
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden; Institute for Global Health, University College London, London, UK.
| |
Collapse
|
4
|
Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M. pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections. Microb Genom 2024; 10:001189. [PMID: 38288762 PMCID: PMC10868605 DOI: 10.1099/mgen.0.001189] [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: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.
Collapse
Affiliation(s)
- Leonor Sánchez-Busó
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Spain
| | - Andrea Sánchez-Serrano
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
| |
Collapse
|
5
|
Gianecini RA, Poklepovich T, Golparian D, Cuenca N, Scocozza L, Bergese S, Canigia LF, Vilches V, Lazzarino Elgart MJ, Unemo M, Campos J, Galarza P. Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC ≥ 256 μg/mL) in Argentina, 2018 to 2022. Microbiol Spectr 2023; 11:e0097023. [PMID: 37338369 PMCID: PMC10433793 DOI: 10.1128/spectrum.00970-23] [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: 03/06/2023] [Accepted: 05/24/2023] [Indexed: 06/21/2023] Open
Abstract
Azithromycin combined with ceftriaxone is the recommended dual therapy for uncomplicated gonorrhea in many countries. Nevertheless, the increasing prevalence of azithromycin resistance compromises the effectiveness of this treatment strategy. From 2018 to 2022, we collected 13 gonococcal isolates with high-level azithromycin resistance (MIC ≥ 256 μg/mL) across Argentina. Whole-genome sequencing revealed that these isolates were mainly represented by the internationally spreading Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) genogroup G12302, containing the 23S rRNA A2059G mutation (in all four alleles) together with mosaic mtrD and mtrR promoter 2 loci. This information is important to develop targeted public health policies to control the spread of azithromycin-resistant N. gonorrhoeae in Argentina and internationally. IMPORTANCE Azithromycin resistance in Neisseria gonorrhoeae has been increasing in numerous populations worldwide, which is of concern, as azithromycin is part of the recommended dual treatment in many countries. Here, we report 13 N. gonorrhoeae isolates with high-level azithromycin resistance (MIC ≥ 256 μg/mL). This study observed that high-level azithromycin-resistant gonococcal strains have shown sustained transmission in Argentina and are related to the successful international clone NG-MAST G12302. Genomic surveillance together with real-time tracing and data-sharing networks will be crucial in controlling the spread of azithromycin resistance in gonococcus.
Collapse
Affiliation(s)
- Ricardo Ariel Gianecini
- World Health Organization Collaborating Centre for Antimicrobial Resistance, National Reference Laboratory of Sexually Transmitted Diseases (STD), National Institute of Infectious Diseases - ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Tomas Poklepovich
- National Center of Genomics and Bioinformatics - ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Örebro University, Örebro, Sweden
| | - Noelia Cuenca
- World Health Organization Collaborating Centre for Antimicrobial Resistance, National Reference Laboratory of Sexually Transmitted Diseases (STD), National Institute of Infectious Diseases - ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Scocozza
- Laboratorio Bacteriología, Hospital Fernández, Ciudad Autónoma de Buenos Aires, Argentina
| | - Silvina Bergese
- Laboratorio Bacteriología, Hospital Alemán, Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Viviana Vilches
- Laboratorio Microbiología, Hospital Universitario Austral, Buenos Aires, Argentina
| | | | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London, London, United Kingdom
| | - Josefina Campos
- National Center of Genomics and Bioinformatics - ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Patricia Galarza
- World Health Organization Collaborating Centre for Antimicrobial Resistance, National Reference Laboratory of Sexually Transmitted Diseases (STD), National Institute of Infectious Diseases - ANLIS “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
6
|
Kakooza F, Golparian D, Matoga M, Maseko V, Lamorde M, Krysiak R, Manabe YC, Chen JS, Kularatne R, Jacobsson S, Godreuil S, Hoffman I, Bercot B, Wi T, Unemo M. Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20. J Antimicrob Chemother 2023; 78:1982-1991. [PMID: 37352017 DOI: 10.1093/jac/dkad193] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVES Global antimicrobial resistance (AMR) surveillance in Neisseria gonorrhoeae is essential. In 2017-18, only five (10.6%) countries in the WHO African Region reported to the WHO Global Gonococcal Antimicrobial Surveillance Programme (WHO GASP). Genomics enhances our understanding of gonococcal populations nationally and internationally, including AMR strain transmission; however, genomic studies from Africa are extremely scarce. We describe the gonococcal genomic lineages/sublineages, including AMR determinants, and baseline genomic diversity among strains in Uganda, Malawi and South Africa, 2015-20, and compare with sequences from Kenya and Burkina Faso. METHODS Gonococcal isolates cultured in Uganda (n = 433), Malawi (n = 154) and South Africa (n = 99) in 2015-20 were genome-sequenced. MICs were determined using ETEST. Sequences of isolates from Kenya (n = 159), Burkina Faso (n = 52) and the 2016 WHO reference strains (n = 14) were included in the analysis. RESULTS Resistance to ciprofloxacin was high in all countries (57.1%-100%). All isolates were susceptible to ceftriaxone, cefixime and spectinomycin, and 99.9% were susceptible to azithromycin. AMR determinants for ciprofloxacin, benzylpenicillin and tetracycline were common, but rare for cephalosporins and azithromycin. Most isolates belonged to the more antimicrobial-susceptible lineage B (n = 780) compared with the AMR lineage A (n = 141), and limited geographical phylogenomic signal was observed. CONCLUSIONS We report the first multi-country gonococcal genomic comparison from Africa, which will support the WHO GASP and WHO enhanced GASP (EGASP). The high prevalence of resistance to ciprofloxacin (and empirical use continues), tetracycline and benzylpenicillin, and the emerging resistance determinants for azithromycin show it is imperative to strengthen the gonococcal AMR surveillance, ideally including genomics, in African countries.
Collapse
Affiliation(s)
- Francis Kakooza
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daniel Golparian
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
| | | | - Venessa Maseko
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Yuka C Manabe
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jane S Chen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ranmini Kularatne
- Labtests Laboratory and Head Office, Mt Wellington, Auckland, New Zealand
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, and MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Irving Hoffman
- UNC Project Malawi, Lilongwe, Malawi
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Beatrice Bercot
- Infectious Agents Department, French National Reference Centre for Bacterial STIs, Associated Laboratory for Gonococci, and APHP, Saint Louis Hospital, Paris, France
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Magnus Unemo
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London, London, UK
| |
Collapse
|
7
|
Tayimetha CY, Njunda LA, Akenji B, Founou RC, Feteh V, Zofou D, Chafa A, Oyono Y, Etogo B, Tseuko D, Fonkoua MC, Harrison OB. Phenotypic and genotypic characterization of Neisseria gonorrhoeae isolates from Yaoundé, Cameroon, 2019 to 2020. Microb Genom 2023; 9:mgen001091. [PMID: 37590058 PMCID: PMC10483411 DOI: 10.1099/mgen.0.001091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
This study investigated antimicrobial resistance (AMR) phenotypes and genotypes exhibited by Neisseria gonorrhoeae from Yaoundé, Cameroon. AMR to tetracycline, penicillin and ciprofloxacin was observed although none of the isolates had reduced susceptibility to azithromycin, cefixime or ceftriaxone. Whole genome sequence (WGS) data were obtained and, using a threshold of 300 or fewer locus differences in the N. gonorrhoeae core gene multilocus sequence typing (cgMLST) scheme, four distinct core genome lineages were identified. Publicly available WGS data from 1355 gonococci belonging to these four lineages were retrieved from the PubMLST database, allowing the Cameroonian isolates to be examined in the context of existing data and compared with related gonococci. Examination of AMR genotypes in this dataset found an association between the core genome and AMR with, for example, isolates belonging to the core genome group, Ng_cgc_300 : 21, possessing GyrA and ParC alleles with amino acid substitutions conferring high-level resistance to ciprofloxacin while lineages Ng_cgc_300 : 41 and Ng_cgc_300 : 243 were predicted to be susceptible to several antimicrobials. A core genome lineage, Ng_cgc_300 : 498, was observed which largely consisted of gonococci originating from Africa. Analyses from this study demonstrate the advantages of using the N. gonorrhoeae cgMLST scheme to find related gonococci to carry out genomic analyses that enhance our understanding of the population biology of this important pathogen.
Collapse
Affiliation(s)
- Carolle Yanique Tayimetha
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
- National Public Health Laboratory, Yaounde, Cameroon
| | | | - Blaise Akenji
- National Public Health Laboratory, Yaounde, Cameroon
| | - Raspail Carrel Founou
- Department of Microbiology, Haematology and Immunology of University of Dschang, Dschang, Cameroon
| | - Vitalis Feteh
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Denis Zofou
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | - Anicet Chafa
- Medical Bacteriology Laboratory of University Hospital Center, Yaoundé, Cameroon
| | - Yannick Oyono
- Faculty of Health Sciences of the University of Buea, Buea, Cameroon
| | | | - Dorine Tseuko
- National Public Health Laboratory, Yaounde, Cameroon
| | - Marie Christine Fonkoua
- Centre Pasteur du Cameroon, Yaoundé, Cameroon
- Cameroonian Society of Microbiology, Yaoundé, Cameroon
| | - Odile B. Harrison
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| |
Collapse
|
8
|
Biochemical Atypia in Russian Neisseria gonorrhoeae Clinical Isolates Belonging to the G807 NG-MAST Genogroup/ST1594 MLST. Microorganisms 2022; 10:microorganisms10112271. [DOI: 10.3390/microorganisms10112271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022] Open
Abstract
Many current gonococcal clinical isolates in Russia show atypical taxonomically significant biochemical activity, which leads to species misidentification. Molecular typing of such cultures according Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) and multilocus sequence typing (MLST) protocols assigned them to the G807 NG-MAST GENOGROUP/ST1594 MLST that has been predominant in Russia in recent years. The goal of the study was to analyze the molecular mechanisms of biochemical atypia in N. gonorrhoeae clinical isolates characterized as the members of G807 NG-MAST GENOGROUP/ST1594 MLST. Sixteen isolates of this genogroup were included in the study, eight showed defective amino acid metabolism or loss of D-glucose fermentation. Comparative bioinformatic analysis based on WGS data divided these isolates into two clusters strictly associated with typical or atypical biochemical activity. Cultures with defective amino acid metabolism had a 5-nucleotide insertion in the pip-gene that caused a stop codon and led to synthesis of the non-functional enzyme. Comparison of the sequenced genomes with publicly available N. gonorrhoeae genomes showed the rarity of this insertion. In the global N. gonorrhoeae phylogenetic tree the G807 NG-MAST GENOGROUP/ST1594 MLST forms a distinct branch characterized by 170 SNPs, most of which are non-synonymous. We hypothesized a unique strategy for G807 NG-MAST GENOGROUP/ST1594 MLST clone persistence in the global N. gonorrhoeae population via escape of antimicrobial therapy due to diagnostic misidentification.
Collapse
|
9
|
Ribeiro ÁCDS, Santos FF, Moses IB, Minarini LADR, Gales AC. Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones. Microb Drug Resist 2022; 28:1037-1042. [DOI: 10.1089/mdr.2022.0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ághata Cardoso da Silva Ribeiro
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Ikechukwu Benjamin Moses
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Luciene Andrade da Rocha Minarini
- Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| |
Collapse
|
10
|
Molecular Mechanisms of Drug Resistance and Epidemiology of Multidrug-Resistant Variants of Neisseria gonorrhoeae. Int J Mol Sci 2022; 23:ijms231810499. [PMID: 36142410 PMCID: PMC9505821 DOI: 10.3390/ijms231810499] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 01/16/2023] Open
Abstract
The paper presents various issues related to the increasing drug resistance of Neisseria gonorrhoeae and the occurrence and spread of multidrug-resistant clones. One of the most important is the incidence and evolution of resistance mechanisms of N. gonorrhoeae to beta-lactam antibiotics. Chromosomal resistance to penicillins and oxyimino-cephalosporins and plasmid resistance to penicillins are discussed. Chromosomal resistance is associated with the presence of mutations in the PBP2 protein, containing mosaic variants and nonmosaic amino acid substitutions in the transpeptidase domain, and their correlation with mutations in the mtrR gene and its promoter regions (the MtrCDE membrane pump repressor) and in several other genes, which together determine reduced sensitivity or resistance to ceftriaxone and cefixime. Plasmid resistance to penicillins results from the production of beta-lactamases. There are different types of beta-lactamases as well as penicillinase plasmids. In addition to resistance to beta-lactam antibiotics, the paper covers the mechanisms and occurrence of resistance to macrolides (azithromycin), fluoroquinolones and some other antibiotics. Moreover, the most important epidemiological types of multidrug-resistant N. gonorrhoeae, prevalent in specific years and regions, are discussed. Epidemiological types are defined as sequence types, clonal complexes and genogroups obtained by various typing systems such as NG-STAR, NG-MAST and MLST. New perspectives on the treatment of N. gonorrhoeae infections are also presented, including new drugs active against multidrug-resistant strains.
Collapse
|
11
|
Golparian D, Kittiyaowamarn R, Paopang P, Sangprasert P, Sirivongrangson P, Franceschi F, Jacobsson S, Wi T, Unemo M. Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018. J Antimicrob Chemother 2022; 77:2171-2182. [PMID: 35542983 DOI: 10.1093/jac/dkac158] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/20/2022] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a substantial global public health problem. Gonococcal infections acquired in or from Asia represent most verified ceftriaxone treatment failures, and several ceftriaxone-resistant strains have emerged in Asia and subsequently spread globally. Additionally, in Thailand the gonorrhoea incidence remains high. Herein, we investigate the genomic diversity, AMR and AMR determinants in gonococcal isolates cultured in 2018 in Bangkok, Thailand. METHODS Gonococcal isolates from males (n = 37) and females (n = 62) were examined by Etest and WGS. AMR determinants and molecular epidemiological STs were characterized. For phylogenomic comparison, raw sequence data were included from China (432 isolates), Japan (n = 270), Vietnam (n = 229), Thailand (n = 3), a global dataset (n = 12 440) and the 2016 WHO reference strains plus WHO Q (n = 15). RESULTS In total, 88, 66 and 41 different NG-MAST, NG-STAR and MLST STs, respectively, and 31 different NG-STAR clonal complexes were found. A remarkably high frequency (88%) of β-lactamase TEM genes was detected and two novel TEM alleles were found. The phylogenomic analysis divided the isolates into the previously described lineages A and B, with a large proportion of Thai isolates belonging to the novel sublineage A3. CONCLUSIONS We describe the first molecular epidemiological study using WGS on gonococcal isolates from Thailand. The high prevalence of AMR and AMR determinants for ciprofloxacin, tetracycline and benzylpenicillin, and some strains belonging to clones/clades especially in sublineage A2 that are prone to develop resistance to extended-spectrum cephalosporins (ESCs) and azithromycin, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Thailand.
Collapse
Affiliation(s)
- Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Rossaphorn Kittiyaowamarn
- Bangrak STIs Center, Division of AIDS and STIs, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Porntip Paopang
- Bangrak STIs Center, Division of AIDS and STIs, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Pongsathorn Sangprasert
- Bangrak STIs Center, Division of AIDS and STIs, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | | | - Francois Franceschi
- Global Antibiotic Research & Development Partnership (GARDP), Geneva, Switzerland
| | - Susanne Jacobsson
- World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI programmes, World Health Organization, Geneva, Switzerland
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London, London, UK
| |
Collapse
|
12
|
Sánchez-Busó L, Cole MJ, Spiteri G, Day M, Jacobsson S, Golparian D, Sajedi N, Yeats CA, Abudahab K, Underwood A, Bluemel B, Aanensen DM, Unemo M, Pleininger S, Indra A, De Baetselier I, Vanden Berghe W, Hunjak B, Blažić TN, Maikanti-Charalambous P, Pieridou D, Zákoucká H, Žemličková H, Hoffmann S, Cowan S, Schwartz LJ, Peetso R, Epstein J, Viktorova J, Ndeikoundam N, Bercot B, Bébéar C, Lot F, Buder S, Jansen K, Miriagou V, Rigakos G, Raftopoulos V, Balla E, Dudás M, Ásmundsdóttir LR, Sigmundsdóttir G, Hauksdóttir GS, Gudnason T, Colgan A, Crowley B, Saab S, Stefanelli P, Carannante A, Parodi P, Pakarna G, Nikiforova R, Bormane A, Dimina E, Perrin M, Abdelrahman T, Mossong J, Schmit JC, Mühlschlegel F, Barbara C, Mifsud F, Van Dam A, Van Benthem B, Visser M, Linde I, Kløvstad H, Caugant D, Młynarczyk-Bonikowska B, Azevedo J, Borrego MJ, Nascimento MLR, Pavlik P, Klavs I, Murnik A, Jeverica S, Kustec T, Vázquez Moreno J, Diaz A, Abad R, Velicko I, Unemo M, Fifer H, Shepherd J, Patterson L. Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study. THE LANCET MICROBE 2022; 3:e452-e463. [DOI: 10.1016/s2666-5247(22)00044-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
|
13
|
Hadad R, Golparian D, Velicko I, Ohlsson AK, Lindroth Y, Ericson EL, Fredlund H, Engstrand L, Unemo M. First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016. Front Microbiol 2022; 12:820998. [PMID: 35095823 PMCID: PMC8794790 DOI: 10.3389/fmicb.2021.820998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 12/05/2022] Open
Abstract
The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.
Collapse
Affiliation(s)
- Ronza Hadad
- World Health Organization 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
| | - Daniel Golparian
- World Health Organization 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
| | | | - Anna-Karin Ohlsson
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Ylva Lindroth
- Department of Laboratory Medicine, Medical Microbiology, Lund University, Skåne Laboratory Medicine, Lund, Sweden
| | - Eva-Lena Ericson
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Sweden
| | - Hans Fredlund
- World Health Organization 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
| | - Lars Engstrand
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Magnus Unemo
- World Health Organization 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
| |
Collapse
|
14
|
Giovannuzzi S, Abutaleb NS, Hewitt CS, Carta F, Nocentini A, Seleem MN, Flaherty DP, Supuran CT. Dithiocarbamates effectively inhibit the α-carbonic anhydrase from Neisseria gonorrhoeae. J Enzyme Inhib Med Chem 2021; 37:1-8. [PMID: 34894954 PMCID: PMC8667944 DOI: 10.1080/14756366.2021.1988945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recently, inorganic anions and sulphonamides, two of the main classes of zinc-binding carbonic anhydrase inhibitors (CAIs), were investigated for inhibition of the α-class carbonic anhydrase (CA, EC 4.2.1.1) from Neisseria gonorrhoeae, NgCA. As an extension to our previous studies, we report that dithiocarbamates (DTCs) derived from primary or secondary amines constitute a class of efficient inhibitors of NgCA. KIs ranging between 83.7 and 827 nM were measured for a series of 31 DTCs that incorporated various aliphatic, aromatic, and heterocyclic scaffolds. A subset of DTCs were selected for antimicrobial testing against N. gonorrhoeae, and three molecules displayed minimum inhibitory concentration (MIC) values less than or equal to 8 µg/mL. As NgCA was recently validated as an antibacterial drug target, the DTCs may lead to development of novel antigonococcal agents.
Collapse
Affiliation(s)
- Simone Giovannuzzi
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Nader S Abutaleb
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Fabrizio Carta
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Alessio Nocentini
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.,Center for Emerging Zoonotic and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Straub C, Thirkell C, Tiong A, Woodhouse R, Szeto J, Dyet KH. The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission. Microb Genom 2021; 7:000701. [PMID: 34755593 PMCID: PMC8743534 DOI: 10.1099/mgen.0.000701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/30/2021] [Indexed: 11/18/2022] Open
Abstract
The increasing use of culture independent diagnostic testing for the diagnosis of Neisseria gonorrhoeae infection has led to gaps in surveillance of antimicrobial resistance (AMR) rates due to limited availability of cultures. Our study reports the findings of a second national survey of N. gonorrhoeae in New Zealand, utilizing whole-genome sequencing (WGS) to study the population structure, prevalence of AMR, epidemiology and transmission of gonorrhoea isolates. We analysed 314 isolates and found a strong correlation between carriage of acquired resistance genes or chromosomal point mutations and phenotypic susceptibility testing results. Overall, the New Zealand rates of azithromycin resistance and decreased susceptibility to ceftriaxone remain lower than in most countries, which are part of the World Health Organization (WHO) Global Gonococcal Antimicrobial Surveillance Programme (GASP). The phylogeny provides evidence of a diverse population significantly associated with sexual behaviour groups. Transmission clustering with a ten single nucleotide polymorphism (SNP) cut-off identified 49 clusters, of which ten were solely associated with men who have sex with men (MSM), whereas remaining clusters included heterosexual patients, as well as MSM, suggesting that bridging of sexual networks is occurring. Utilizing pairwise SNP differences between isolates of the same sequence types we determined genetic variation for the three typing schemes used in this study [Multi locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST), and sequence typing for antimicrobial resistance (NG-STAR)]. A median of 0.0 to 52.5 pairwise SNP differences within a single NG-STAR sequence type underlines previous findings of the superiority of the NG-STAR typing scheme in terms of genomic inherency. With our analysis incorporating epidemiological and genomic data, we were able to show a comprehensive overview of the N. gonorrhoeae population circulating in New Zealand, focussing on AMR and transmission within sexual networks. Regular surveillance studies to understand the origin, evolution and spread of AMR for gonorrhoea remain necessary to make informed decisions about public health guidelines, as the internationally rising rates of ceftriaxone and azithromycin resistance have already led to adaptation of current treatment guidelines in the UK and the USA, highlighting the importance of regular surveillance in individual countries.
Collapse
Affiliation(s)
- Christina Straub
- The Institute of Environmental Science and Research, Auckland 1025, New Zealand
- Genomics Aotearoa, New Zealand
| | - Callum Thirkell
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Audrey Tiong
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Rosemary Woodhouse
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Jenny Szeto
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Kristin H. Dyet
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| |
Collapse
|
17
|
Handsfield HH. Gonococcal Infection of Penile Skin and Accessory Structures. Sex Transm Dis 2021; 48:787-788. [PMID: 33783410 DOI: 10.1097/olq.0000000000001428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- H Hunter Handsfield
- From the Center for AIDS and STD and the Department of Medicine, University of Washington School of Medicine, Seattle, WA
| |
Collapse
|
18
|
Singh R, Kusalik A, Dillon JAR. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Brief Funct Genomics 2021; 21:78-89. [PMID: 34170311 DOI: 10.1093/bfgp/elab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
Collapse
Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology
| | - Anthony Kusalik
- Department of Computer Science at the University of Saskatchewan
| | - Jo-Anne R Dillon
- Department of Biochemistry Microbiology and Immunology, College of Medicine, c/o Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N5E3, Canada
| |
Collapse
|
19
|
Nocentini A, Hewitt CS, Mastrolorenzo MD, Flaherty DP, Supuran CT. Anion inhibition studies of the α-carbonic anhydrases from Neisseria gonorrhoeae. J Enzyme Inhib Med Chem 2021; 36:1061-1066. [PMID: 34030562 PMCID: PMC8158254 DOI: 10.1080/14756366.2021.1929202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The bacterial pathogen Neisseria gonorrhoeae encodes for an α-class carbonic anhydrase (CA, EC 4.2.1.1), NgCA, which was investigated for its inhibition with a series of inorganic and organic anions. Perchlorate and hexafluorophosphate did not significantly inhibit NgCA CO2 hydrase activity, whereas the halides, azide, bicarbonate, carbonate, stannate, perosmate, diphosphate, divanadate, perruthenate, and trifluoromethanesulfonate showed inhibition constants in the range of 1.3–9.6 mM. Anions/small molecules such as cyanate, thiocyanate, nitrite, nitrate, bisulphite, sulphate, hydrogensulfide, phenylboronic acid, phenylarsonic acid, selenate, tellurate, tetraborate, perrhenate, peroxydisulfate, selenocyanate, iminodisulfonate, and fluorosulfonate showed KIs in the range of 0.15–1.0 mM. The most effective inhibitors detected in this study were sulfamide, sulfamate, trithiocarbonate and N,N-diethyldithiocarbamate, which had KIs in the range of 5.1–88 µM. These last compounds incorporating the CS2- zinc-binding group may be used as leads for developing even more effective NgCA inhibitors in addition to the aromatic/heterocyclic sulphonamides, as this enzyme was recently validated as an antibacterial drug target for obtaining novel antigonococcal agents
Collapse
Affiliation(s)
- Alessio Nocentini
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Chad S Hewitt
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Margaret D Mastrolorenzo
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy.,University of California, San Diego (UCSD), San Diego, CA, USA
| | - Daniel P Flaherty
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.,Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione di Scienze Farmaceutiche e Nutraceutiche, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| |
Collapse
|
20
|
Smolarczyk K, Mlynarczyk-Bonikowska B, Rudnicka E, Szukiewicz D, Meczekalski B, Smolarczyk R, Pieta W. The Impact of Selected Bacterial Sexually Transmitted Diseases on Pregnancy and Female Fertility. Int J Mol Sci 2021; 22:2170. [PMID: 33671616 PMCID: PMC7926516 DOI: 10.3390/ijms22042170] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Sexually transmitted infections (STIs) caused by Neisseria gonorrhoeae, Chlamydia trachomatis and Mycoplasma genitalium are a common cause of pelvic inflammatory disease (PID) which can lead to tubal factor infertility (TFI). TFI is one of the most common causes of infertility, accounting for 30% of female fertility problems. STIs can also have an impact on pregnancy, leading to adverse pregnancy outcomes. Escalating antibiotic resistance in Neisseria gonorrhoeae and Mycoplasma genitalium represents a significant problem and can be therapeutically challenging. We present a comprehensive review of the current treatment options, as well as the molecular approach to this subject. We have given special attention to molecular epidemiology, molecular diagnostics, current and new treatments, and drug resistance.
Collapse
MESH Headings
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Chlamydia Infections/drug therapy
- Chlamydia Infections/etiology
- Chlamydia Infections/microbiology
- Drug Resistance, Bacterial/drug effects
- Fallopian Tubes/microbiology
- Fallopian Tubes/pathology
- Female
- Gonorrhea/drug therapy
- Gonorrhea/etiology
- Humans
- Infertility, Female/microbiology
- Molecular Diagnostic Techniques
- Molecular Epidemiology/methods
- Mycoplasma Infections/drug therapy
- Mycoplasma Infections/etiology
- Mycoplasma genitalium/pathogenicity
- Pregnancy
- Pregnancy Complications, Infectious/diagnosis
- Pregnancy Complications, Infectious/drug therapy
- Pregnancy Complications, Infectious/epidemiology
- Pregnancy Complications, Infectious/etiology
- Sexually Transmitted Diseases, Bacterial/complications
- Sexually Transmitted Diseases, Bacterial/diagnosis
- Sexually Transmitted Diseases, Bacterial/drug therapy
- Sexually Transmitted Diseases, Bacterial/epidemiology
Collapse
Affiliation(s)
- Katarzyna Smolarczyk
- Department of Dermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland; (K.S.); (B.M.-B.)
| | - Beata Mlynarczyk-Bonikowska
- Department of Dermatology and Venereology, Medical University of Warsaw, 02-008 Warsaw, Poland; (K.S.); (B.M.-B.)
| | - Ewa Rudnicka
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Dariusz Szukiewicz
- Department of General and Experimental Pathology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Blazej Meczekalski
- Department of Gynaecological Endocrinology, Poznan University of Medical Sciences, 60-535 Poznan, Poland;
| | - Roman Smolarczyk
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Wojciech Pieta
- Department of Gynaecological Endocrinology, Medical University of Warsaw, 02-091 Warsaw, Poland;
| |
Collapse
|