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Osman R, Dema E, David A, Hughes G, Field N, Cole M, Didelot X, Saunders J. Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care. J Infect 2024; 88:106168. [PMID: 38670270 DOI: 10.1016/j.jinf.2024.106168] [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: 01/10/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. METHODS We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. RESULTS We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n = 7) and gonorrhoea (n = 1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n = 2), inform antimicrobial therapy (n = 5) and identify cross-contamination (n = 1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. CONCLUSIONS While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.
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Affiliation(s)
- Roeann Osman
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom.
| | - Emily Dema
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Alexandra David
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Nigel Field
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Michelle Cole
- UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Genomics and Enabling Data at Warwick University, United Kingdom
| | - John Saunders
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom; UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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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.
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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
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3
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Phillips LT, Witney AA, Furegato M, Laing KG, Zhou L, Sadiq ST. Time Required for Nanopore Whole-Genome Sequencing of Neisseria gonorrhoeae for Identification of Phylogenetic Relationships. J Infect Dis 2023; 228:1179-1188. [PMID: 37216766 PMCID: PMC10629711 DOI: 10.1093/infdis/jiad170] [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: 12/05/2022] [Revised: 03/20/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health challenge. Limitations to AMR surveillance reporting, alongside reduction in culture-based susceptibility testing, has resulted in a need for rapid diagnostics and strain detection. We investigated Nanopore sequencing time, and depth, to accurately identify closely related N. gonorrhoeae isolates, compared to Illumina sequencing. METHODS N. gonorrhoeae strains collected from a London sexual health clinic were cultured and sequenced with MiSeq and MinION sequencing platforms. Accuracy was determined by comparing variant calls at 68 nucleotide positions (37 resistance-associated markers). Accuracy at varying MinION sequencing depths was determined through retrospective time-stamped read analysis. RESULTS Of 22 MinION-MiSeq pairs reaching sufficient sequencing depth, agreement of variant call positions passing quality control criteria was 185/185 (100%; 95% confidence interval [CI], 98.0%-100.0%), 502/503 (99.8%; 95% CI, 98.9%-99.9%), and 564/565 (99.8%; 95% CI, 99.0%-100.0%) at 10x, 30x, and 40x MinION depth, respectively. Isolates identified as closely related by MiSeq, within one yearly evolutionary distance of ≤5 single nucleotide polymorphisms, were accurately identified via MinION. CONCLUSIONS Nanopore sequencing shows utility as a rapid surveillance tool, identifying closely related N. gonorrhoeae strains, with just 10x sequencing depth, taking a median time of 29 minutes. This highlights its potential for tracking local transmission and AMR markers.
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Affiliation(s)
- Laura T Phillips
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Adam A Witney
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Martina Furegato
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Ken G Laing
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Liqing Zhou
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
| | - S Tariq Sadiq
- Institute for Infection and Immunity, St George’s University of London, London, United Kingdom
- Infection Clinical Academic Group, St George's University Hospitals NHS Trust, London, United Kingdom
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Mitjà O, Padovese V, Folch C, Rossoni I, Marks M, Rodríguez i Arias MA, Telenti A, Ciuffi A, Blondeel K, Mårdh O, Casabona J. Epidemiology and determinants of reemerging bacterial sexually transmitted infections (STIs) and emerging STIs in Europe. THE LANCET REGIONAL HEALTH. EUROPE 2023; 34:100742. [PMID: 37927427 PMCID: PMC10625005 DOI: 10.1016/j.lanepe.2023.100742] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 11/07/2023]
Abstract
In this scoping review, we offer a comprehensive understanding of the current and recent epidemiology, challenges, and emerging issues related to bacterial sexually transmitted infections (STIs) in the WHO European Region. We endeavour in collating data from both EU/EEA and non- EU/EEA countries, thereby giving a complete picture of the region which highlights the higher notification rates in Northern and Western countries than other regions, likely due to differences in testing, access to testing, and surveillance capacity. We provide an up-to-date review on the current knowledge of determinants and persistent inequities in key populations as well as the use of molecular epidemiology for identifying transmission networks in gonorrhoea and syphilis, and detecting chlamydia mutations that evade molecular diagnosis. Finally, we explore the emerging STIs in the region and the evolving transmission routes of food and waterborne diseases into sexual transmission. Our findings call for harmonized STI surveillance systems, proactive strategies, and policies to address social factors, and staying vigilant for emerging STIs.
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Affiliation(s)
- Oriol Mitjà
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
- School of Medicine and Health Sciences, University of Papua New Guinea, Port Moresby, Papua New Guinea
| | - Valeska Padovese
- Genitourinary Clinic, Department of Dermatology and Venereology, Mater Dei Hospital, Msida, Malta
| | - Cinta Folch
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
| | - Isotta Rossoni
- Van Vollenhoven Institute for Law, Governance and Society, Leiden University, Netherland
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, United Kingdom
- Division of Infection and Immunology, University College London, London, UK
- Hospital for Tropical Diseases, University College London Hospital, London, UK
| | - Miquel Angel Rodríguez i Arias
- Skin Neglected Tropical Diseases and Sexually Transmitted Infections Section, Hospital Universitari Germans Trías i Pujol, Badalona, Spain
- Fight Infectious Diseases Foundation, Badalona, Spain
| | | | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Karel Blondeel
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Otilia Mårdh
- STI, Blood Borne Viruses and TB Section, Disease Programmes Unit, European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Jordi Casabona
- Centre of Epidemiological Studies of HIV/AIDS and STI of Catalonia (CEEISCAT), Health Department, Generalitat de Catalunya, Badalona, Spain
- Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, Badalona, Spain
- CIBER Epidemiología Y Salud Pública (CIBERESP), Madrid, Spain
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5
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Mortimer TD, Grad YH. A Genomic Perspective on the Near-term Impact of Doxycycline Post-exposure Prophylaxis on Neisseria gonorrhoeae Antimicrobial Resistance. Clin Infect Dis 2023; 77:788-791. [PMID: 37138444 PMCID: PMC10495131 DOI: 10.1093/cid/ciad279] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/05/2023] Open
Abstract
Pre-existing tetracycline resistance in Neisseria gonorrhoeae limits the effectiveness of post-exposure prophylaxis (PEP) with doxycycline against gonorrhea, and selection for tetracycline resistance may influence prevalence of multi-drug resistant strains. Using genomic and antimicrobial susceptibility data from N. gonorrhoeae, we assessed the near-term impact of doxycycline PEP on N. gonorrhoeae resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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6
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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.
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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
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7
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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.
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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
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8
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Mortimer TD, Grad YH. A genomic perspective on the near-term impact of doxycycline post-exposure prophylaxis on Neisseria gonorrhoeae antimicrobial resistance. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.14.23287223. [PMID: 36993406 PMCID: PMC10055447 DOI: 10.1101/2023.03.14.23287223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Post-exposure prophylaxis with doxycycline (doxyPEP) is being introduced to prevent bacterial sexually transmitted infections (STIs). Pre-existing tetracycline resistance in Neisseria gonorrhoeae limits doxyPEP effectiveness against gonorrhea, and selection for tetracycline resistant lineages may influence prevalence of resistance to other antimicrobials via selection for multi-drug resistant strains. Using genomic and antimicrobial susceptibility data from 5,644 clinical isolates of N. gonorrhoeae , we assessed the near-term impact of doxyPEP on N. gonorrhoeae antimicrobial resistance. We found that the impact on antimicrobial resistance is likely to be influenced by the strength of selection for plasmid-encoded and chromosomally-encoded tetracycline resistance, as isolates with high-level, plasmid-encoded resistance had lower minimum inhibitory concentrations to other antimicrobials compared to isolates with low-level tetracycline resistance. The impact of doxyPEP may differ across demographic groups and geographic regions within the United States due to variation in pre-existing tetracycline resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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9
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Corwin LMB, Ingebretsen A, Campbell P, Alfsnes K, Müller F, Mauder N, Koomey M, Bjørnholt JV. Fourier transform infrared spectroscopy; can it be used as a rapid typing method of Neisseria gonorrhoeae? J Microbiol Methods 2023; 205:106675. [PMID: 36681126 DOI: 10.1016/j.mimet.2023.106675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/16/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Typing of Neisseria gonorrhoeae is necessary for epidemiologic surveillance, while time consuming and resource intensive. Fourier transform infrared (FTIR) spectroscopy has shown promising results when typing several bacterial species. This study investigates whether FTIR spectroscopy can be used as a rapid method for typing clinical N. gonorrhoeae isolates, comparing FTIR spectroscopy to multi locus sequence typing (MLST), N. gonorrhoeae multi antigen sequence typing (NG-MAST) and whole genome sequencing (WGS). METHODS Sixty consecutive isolates from a venereology clinic and three isolates from an outbreak were included. Isolates were analysed with FTIR spectroscopy on the IR Biotyper system (Bruker Daltonik) with the IR Biotyper software (version 2.1) with default analysis settings (spectral range 1300-800 cm-1). Four technical replicates of each isolate were analysed in three different runs. The output was a hierarchical cluster analysis (HCA) presented as a dendrogram; a tree-like overview of how closely different isolates are related. FTIR spectroscopy was compared to MLST, NG-MAST and WGS to see if the FTIR spectroscopy-dendrogram grouped the isolates in the same clusters. RESULTS Fifty-one out of 60 isolates, and the three outbreak isolates, produced at least one spectrum in each run and were included. No agreement between FTIR spectroscopy and MLST or NG-MAST or WGS was shown. The FTIR spectroscopy-dendrogram failed to cluster the outbreak isolates. CONCLUSION FTIR spectroscopy (spectral range 1300-800 cm-1) is not yet suitable for epidemiologic typing of N. gonorrhoeae. Absence of a capsule as well as phase- and antigenic variation of carbohydrate surface structures of the gonococcal cell wall may contribute to our findings. Future studies should include analysis of a wider range of the spectrum recorded (4000-500 cm-1), and should also explore further mathematical analytic approaches of the similarity between spectra.
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Affiliation(s)
- Linn Merete Brendefur Corwin
- Microbiology Dept Rikshospitalet, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway; University of Oslo (UiO), Institute of Clinical Medicine, PO Box 1072 Blindern, 0316 Oslo, Norway.
| | - André Ingebretsen
- Microbiology Dept Rikshospitalet, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway.
| | - Patricia Campbell
- University of Oslo (UiO), Institute of Clinical Medicine, PO Box 1072 Blindern, 0316 Oslo, Norway; Microbiology Dept, Akershus University Hospital, PO Box 1000, 1478 Lørenskog, Norway.
| | - Kristian Alfsnes
- Norwegian Institute of Public Health (NIPH), PO Box 222 Skøyen, 0213 Oslo, Norway.
| | - Fredrik Müller
- Microbiology Dept Rikshospitalet, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway; University of Oslo (UiO), Institute of Clinical Medicine, PO Box 1072 Blindern, 0316 Oslo, Norway.
| | - Norman Mauder
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany.
| | - Michael Koomey
- University of Oslo (UiO), Department of Biosciences, PO Box 1072 Blindern, 0316 Oslo, Norway.
| | - Jørgen Vildershøj Bjørnholt
- Microbiology Dept Rikshospitalet, Oslo University Hospital, PO Box 4950 Nydalen, 0424 Oslo, Norway; University of Oslo (UiO), Institute of Clinical Medicine, PO Box 1072 Blindern, 0316 Oslo, Norway.
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10
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Martin SL, Mortimer TD, Grad YH. Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests. Ann N Y Acad Sci 2023; 1520:74-88. [PMID: 36573759 PMCID: PMC9974846 DOI: 10.1111/nyas.14549] [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] [Indexed: 12/28/2022]
Abstract
Neisseria gonorrhoeae is an urgent public health threat due to the emergence of antibiotic resistance. As most isolates in the United States are susceptible to at least one antibiotic, rapid molecular antimicrobial susceptibility tests (ASTs) would offer the opportunity to tailor antibiotic therapy, thereby expanding treatment options. With genome sequence and antibiotic resistance phenotype data for nearly 20,000 clinical N. gonorrhoeae isolates now available, there is an opportunity to use statistical methods to develop sequence-based diagnostics that predict antibiotic susceptibility from genotype. N. gonorrhoeae, therefore, provides a useful example illustrating how to apply machine learning models to aid in the design of sequence-based ASTs. We present an overview of this framework, which begins with establishing the assay technology, the performance criteria, the population in which the diagnostic will be used, and the clinical goals, and extends to the choices that must be made to arrive at a set of features with the desired properties for predicting susceptibility phenotype from genotype. While we focus on the example of N. gonorrhoeae, the framework generalizes to other organisms for which large-scale genotype and antibiotic resistance data can be combined to aid in diagnostics development.
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Affiliation(s)
- Skylar L. Martin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tatum D. Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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11
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Chaguza C, Smith JT, Bruce SA, Gibson R, Martin IW, Andam CP. Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation. CELL GENOMICS 2022; 2:100194. [PMID: 36465278 PMCID: PMC9718559 DOI: 10.1016/j.xgen.2022.100194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA,Corresponding author
| | | | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA
| | - Robert Gibson
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, New York, USA,Corresponding author
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12
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Nakku-Joloba E, Mboowa G, Ssengooba W, Kiyimba A, Kigozi E, Baluku H, Alinaitwe L, Nyote R, Kabahita JM, Mutumba P, Katabazi FA, Kiwanuka N, Sewankambo N, Kateete DP. Prevalence and antimicrobial resistance profiles of Neisseria gonorrhea and Chlamydia trachomatis isolated from individuals attending STD clinics in Kampala, Uganda. Afr Health Sci 2022; 22:62-71. [PMID: 36910377 PMCID: PMC9993296 DOI: 10.4314/ahs.v22i3.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Sexually transmitted diseases (STDs) management in sub-Saharan Africa is syndromic but molecular diagnostics provide quicker, sensitive diagnosis and treatment. Effective STD control hinges on identification and treatment of infected persons and sexual partner contact tracing. Objectives This study assessed feasibility of using the Xpert CT/NG test to identify prevalent Chlamydia trachomatis (CT) and Neisseria gonorrhea (NG) infections among STD clinic attendees and their sexual partners and tested for antimicrobial resistance for N. gonorrhea. Methods A cross-sectional study was conducted at 4 outpatient STD clinics in Kampala, Uganda from February 2019 to October 2019. Participants received a syndromic diagnosis, were tested for NG and CT, as well as their sexual partners. Urine (men) and high vaginal swabs (women) were collected, examined using Xpert CT/NG assay. A total of 79 participants were enrolled at baseline of whom 25 had CT/NG. 21 partners of infected baseline participants and 7 partners of the 21 primary partners were enrolled. Results The mean age of the reported sexual partners was 26 (18-43) years. The prevalence of NG was 25% at baseline and 18 % for CT. Nine (11.4%) people were dually infected. Men were more likely to have NG (p<0.001) at multivariable level. Two participants tested HIV-1 positive. On microbiological culture, 8 samples (2.5%) grew NG and all were resistant to penicillin, ciprofloxacin. For CT, we found a preponderance of the F-serovar in this population. Conclusion The most prevalent organism was Neisseria gonorrhea. Generally, the prevalence of CT and NG was high. Infection proportions increased among primary partners, particularly women. Etiologic testing without partner tracing and treatment may underestimate burden of CT/NG in this population and contribute to re-infection.
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Affiliation(s)
- Edith Nakku-Joloba
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda.,STD Clinic/Ward 12 Mulago National Referral Hospital
| | - Gerald Mboowa
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Anthony Kiyimba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Hannington Baluku
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | | | - Ronnie Nyote
- STD Clinic/Ward 12 Mulago National Referral Hospital
| | - Jupiter Marina Kabahita
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Paul Mutumba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Fred A Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
| | - Nelson Sewankambo
- Department of Medicine, and Clinical Epidemiology Unit, Makerere University College of Health Sciences. P.O.Box 7072, Kampala, Uganda
| | - David P Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences. P.O. Box 7072, Kampala, Uganda
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13
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Vollan HS, Caugant DA, Eldholm V, Alfsnes K, Debech N, Brynildsrud O. Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing. Microb Genom 2022; 8. [PMID: 36136059 DOI: 10.1099/mgen.0.000889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The abcZ gene is an essential housekeeping gene in all the Neisseria species. It is one of the seven genes used for multilocus sequence typing (MLST) this genus. It encodes the cytosolic component of an ATP-binding cassette (ABC) transporter complex of unknown function. We report here the finding of a strain of Neisseria gonorrhoeae with a 485 base pair deletion in the 5' region of the abcZ gene that truncates the protein product from 636 amino acids to 89 amino acids. A second open reading frame (ORF), encoding the latter 388 amino acids of the abcZ gene, was predicted downstream. The deletion will affect MLST profiling; interrogation of genomic sequences from PubMLST revealed that this isolate is not an anomaly. Deletions in abcZ were identified in 256 Neisseria genomes, roughly 0.6% of isolates. Furthermore, these deletions could leave the abcZ gene in a pseudogenized state. Our strain, isolated from a patient with symptoms of gonorrheal infection, nevertheless behaved normal in terms of growth and in vitro phenotypic properties.
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Affiliation(s)
- Hilde Synnøve Vollan
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Dominique A Caugant
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway.,Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vegard Eldholm
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristian Alfsnes
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Nadia Debech
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola Brynildsrud
- Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway.,Food Safety and Infection Biology, Norwegian University of Life Science, Ås, Norway
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14
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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.
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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
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15
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de Korne-Elenbaas J, Bruisten SM, de Vries HJC, van Dam AP. Within-Host Genetic Variation in Neisseria gonorrhoeae over the Course of Infection. Microbiol Spectr 2022; 10:e0031322. [PMID: 35467402 PMCID: PMC9241688 DOI: 10.1128/spectrum.00313-22] [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: 01/26/2022] [Accepted: 04/02/2022] [Indexed: 11/20/2022] Open
Abstract
Knowledge of within-host genetic variation informs studies on transmission dynamics. We studied within-host genetic variation in Neisseria gonorrhoeae over the course of infection and across different anatomical locations. Isolates were obtained during a clinical trial, and isolates from consecutive time points reflected persistent infections after treatment failure. We compared sequence types (STs) and recombination unfiltered- and filtered core genome single nucleotide polymorphism (SNP) distances in 65 within-host isolate pairs from the same anatomical location over time-obtained with a median interval of 7 days-and 65 isolate pairs across different anatomical locations at one time point. Isolates with different Multi-Locus Sequence Types (MLST), NG-Sequence Types for Antimicrobial Resistance (NG-STAR) and NG-Multi Antigen Sequence Types (NG-MAST) had a median of 1466 recombination filtered SNPs, whereas a median of 1 SNP was found between isolates with identical STs or a different NG-MAST only. The threshold for differentiating between strains was set at 10 recombination filtered SNPs, showing that isolates from persistent infections could have different NG-MASTs. Antibiotic pressure applied through treatment did not lead to an increase in genetic variation in specific genes or in overall extent of variation, compared to variation across anatomical locations. Instead, within-host genetic variation was proposedly driven by the host immune response, as it was concentrated in genomic regions encoding surface exposed proteins involved in host-microbe interaction. Ultimately, 15/228 (6.5%) between-host pairs contained a single strain, suggesting between-host transmission. However, patient reported data are needed to differentiate within-host persistence from between-host transmission. IMPORTANCE Understanding transmission dynamics of Neisseria gonorrhoeae (Ng) is based on the identification of transmission events. These can be identified by assessing genetic relatedness between Ng isolates, expressed as core genome SNP distances. However, a SNP threshold to differentiate between strains needs to be defined, using knowledge on within- and between-host genetic variation. Here, we assessed within-host genetic variation, using a unique set of within-host Ng isolates from the same anatomical location over time or across different anatomical locations at one time point. The insights in genetic variation that occurred during the infection period contribute to the understanding of infection dynamics. In addition, the obtained knowledge can be used for future research on transmission dynamics and development of public health interventions based on bacterial genomic data.
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Affiliation(s)
- Jolinda de Korne-Elenbaas
- Department of Infectious Diseases, Public Health Laboratory, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AII), location Academic Medical Center, Amsterdam, the Netherlands
| | - Sylvia M. Bruisten
- Department of Infectious Diseases, Public Health Laboratory, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Amsterdam, the Netherlands
| | - Henry J. C. de Vries
- Amsterdam UMC, University of Amsterdam, Department of Dermatology, Amsterdam Institute for Infection and Immunity (AII), location Academic Medical Center, Amsterdam, the Netherlands
- Center for Sexual Health, Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Alje P. van Dam
- Department of Infectious Diseases, Public Health Laboratory, Public Health Service of Amsterdam, Amsterdam, the Netherlands
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology, Amsterdam Institute for Infection and Immunity (AII), location Academic Medical Center, Amsterdam, the Netherlands
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16
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Penedos AR, Fernández-García A, Lazar M, Ralh K, Williams D, Brown KE. Mind your Ps: A probabilistic model to aid the interpretation of molecular epidemiology data. EBioMedicine 2022; 79:103989. [PMID: 35398788 PMCID: PMC9006250 DOI: 10.1016/j.ebiom.2022.103989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/18/2022] [Accepted: 03/23/2022] [Indexed: 11/26/2022] Open
Abstract
Background Assessing relatedness of pathogen sequences in clinical samples is a core goal in molecular epidemiology. Tools for Bayesian analysis of phylogeny, such as the BEAST software package, have been typically used in the analysis of sequence/time data in public health. However, they are computationally-, time-, and knowledge-intensive, demanding resources that many laboratories do not have available or cannot allocate frequently. Methods To evaluate a faster and simpler alternative method to support the routine interpretation of sequence data for epidemiology, we obtained sequences for two regions in the measles virus genome, N-450 and MF-NCR, from patient samples of genotypes B3, D4 and D8 taken between 2011 and 2017 in the UK and Romania. A mathematical model incorporating time, possible shared ancestry and the Poisson distribution describing the number of expected substitutions at a given time point was developed to exclude epidemiological relatedness between pairs of sequences. The model was validated against the commonly used Bayesian phylogenetic method using an independent dataset collected in 2017–19. Findings We demonstrate that our model, using time and sequence information to predict whether two samples may be related within a given time frame, minimises the risk of erroneous exclusion of relatedness. An easy-to-use implementation in the form of a guide and spreadsheet is provided for convenient application. Interpretation The proposed model only requires a previously calculated substitution rate for the locus and pathogen of interest. It allows for an informed but quick decision on the likelihood of relatedness between two samples within a time frame, without the need for phylogenetic reconstruction, thus facilitating rapid epidemiological interpretation of sequence data. Funding This work was funded by the United Kingdom Health Security Agency (UKHSA). The World Health Organization European Regional Office funded Aurora Fernández-García and Mihaela Lazar training visits to UKHSA.
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17
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Shaskolskiy B, Kravtsov D, Kandinov I, Gorshkova S, Kubanov A, Solomka V, Deryabin D, Dementieva E, Gryadunov D. Comparative Whole-Genome Analysis of Neisseria gonorrhoeae Isolates Revealed Changes in the Gonococcal Genetic Island and Specific Genes as a Link to Antimicrobial Resistance. Front Cell Infect Microbiol 2022; 12:831336. [PMID: 35252037 PMCID: PMC8895040 DOI: 10.3389/fcimb.2022.831336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 12/24/2022] Open
Abstract
Comparative whole-genome analysis was performed for Neisseria gonorrhoeae isolates belonging to the Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) types predominant worldwide — 225, 1407, 2400, 2992, and 4186 — and to genogroup 807, the most common genogroup in the Russian Federation. Here, for the first time, the complete genomes of 25 N. gonorrhoeae isolates from genogroup 807 were obtained. For NG-MAST types 225, 1407, 2400, 2992, and 4186, genomes from the Pathogenwatch database were used. The phylogenetic network constructed for 150 genomes showed that the clustering according to NG-MAST type corresponded to the clustering according to genome. Comparisons of genomes of the six sequence types revealed 8-20 genes specific to each sequence type, including the loci for phase variations and genetic components of the gonococcal genetic island (GGI). NG-MAST type 2992 and 4186 isolates either lacked the GGI or carried critical mutations in genes essential for DNA secretion. In all analyzed genogroup 807 isolates, substitution of the essential atlA gene with the eppA gene was found, accompanied by a change in the traG allele, replacement of the ych gene with ych1, and the absence of the exp1 gene, which is likely to result in loss of GGI functionality. For the NG-MAST type 225, 1407 and 2400 isolates, no premature stop codons or reading frameshifts were found in the genes essential for GGI function. A relationship between isolate susceptibility to ciprofloxacin, penicillin, tetracycline and the presence of lesions in GGI genes necessary for DNA secretion was established. The N. gonorrhoeae evolutionary pathways, which allow a particular sequence type to maintain long-term predominance in the population, may include changes in genes responsible for adhesion and virulence, changes in the GGI structure, preservation of genes carrying drug resistance determinants, and changes in genes associated with host adaptation or encoding enzymes of biochemical pathways.
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Affiliation(s)
- Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Boris Shaskolskiy,
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sofya Gorshkova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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18
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Eyre DW. Infection prevention and control insights from a decade of pathogen whole-genome sequencing. J Hosp Infect 2022; 122:180-186. [PMID: 35157991 PMCID: PMC8837474 DOI: 10.1016/j.jhin.2022.01.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
Pathogen whole-genome sequencing has become an important tool for understanding the transmission and epidemiology of infectious diseases. It has improved our understanding of sources of infection and transmission routes for important healthcare-associated pathogens, including Clostridioides difficile and Staphylococcus aureus. Transmission from known infected or colonized patients in hospitals may explain fewer cases than previously thought and multiple introductions of these pathogens from the community may play a greater a role. The findings have had important implications for infection prevention and control. Sequencing has identified heterogeneity within pathogen species, with some subtypes transmitting and persisting in hospitals better than others. It has identified sources of infection in healthcare-associated outbreaks of food-borne pathogens, Candida auris and Mycobacterium chimera, as well as individuals or groups involved in transmission and historical sources of infection. SARS-CoV-2 sequencing has been central to tracking variants during the COVID-19 pandemic and has helped understand transmission to and from patients and healthcare workers despite prevention efforts. Metagenomic sequencing is an emerging technology for culture-independent diagnosis of infection and antimicrobial resistance. In future, sequencing is likely to become more accessible and widely available. Real-time use in hospitals may allow infection prevention and control teams to identify transmission and to target interventions. It may also provide surveillance and infection control benchmarking. Attention to ethical and wellbeing issues arising from sequencing identifying individuals involved in transmission is important. Pathogen whole-genome sequencing has provided an incredible new lens to understand the epidemiology of healthcare-associated infection and to better control and prevent these infections.
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Affiliation(s)
- D W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK; National Institiute for Health Research, Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK; Oxford University Hospitals, Oxford, UK.
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19
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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.
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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
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Vickram A, Dhama K, Thanigaivel S, Chakraborty S, Anbarasu K, Dey N, Karunakaran R. Strategies for successful designing of immunocontraceptive vaccines and recent updates in vaccine development against sexually transmitted infections - A Review. Saudi J Biol Sci 2022; 29:2033-2046. [PMID: 35531220 PMCID: PMC9073025 DOI: 10.1016/j.sjbs.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 11/28/2022] Open
Abstract
Background Objective Methods Results Conclusion
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Affiliation(s)
- A.S. Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Tamil Nadu, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - S. Thanigaivel
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Tamil Nadu, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences &, Animal Husbandry, R.K.Nagar, West Tripura, Pin- 799008, India
| | - K. Anbarasu
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Tamil Nadu, India
| | - Nibedita Dey
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Tamil Nadu, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling, Bedong, Kedah, Malaysia
- Corresponding author.
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21
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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22
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Town K, Learner ER, Chivukula VL, Mauk K, Reimche JL, Schmerer MW, Black J, Pathela P, Bhattacharyya S, Kerani RP, Gieseker KE, Fukuda A, Sankaran M, McNeil CJ, Spicknall IH, Raphael BH, St Cyr SB, Bernstein K, Kersh EN, Kirkcaldy RD, Schlanger K, Gernert KM. Exploring and Comparing the Structure of Sexual Networks Affected by Neisseria gonorrhoeae Using Sexual Partner Services Investigation and Genomic Data. Sex Transm Dis 2021; 48:S131-S136. [PMID: 34310528 DOI: 10.1097/olq.0000000000001520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Sexual networks are difficult to construct because of incomplete sexual partner data. The proximity of people within a network may be inferred from genetically similar infections. We explored genomic data combined with partner services investigation (PSI) data to extend our understanding of sexual networks affected by Neisseria gonorrhoeae (NG). METHODS We used 2017-2019 PSI and whole-genome sequencing (WGS) data from 8 jurisdictions participating in Centers for Disease Control and Prevention's Strengthening the US Response to Resistant Gonorrhea (SURRG) project. Clusters were identified from sexual contacts and through genetically similar NG isolates. Sexual mixing patterns were characterized by describing the clusters by the individual's gender and gender of their sex partners. RESULTS Our study included 4627 diagnoses of NG infection (81% sequenced), 2455 people received a PSI, 393 people were negative contacts of cases, and 495 were contacts with an unknown NG status. We identified 823 distinct clusters using PSI data combined with WGS data. Of cases that were not linked to any other case using PSI data, 37% were linked when using WGS data. Overall, 40% of PSI cases were allocated to a larger cluster when PSI and WGS data were combined compared with PSI data alone. Mixed clusters containing women, men who report sex with women, and men who report sex with men were common when using the WGS data either alone or in combination with the PSI data. CONCLUSIONS Combining PSI and WGS data improves our understanding of sexual network connectivity.
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Affiliation(s)
- Katy Town
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Emily R Learner
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Kerry Mauk
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Matthew W Schmerer
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Jamie Black
- Division of HIV/STD/Viral Hepatitis, Indiana Department of Health, Indianapolis, IN
| | - Preeti Pathela
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, Queens, NY
| | | | | | - Karen E Gieseker
- Colorado Department of Public Health and Environment, Denver, CO
| | | | | | - Candice J McNeil
- Department of Health, Wake Forest University School of Medicine/Guilford County, NC
| | - Ian H Spicknall
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Brian H Raphael
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Sancta B St Cyr
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kyle Bernstein
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ellen N Kersh
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Robert D Kirkcaldy
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Karen Schlanger
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kim M Gernert
- From the Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA
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Cherdtrakulkiat T, Wongsurawat T, Jenjaroenpun P, Sutheeworapong S, Leelawiwat W, Woodring JV, Dunne EF, Papp JR, Srifuengfung S, Tribuddharat C. Complete Genome Sequence of Neisseria gonorrhoeae Multilocus Sequence Type ST7363 Isolated from Thailand. Microbiol Resour Announc 2021; 10:e0057321. [PMID: 34647806 PMCID: PMC8515890 DOI: 10.1128/mra.00573-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
A Neisseria gonorrhoeae multilocus sequence type (MLST) ST7363 strain was isolated from a patient at the Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand, in 2010 and completely sequenced. This strain is susceptible to ceftriaxone and cefixime. A complete circular chromosome and circular plasmids were assembled from combined Oxford Nanopore Technologies (ONT) and Illumina sequencing.
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Affiliation(s)
- Thitima Cherdtrakulkiat
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
- Molecular Medicine Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Sawannee Sutheeworapong
- Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Wanna Leelawiwat
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Joseph V. Woodring
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Eileen F. Dunne
- Division of HIV/AIDS Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Thailand Ministry of Public Health-U.S. Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - John R. Papp
- Division of Sexually Transmitted Disease Prevention, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Chanwit Tribuddharat
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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24
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Kong LY, Wilson JD, Moura IB, Fawley W, Kelly L, Walker AS, Eyre DW, Wilcox MH. Utility of Whole Genome Sequencing in Assessing and Enhancing Partner Notification of Neisseria gonorrhoeae Infection. Sex Transm Dis 2021; 48:773-780. [PMID: 34110743 DOI: 10.1097/olq.0000000000001419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Gonorrhea is a sexually transmitted infection of global concern. We investigated whole-genome sequencing (WGS) as a tool to measure and enhance partner notification (PN) in gonorrhea management. METHODS Between May and November 2018, all N. gonorrhoeae isolated from patients attending Leeds Sexual Health, United Kingdom, underwent WGS. Reports listing sequences within 20 single-nucleotide polymorphisms (SNPs) of study isolates within a database containing select isolates from April 1, 2016, to November 15, 2018, were issued to clinicians. The proportion of cases with a potential transmission partner identified by PN was determined from patient and PN data. The WGS reports were reviewed to identify additional cases within 6 SNPs or less and verified for PN concordance. RESULTS Three hundred eighty isolates from 377 cases were successfully sequenced; 292 had traceable/contactable partners and 69 (18%) had a potential transmission partner identified by PN. Concordant PN and WGS links were identified in 47 partner pairs. Of 308 cases with no transmission partner by PN, 185 (60%) had a case within 6 SNPs or less; examination of these cases' PN data identified 7 partner pairs with previously unrecognized PN link, giving a total of 54 pairs; all had 4 or less SNP differences. The WGS clusters confirmed gaps in partner finding, at individual and group levels. Despite the clinic providing sexual health services to the whole city, 35 cases with multiple partners had no genetically related case, suggesting multiple undiagnosed infections. CONCLUSIONS Whole-genome sequencing could improve gonorrhea PN and control by identifying new links and clusters with significant gaps in partner finding.
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Affiliation(s)
| | | | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds
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25
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Gianecini RA, Poklepovich T, Golparian D, Cuenca N, Tuduri E, Unemo M, Campos J, Galarza P. Genomic Epidemiology of Azithromycin-Nonsusceptible Neisseria gonorrhoeae, Argentina, 2005-2019. Emerg Infect Dis 2021; 27:2369-2378. [PMID: 34424175 PMCID: PMC8386799 DOI: 10.3201/eid2709.204843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Azithromycin-nonsusceptible Neisseria gonorrhoeae strains are an emerging global public health threat. During 2015–2018, the prevalence of azithromycin-nonsusceptible gonococcal infection increased significantly in Argentina. To investigate the genomic epidemiology and resistance mechanisms of these strains, we sequenced 96 nonsusceptible isolates collected in Argentina during 2005–2019. Phylogenomic analysis revealed 2 main clades, which were characterized by a limited geographic distribution, circulating during January 2015–November 2019. These clades included the internationally spreading multilocus sequence types (STs) 1580 and 9363. The ST1580 isolates, which had MICs of 2–4 μg/mL, had mutations in the 23S rRNA. The ST9363 isolates, which had MICs of 2–4 or >256 μg/mL, had mutations in the 23S rRNA, a mosaic mtr locus, or both. Identifying the geographic dissemination and characteristics of these predominant clones will guide public health policies to control the spread of azithromycin-nonsusceptible N. gonorrhoeae in Argentina.
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26
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Moloney G, Eyre DW, Mac Aogáin M, McElroy MC, Vaughan A, Peto TE, Crook DW, Rogers TR. Human and Porcine Transmission of Clostridioides difficile Ribotype 078, Europe. Emerg Infect Dis 2021; 27:2294-2300. [PMID: 34423760 PMCID: PMC8386809 DOI: 10.3201/eid2709.203468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genomic analysis of a diverse collection of Clostridioides difficile ribotype 078 isolates from Ireland and 9 countries in Europe provided evidence for complex regional and international patterns of dissemination that are not restricted to humans. These isolates are associated with C. difficile colonization and clinical illness in humans and pigs.
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27
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van der Veer BMJW, Wolffs PFG, Hoebe CJPA, Wijers JNAP, van Liere GAFS, Werner MILS, Verhaegh A, Dukers-Muijrers NHTM, van Alphen LB. Culture-Independent Genotyping Revealed 3 Strain Clusters in a Potential Neisseria gonorrhoeae Outbreak in Young Heterosexuals (<25 Years), the Netherlands, October 2017 to March 2019. Sex Transm Dis 2021; 48:536-541. [PMID: 34110758 DOI: 10.1097/olq.0000000000001370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Investigation was undertaken to determine the genetic relatedness of Neisseria gonorrhoeae (NG) isolates of young (<25 years) heterosexuals of a potential outbreak from October 2017 to March 2019 in South-Limburg, the Netherlands. METHODS Data and residual sample material of routine diagnostics were retrieved for outbreak cases (78/81), young heterosexuals at baseline (January 2016 to September 2017, n = 30), and men who have sex with men (2018, n = 47). Total DNA was isolated, and NG was genotyped using culture-free NG multiantigen sequence typing. Sanger sequence data were used to construct a phylogenetic tree. Cases of outbreak clusters were geographically mapped, and descriptive analyses were performed on patient characteristics, comparing these clusters. RESULTS Outbreak investigation showed 81 cases of young heterosexuals between October 2017 and March 2019 (4.5 per month) compared with 30 between January 2016 and September 2017 (1.4 per month), which was considered as baseline. Culture-independent genotyping of NG was performed to assess the genetic relatedness, as only 21 outbreak cases were culture confirmed. This revealed 3 independent outbreak clusters G2 (n = 18), G13113 (n = 11), and GNewST (n = 24). None of the clusters were geographically linked or introduced by bridging with men who have sex with men networks. Number of sex partners reported by men and Chlamydia trachomatis coinfection were associated with clusters G2 and GNewST, respectively. CONCLUSIONS Culture-independent typing proved to be essential to identify the 3 outbreak clusters. However, targeted interventions were difficult because information on sex partners was limited. Therefore, prospective culture-independent typing could be used for early outbreak detection and aid in transmission prevention.
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Affiliation(s)
- Brian M J W van der Veer
- From the Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht
| | - Petra F G Wolffs
- From the Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht
| | | | | | | | - Marita I L S Werner
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen
| | - Amanja Verhaegh
- Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen
| | | | - Lieke B van Alphen
- From the Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht
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DNA-nanopore technology: a human perspective. Emerg Top Life Sci 2021; 5:455-463. [PMID: 34282838 DOI: 10.1042/etls20200282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/17/2022]
Abstract
The purpose of this article is to give a brief overview of the current state of nanopore sequencing in relation to forensic science with a brief outline of where it stands in relation to current methods, its potential uses in forensic science and factors which may influence acceptance of this technology by forensic practitioners, the judiciary and law enforcement. Perhaps most importantly consideration is also given to concerns which may influence the acceptance of the technology by the general public.
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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.
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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
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30
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Golparian D, Bazzo ML, Golfetto L, Gaspar PC, Schörner MA, Schwartz Benzaken A, Ramos MC, Ferreira WA, Alonso Neto JB, Mendes Pereira GF, Unemo M. Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16. J Antimicrob Chemother 2021; 75:3163-3172. [PMID: 32785692 DOI: 10.1093/jac/dkaa318] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/22/2020] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is imperative internationally, but only eight (22.9%) countries in the WHO Region of the Americas reported complete AMR data to the WHO Global Gonococcal Antimicrobial Surveillance Program (WHO GASP) in 2016. Genomic studies are ideal for enhanced understanding of gonococcal populations, including the spread of AMR strains. To elucidate the circulating gonococcal lineages/sublineages, including their AMR determinants, and the baseline genomic diversity among gonococcal strains in Brazil, we conducted WGS on 548 isolates obtained in 2015-16 across all five macroregions in Brazil. METHODS A total of 548 gonococcal isolates cultured across Brazil in 2015-16 were genome sequenced. AMR was determined using agar dilution and/or Etest. Genome sequences of isolates from Argentina (n = 158) and the 2016 WHO reference strains (n = 14) were included in the analysis. RESULTS We found 302, 68 and 214 different NG-MAST, MLST and NG-STAR STs, respectively. The phylogenomic analysis identified one main antimicrobial-susceptible lineage and one AMR lineage, which was divided into two sublineages with different AMR profiles. Determination of NG-STAR networks of clonal complexes was shown as a new and valuable molecular epidemiological analysis. Several novel mosaic mtrD (and mtrR and mtrE) variants associated with azithromycin resistance were identified. CONCLUSIONS We describe the first genomic baseline data to support the Brazilian GASP. The high prevalence of resistance to ciprofloxacin, tetracycline and benzylpenicillin, and the high number of isolates with mosaic penA and azithromycin resistance mutations, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Brazil.
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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, Örebro, Sweden
| | - Maria Luiza Bazzo
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Lisléia Golfetto
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Pamela Cristina Gaspar
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, Brazil
| | - Marcos André Schörner
- Molecular Biology, Microbiology and Serology Laboratory, Federal University of Santa Catarina, Florianópolis, Brazil
| | | | | | | | - José Boullosa Alonso Neto
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, Brazil
| | - Gerson Fernando Mendes Pereira
- Department of Diseases of Chronic Condition and Sexually Transmitted Infection, Secretariat of Health Surveillance, 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, Örebro, Sweden
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Xiu L, Yuan Q, Li Y, Zhang C, Tang L, Peng J. Emergence of ceftriaxone-resistant Neisseria gonorrhoeae strains harbouring a novel mosaic penA gene in China. J Antimicrob Chemother 2021; 75:907-910. [PMID: 31899504 DOI: 10.1093/jac/dkz530] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The continuous emergence of ceftriaxone-resistant Neisseria gonorrhoeae strains threatens the effectiveness of current treatment regimens for gonorrhoea. The objective of the present study was to characterize three ceftriaxone-resistant N. gonorrhoeae strains with a novel mosaic penA allele isolated in China. METHODS Three ceftriaxone-resistant Neisseria gonorrhoeae strains (GC150, GC161 and GC208) isolated in 2017 were characterized by N. gonorrhoeae multiantigen sequence typing (NG-MAST), MLST and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR). Recombination analyses were performed using the SimPlot software. RESULTS Three strains had the same antibiotic resistance profiles, with resistance to ceftriaxone (MIC 0.5 mg/L), ciprofloxacin (MIC 8.0 mg/L), penicillin (MIC 2.0 mg/L) and tetracycline (MIC 2.0-8.0 mg/L). STs were assigned as MLST7360, NG-MAST14292 and NG-STAR1611/NG-STAR1612. The penA gene of these three strains differed from previous ceftriaxone-resistant gonococcal strains and harboured a novel mosaic allele (penA-121.001). Like N. gonorrhoeae FC428, a widely disseminated ceftriaxone-resistant strain that was initially described in Japan in 2015, all strains also possessed substitutions A311V and T483S in PBP2, which are associated with resistance to ceftriaxone. Potential recombination events were detected in penA between N. gonorrhoeae strain FC428 and commensal Neisseria species. Our results provide further evidence that the commensal Neisseria species (Neisseria cinerea and Neisseria perflava) can serve as a reservoir of ceftriaxone resistance-mediating penA sequences in clinical gonococcal strains. CONCLUSIONS The emergence of such strains may be the result of the interspecies recombination of penA genes between N. gonorrhoeae strain FC428 and commensal Neisseria species.
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Affiliation(s)
- Leshan Xiu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qianqin Yuan
- Department of Laboratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yamei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lingli Tang
- Department of Laboratory Medicine, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Lan PT, Golparian D, Ringlander J, Van Hung L, Van Thuong N, Unemo M. Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16. J Antimicrob Chemother 2021; 75:1432-1438. [PMID: 32068837 PMCID: PMC7382555 DOI: 10.1093/jac/dkaa040] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/13/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Antimicrobial resistance (AMR) in Neisseria gonorrhoeae, compromising gonorrhoea treatment, is a threat to reproductive health globally. South-East and East Asia have been major sources of emergence and subsequent international spread of AMR gonococcal strains during recent decades. We investigated gonococcal isolates from 2011 and 2015-16 in Vietnam using AMR testing, WGS and detection of AMR determinants. METHODS Two hundred and twenty-nine gonococcal isolates cultured in 2015-16 (n = 121) and 2011 (n = 108) in Vietnam were examined. AMR testing was performed using Etest and WGS with Illumina MiSeq. RESULTS Resistance among the 2015-16 isolates was as follows: ciprofloxacin, 100%; tetracycline, 79%; benzylpenicillin, 50%; cefixime, 15%; ceftriaxone, 1%; spectinomycin, 0%; and 5% were non-WT to azithromycin. Eighteen (15%) isolates were MDR. The MIC range for gentamicin was 2-8 mg/L. Among the 2015-16 isolates, 27% (n = 33) contained a mosaic penA allele, while no isolates had a mosaic penA allele in 2011. Phylogenomic analysis revealed introduction after 2011 of two mosaic penA-containing clones (penA-10.001 and penA-34.001), which were related to cefixime-resistant strains spreading in Japan and Europe, and a minor clade (eight isolates) relatively similar to the XDR strain WHO Q. CONCLUSIONS From 2011 to 2015-16, resistance in gonococci from Vietnam increased to all currently and previously used antimicrobials except ceftriaxone, spectinomycin and tetracycline. Two mosaic penA-containing clones were introduced after 2011, explaining the increased cefixime resistance. Significantly increased AMR surveillance, antimicrobial stewardship and use of WGS for molecular epidemiology and AMR prediction for gonococcal isolates in Vietnam and other Asian countries are crucial.
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Affiliation(s)
- Pham Thi Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Swedish Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Johan Ringlander
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Swedish Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Infectious Diseases at Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Le Van Hung
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Nguyen Van Thuong
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Swedish Reference Laboratory for STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Thomas JC, Joseph SJ, Cartee JC, Pham CD, Schmerer MW, Schlanger K, St Cyr SB, Kersh EN, Raphael BH. Phylogenomic analysis reveals persistence of gonococcal strains with reduced-susceptibility to extended-spectrum cephalosporins and mosaic penA-34. Nat Commun 2021; 12:3801. [PMID: 34155204 PMCID: PMC8217231 DOI: 10.1038/s41467-021-24072-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/28/2021] [Indexed: 12/03/2022] Open
Abstract
The recent emergence of strains of Neisseria gonorrhoeae associated with treatment failures to ceftriaxone, the foundation of current treatment options, has raised concerns over a future of untreatable gonorrhea. Current global data on gonococcal strains suggest that several lineages, predominately characterized by mosaic penA alleles, are associated with elevated minimum inhibitory concentrations (MICs) to extended spectrum cephalosporins (ESCs). Here we report on whole genome sequences of 813 N. gonorrhoeae isolates collected through the Gonococcal Isolate Surveillance Project in the United States. Phylogenomic analysis revealed that one persisting lineage (Clade A, multi-locus sequence type [MLST] ST1901) with mosaic penA-34 alleles, contained the majority of isolates with elevated MICs to ESCs. We provide evidence that an ancestor to the globally circulating MLST ST1901 clones potentially emerged around the early to mid-20th century (1944, credibility intervals [CI]: 1935-1953), predating the introduction of cephalosporins, but coinciding with the use of penicillin. Such results indicate that drugs with novel mechanisms of action are needed as these strains continue to persist and disseminate globally.
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Affiliation(s)
- Jesse C Thomas
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Sandeep J Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John C Cartee
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cau D Pham
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew W Schmerer
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Karen Schlanger
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sancta B St Cyr
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellen N Kersh
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Raphael
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Manoharan-Basil SS, Laumen JGE, Van Dijck C, De Block T, De Baetselier I, Kenyon C. Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae. Front Microbiol 2021; 12:683901. [PMID: 34177869 PMCID: PMC8222677 DOI: 10.3389/fmicb.2021.683901] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.
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Affiliation(s)
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Tessa De Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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35
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Sánchez-Busó L, Yeats CA, Taylor B, Goater RJ, Underwood A, Abudahab K, Argimón S, Ma KC, Mortimer TD, Golparian D, Cole MJ, Grad YH, Martin I, Raphael BH, Shafer WM, Town K, Wi T, Harris SR, Unemo M, Aanensen DM. A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch. Genome Med 2021; 13:61. [PMID: 33875000 PMCID: PMC8054416 DOI: 10.1186/s13073-021-00858-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance. METHODS Here we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch ( https://pathogen.watch/ngonorrhoeae ). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization. RESULTS AMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern. CONCLUSIONS The N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.
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Affiliation(s)
- Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain.
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Benjamin Taylor
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Richard J Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
- European Molecular Biology Lab, Heidelberg, Baden-Wuerttemberg, Germany
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Daniel Golparian
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Brian H Raphael
- Division of STD prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - William M Shafer
- Department of Microbiology and Immunology and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
- Laboratories of Bacterial Pathogenesis, Veterans Affairs Medical Center, Decatur, GA, USA
| | - Katy Town
- Division of STD prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, World Health Organization, Geneva, Switzerland
| | - Simon R Harris
- Microbiotica, Biodata Innovation Centre, Cambridge, Cambridgeshire, UK
| | - Magnus Unemo
- World Health Organization Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Cambridgeshire, UK.
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Abstract
We report a multidrug-resistant Neisseria gonorrhoeae exhibiting resistance to ceftriaxone and cefixime, isolated in Portugal in 2019. Whole-genome sequencing was performed for typing and identification of genetic determinants of antimicrobial resistance. Because of its antimicrobial susceptibility profile, awareness should be raised for the circulation of this strain.
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37
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Town K, Harris S, Sánchez-Busó L, Cole MJ, Pitt R, Fifer H, Mohammed H, Field N, Hughes G. Genomic and Phenotypic Variability in Neisseria gonorrhoeae Antimicrobial Susceptibility, England. Emerg Infect Dis 2021; 26:505-515. [PMID: 32091356 PMCID: PMC7045833 DOI: 10.3201/eid2603.190732] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global concern. Phylogenetic analyses resolve uncertainties regarding genetic relatedness of isolates with identical phenotypes and inform whether AMR is due to new mutations and clonal expansion or separate introductions by importation. We sequenced 1,277 isolates with associated epidemiologic and antimicrobial susceptibility data collected during 2013–2016 to investigate N. gonorrhoeae genomic variability in England. Comparing genetic markers and phenotypes for AMR, we identified 2 N. gonorrhoeae lineages with different antimicrobial susceptibility profiles and 3 clusters with elevated MICs for ceftriaxone, varying mutations in the penA allele, and different epidemiologic characteristics. Our results indicate N. gonorrhoeae with reduced antimicrobial susceptibility emerged independently and multiple times in different sexual networks in England, through new mutation or recombination events and by importation. Monitoring and control for AMR in N. gonorrhoeae should cover the entire population affected, rather than focusing on specific risk groups or locations.
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38
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Vegvari C, Grad YH, White PJ, Didelot X, Whittles LK, Scangarella-Oman NE, Mitrani-Gold FS, Dumont E, Perry CR, Gilchrist K, Hossain M, Mortimer TD, Anderson RM, Gardiner D. Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea. ACTA ACUST UNITED AC 2021; 25. [PMID: 33124551 PMCID: PMC7596916 DOI: 10.2807/1560-7917.es.2020.25.43.1900210] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Background The first cases of extensively drug resistant gonorrhoea were recorded in the United Kingdom in 2018. There is a public health need for strategies on how to deploy existing and novel antibiotics to minimise the risk of resistance development. As rapid point-of-care tests (POCTs) to predict susceptibility are coming to clinical use, coupling the introduction of an antibiotic with diagnostics that can slow resistance emergence may offer a novel paradigm for maximising antibiotic benefits. Gepotidacin is a novel antibiotic with known resistance and resistance-predisposing mutations. In particular, a mutation that confers resistance to ciprofloxacin acts as the ‘stepping-stone’ mutation to gepotidacin resistance. Aim To investigate how POCTs detecting Neisseria gonorrhoeae resistance mutations for ciprofloxacin and gepotidacin can be used to minimise the risk of resistance development to gepotidacin. Methods We use individual-based stochastic simulations to formally investigate the aim. Results The level of testing needed to reduce the risk of resistance development depends on the mutation rate under treatment and the prevalence of stepping-stone mutations. A POCT is most effective if the mutation rate under antibiotic treatment is no more than two orders of magnitude above the mutation rate without treatment and the prevalence of stepping-stone mutations is 1–13%. Conclusion Mutation frequencies and rates should be considered when estimating the POCT usage required to reduce the risk of resistance development in a given population. Molecular POCTs for resistance mutations and stepping-stone mutations to resistance are likely to become important tools in antibiotic stewardship.
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Affiliation(s)
- Carolin Vegvari
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Yonatan H Grad
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Peter J White
- Modelling and Economics Unit, National Infection Service, Public Health England, London, United Kingdom.,MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Xavier Didelot
- Current affiliation: School of Life Sciences and Department of Statistics, University of Warwick, United Kingdom.,MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Lilith K Whittles
- MRC Centre for Global Infectious Disease Analysis and NIHR Health Protection Research Unit in Modelling and Health Economics, School of Public Health, Imperial College London, London, United Kingdom.,Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | | | | | - Etienne Dumont
- GlaxoSmithKline, Collegeville, Pennsylvania, United States
| | | | - Kim Gilchrist
- Current affiliation: Pfizer, Inc, Pennsylvania, United States.,GlaxoSmithKline, Collegeville, Pennsylvania, United States
| | | | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - David Gardiner
- GlaxoSmithKline, Collegeville, Pennsylvania, United States
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Holderman JL, Thomas JC, Schlanger K, Black JM, Town K, St. Cyr SB, Pham CD, Kirkcaldy RD. Sustained Transmission of Neisseria gonorrhoeae with High-Level Resistance to Azithromycin, in Indianapolis, Indiana, 2017–2018. Clin Infect Dis 2021; 73:808-815. [PMID: 34492693 PMCID: PMC10183473 DOI: 10.1093/cid/ciab132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/11/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Since 2014, Neisseria gonorrhoeae azithromycin (AZM) susceptibility has declined in the United States, but high-level AZM resistance (HL-AZMR) has been infrequent and sporadic. We describe a cluster of 14 N. gonorrhoeae isolates with HL-AZMR identified in Indianapolis over 13 months.
Methods
N. gonorrhoeae culture specimens (genital and extragenital) were collected from attendees of the Bell Flower Clinic. Isolates underwent antimicrobial susceptibility testing (AST) using Etest. AZM minimum inhibitory concentrations ≥256 µg/mL were classified as HL-AZMR. Local disease intervention specialists interviewed patients whose isolates demonstrated HL-AZMR and conducted partner services. Relatedness of isolates was investigated by genomic analyses.
Results
During 2017–2018, AST was performed in 1016 N. gonorrhoeae isolates collected at the Bell Flower Clinic. Fourteen isolates (1.4%) from 12 men collected over 13 months demonstrated HL-AZMR; all were cephalosporin susceptible. Of the 12 men, 9 were white and reported male sex partners. Nine of the men were able to be retested; all were cured with 250-mg ceftriaxone plus 1-g AZM. Two men named each other as partners; no other partners in common were reported. Genomic analysis demonstrated close relatedness of the HL-AZMR isolates and a novel combination of a mosaic-mtrR promoter along with 23S ribosomal RNA mutations that appear to have emerged from circulating strains.
Conclusions
The close genetic relatedness with limited epidemiologic linkages between patients highlights the challenges of gonorrhea partner investigations and suggests undetected local transmission. Local AST, rapid public health action, and epidemiologic investigations combined with genomic analysis provides a multipronged approach to understanding an outbreak of sexually transmitted disease.
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Affiliation(s)
- Justin L Holderman
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Division of HIV, STD, and Viral Hepatitis Prevention, Indiana Department of Health, Indianapolis, Indiana, USA
| | - Jesse C Thomas
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen Schlanger
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jamie M Black
- Division of HIV, STD, and Viral Hepatitis Prevention, Indiana Department of Health, Indianapolis, Indiana, USA
| | - Katy Town
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sancta B St. Cyr
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cau D Pham
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert D Kirkcaldy
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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40
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Pinto M, Borges V, Isidro J, Rodrigues JC, Vieira L, Borrego MJ, Gomes JP. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microb Genom 2021; 7:000481. [PMID: 33245688 PMCID: PMC8208699 DOI: 10.1099/mgen.0.000481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.
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Affiliation(s)
- Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Carlos Rodrigues
- Laboratory of Microbiology, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculty of Medical Sciences, New University of Lisbon, Lisbon, Portugal
| | - Maria José Borrego
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
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Eyre DW, Laager M, Walker AS, Cooper BS, Wilson DJ. Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. PLoS Comput Biol 2021; 17:e1008417. [PMID: 33444378 PMCID: PMC7840057 DOI: 10.1371/journal.pcbi.1008417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 01/27/2021] [Accepted: 10/05/2020] [Indexed: 12/28/2022] Open
Abstract
Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007-2011. 262 (21% [95% credibility interval 20-22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.
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Affiliation(s)
- David W. Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, United Kingdom
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, United Kingdom
| | - Mirjam Laager
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, United Kingdom
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, United Kingdom
| | - Ben S. Cooper
- Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, United Kingdom
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Osnes MN, Didelot X, de Korne-Elenbaas J, Alfsnes K, Brynildsrud OB, Syversen G, Nilsen ØJ, De Blasio BF, Caugant DA, Eldholm V. Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway. Microb Genom 2020; 6:mgen000480. [PMID: 33200978 PMCID: PMC8116678 DOI: 10.1099/mgen.0.000480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/02/2020] [Indexed: 01/01/2023] Open
Abstract
Neisseria gonorrhoeae multilocus sequence type (ST)-7827 emerged in a dramatic fashion in Norway in the period 2016-2018. Here, we aim to shed light on the provenance and expansion of this ST. ST-7827 was found to be polyphyletic, but the majority of members belonged to a monophyletic clade we termed PopPUNK cluster 7827 (PC-7827). In Norway, both PC-7827 and ST-7827 isolates were almost exclusively isolated from men. Phylogeographical analyses demonstrated an Asian origin of the genogroup, with multiple inferred exports to Europe and the USA. The genogroup was uniformly resistant to fluoroquinolones, and associated with reduced susceptibility to both azithromycin and the extended-spectrum cephalosporins (ESCs) cefixime and ceftriaxone. From a genetic background including the penA allele 13.001, associated with reduced ESC susceptibility, we identified repeated events of acquisition of porB alleles associated with further reduction in ceftriaxone susceptibility. Transmission of the strain was significantly reduced in Norway in 2019, but our results indicate the existence of a recently established global reservoir. The worrisome drug-resistance profile and rapid emergence of PC-7827 calls for close monitoring of the situation.
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Affiliation(s)
- Magnus N. Osnes
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | | | - Kristian Alfsnes
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ola B. Brynildsrud
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Gaute Syversen
- Department of Microbiology, Oslo University Hospital Ullevål, Oslo, Norway
| | - Øivind Jul Nilsen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Birgitte Freiesleben De Blasio
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Dominique A. Caugant
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- AMR Centre, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- AMR Centre, Norwegian Institute of Public Health, Oslo, Norway
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Harrison OB, Cehovin A, Skett J, Jolley KA, Massari P, Genco CA, Tang CM, Maiden MCJ. Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance. J Infect Dis 2020; 222:1816-1825. [PMID: 32163580 PMCID: PMC7653085 DOI: 10.1093/infdis/jiaa002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. METHODS In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes. RESULTS A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups. CONCLUSIONS Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Ana Cehovin
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jessica Skett
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Paola Massari
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Caroline Attardo Genco
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christoph M Tang
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
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Cehovin A, Jolley KA, Maiden MCJ, Harrison OB, Tang CM. Association of Neisseria gonorrhoeae Plasmids With Distinct Lineages and The Economic Status of Their Country of Origin. J Infect Dis 2020; 222:1826-1836. [PMID: 32163577 PMCID: PMC7653084 DOI: 10.1093/infdis/jiaa003] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022] Open
Abstract
Plasmids are vehicles for horizontal gene transfer between bacteria, and in Neisseria gonorrhoeae plasmids can mediate high-level antimicrobial resistance (AMR). Using genomic and phylogenetic analyses, we show that plasmids are widespread in a collection of 3724 gonococcal isolates from 56 countries, and characterized the conjugative, β-lactamase and cryptic plasmids. We found that variants of the conjugative plasmid (which can mediate tetracycline resistance) and the β-lactamase plasmid expressing TEM-135 are associated with distinct gonococcal lineages. Furthermore, AMR plasmids are significantly more prevalent in gonococci from less wealthy countries, highlighting the need for further studies. More than 94% of gonococci possess the cryptic plasmid, with its absence correlated with the presence of a novel chromosomal type IV secretion system. Our results reveal the extent of plasmid-mediated AMR in the gonococcus, particularly in less wealthy countries, where diagnostic and therapeutic options can be limited, and highlight the risk of their global spread.
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Affiliation(s)
- Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Odile B Harrison
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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45
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Dong Y, Yang Y, Wang Y, Martin I, Demczuk W, Gu W. Shanghai Neisseria gonorrhoeae Isolates Exhibit Resistance to Extended-Spectrum Cephalosporins and Clonal Distribution. Front Microbiol 2020; 11:580399. [PMID: 33123111 PMCID: PMC7573285 DOI: 10.3389/fmicb.2020.580399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The emergence of Neisseria gonorrhoeae strains with resistance (R) to extended-spectrum cephalosporins (ESCsR) represents a public health threat of untreatable gonococcal infections. This study was designed to determine the prevalence and molecular mechanisms of ESCR of Shanghai N. gonorrhoeae isolates. A total of 366 N. gonorrhoeae isolates were collected in 2017 in Shanghai. Susceptibility to ceftriaxone (CRO), cefixime (CFM), azithromycin (AZM), ciprofloxacin (CIP), spectinomycin, penicillin, and tetracycline was determined using the agar dilution method. A subset of 124 isolates was subjected to phylogenetic analysis for nine antimicrobial resistance-associated genes, i.e., penA, porB, ponA, mtrR, 23S rRNA, gyrA, parC, 16S rRNA, and rpsE. Approximately 20.0% of the isolates exhibited CFMR [minimum inhibitory concentration (MIC) >0.125 mg/L], and 5.5% were CROR (MIC > 0.125 mg/L). In total, 72.7% of ESCR isolates were clonal and associated with mosaic penA 10 and 60 alleles. Non-mosaic penA 18 allele and substitutions of PenA A501T, G542S, and PorB1b G213S/Y were observed in non-clonal ESCR. Approximately 6.8% of the isolates showed AZM MIC above the epidemiological cutoff (ECOFF, 1 mg/L), were associated with 23S rRNA A2059G mutation, and did not exhibit clonal distribution. Almost all isolates were CIPR (resistance to ciprofloxacin) and associated with GyrA-91/92 and ParC-85/86/87/88/89/91 alterations. Isolates with ParC S88P substitution were clustered into the ESCR clade. The Shanghai isolates exhibited a high level of ESCR and distinct resistant patterns.
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Affiliation(s)
- Yuan Dong
- Shanghai Skin Disease Hospital, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yang Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Ying Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Walter Demczuk
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Weiming Gu
- Shanghai Skin Disease Hospital, Shanghai, China
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46
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Antimicrobial Resistance of Neisseria gonorrhoeae Isolates from High-Risk Men in Johannesburg, South Africa. Antimicrob Agents Chemother 2020; 64:AAC.00906-20. [PMID: 32868325 DOI: 10.1128/aac.00906-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022] Open
Abstract
Neisseria gonorrhoeae antimicrobial drug resistance has emerged worldwide; however, the situation in sub-Saharan Africa is not well documented. We investigated the molecular epidemiology and occurrence of antimicrobial resistance in Neisseria gonorrhoeae infections in two core transmission groups of men in Johannesburg, South Africa. We recruited men who have sex with men (MSM) presenting with urethral discharge and men with recurrent episodes of urethral discharge. Molecular testing and culture for N. gonorrhoeae were performed, followed by antimicrobial susceptibility testing. Whole-genome sequencing (WGS) was used to identify resistance-conferring mutations and to determine the genetic relatedness of the isolates. In all, 51 men were recruited; 42 (82%) had N. gonorrhoeae infections. Most gonococcal isolates were resistant to ciprofloxacin (78%) and tetracycline (74%); 33% were penicillin resistant. All gonococcal isolates were susceptible to cephalosporins and spectinomycin. Azithromycin resistance was observed in 4 (15%) isolates (epidemiological cutoff), all with mutations in the mtrR promoter region. Most of the isolates (19/27) harbored the gonococcal genetic island, which is associated with antimicrobial resistance. WGS revealed a diverse epidemic with mostly novel NG-STAR (70%) and NG-MAST (70%) sequence types. Thus, we demonstrate a high prevalence of antimicrobial resistance in Neisseria gonorrhoeae strains obtained from high-risk men in South Africa. The introduction of diagnostics and scale-up of surveillance are warranted to prevent the emergence of multidrug-resistant infections.
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47
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Buckley C, Beatson SA, Limnios A, Lahra MM, Whiley DM, Forde BM. Whole-genome sequencing as an improved means of investigating Neisseria gonorrhoeae treatment failures. Sex Health 2020; 16:500-507. [PMID: 31481151 DOI: 10.1071/sh19012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/22/2019] [Indexed: 11/23/2022]
Abstract
Background Although rare, Neisseria gonorrhoeae treatment failures associated with ceftriaxone have been reported. The World Health Organization (WHO) recommends standardised protocols to verify these cases. Two cases from Australia were previously investigated using N. gonorrhoeae multiantigen sequence typing (NG-MAST), which has been used extensively to assess treatment failures. Case 1 pharyngeal isolates were indistinguishable, whereas Case 2 pharyngeal isolates were distinguished based on an 18-bp deletion in the major outer membrane porin encoded by the porB gene, questioning the reliability of NG-MAST results. Here we used whole-genome sequencing (WGS) to reinvestigate Cases 1 and 2, with a view to examining WGS to assess treatment failures. METHODS Pre- and post-treatment isolates for each case underwent Illumina sequencing, and the two post-treatment isolates underwent additional long-read sequencing using Pacific Biosciences. Sequence data were interrogated to identify differences at single nucleotide resolution. RESULTS WGS identified variation in the pilin subunit encoded by the pilE locus for both cases and the specific 18-bp porB deletion in Case 2 was confirmed, but otherwise the isolates in each case were indistinguishable. CONCLUSIONS The WHO recommends standardised protocols for verifying N. gonorrhoeae treatment failures. Case 2 highlights the enhanced resolution of WGS over NG-MAST and emphasises the immediate effect that WGS can have in a direct clinical application for N. gonorrhoeae. Assessing the whole genome compared with two highly variable regions also provides a more confident predictor for determining treatment failure. Furthermore, WGS facilitates rapid comparisons of these cases in the future.
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Affiliation(s)
- Cameron Buckley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, Qld 4029, Australia
| | - Scott A Beatson
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld 4072, Australia; and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld 4072, Australia; and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Athena Limnios
- WHO Collaborating Centre for STI and AMR, Microbiology Department, New South Wales Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for STI and AMR, Microbiology Department, New South Wales Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia; and School of Medical Sciences, UNSW, Sydney, NSW 2052, Australia
| | - David M Whiley
- Faculty of Medicine, UQ Centre for Clinical Research, The University of Queensland, Herston, Qld 4029, Australia; and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld 4072, Australia; and Pathology Queensland, Microbiology Department, Herston, Qld 4029, Australia
| | - Brian M Forde
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Qld 4072, Australia; and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld 4072, Australia; and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld 4072, Australia; and Corresponding author:
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48
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Hanrahan JK, Hogan TR, Buckley C, Trembizki E, Mitchell H, Lau CL, Whiley DM, Lahra MM. Emergence and spread of ciprofloxacin-resistant Neisseria gonorrhoeae in New South Wales, Australia: lessons from history. J Antimicrob Chemother 2020; 74:2214-2219. [PMID: 31170281 DOI: 10.1093/jac/dkz182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/10/2019] [Accepted: 04/05/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES Our aim was to investigate the emergence and spread of ciprofloxacin resistance in clinical Neisseria gonorrhoeae isolates in New South Wales, Australia, from the first reported case in 1991 until ciprofloxacin resistance was sustained at or above the WHO threshold for treatment change of 5% (1999), to inform future strategies for controlling gonococcal antimicrobial resistance. METHODS The index isolate and all subsequent clinical isolates of ciprofloxacin-resistant N. gonorrhoeae in New South Wales from 1991 to 1999 were genotyped using a previously described method on the Agena MassARRAY iPLEX platform. Region of acquisition data, where available, were used to determine whether cases were travel associated. RESULTS In New South Wales, of the 325 ciprofloxacin-resistant N. gonorrhoeae isolates reported from 1991 to 1999, 98% (320/325) were able to be recovered and 100% (320/320) were genotyped. There were 66 different genotypes, comprising 1-99 isolates each. Notably no single clone was found to account for ciprofloxacin resistance being sustained in the population, with considerable variability in genotype prevalence observed throughout the study period. A total of 65% (209/320) of genotyped isolates had information regarding the likely place of acquisition; of these, 44% (93/209) were associated with overseas travel or sexual contact with an overseas visitor. The first ciprofloxacin-resistant N. gonorrhoeae in New South Wales was associated with travel to Thailand. Index cases of each resistant genotype were significantly more likely to have been acquired overseas (51.5%), predominantly in Asia (45%, 30/66). CONCLUSIONS The continued importation of multiple genotypes, rather than the expansion of a single genotype, led to ciprofloxacin-resistant N. gonorrhoeae being established in New South Wales.
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Affiliation(s)
- Jane K Hanrahan
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, NSWHP Microbiology, Prince of Wales Hospital, Sydney, New South Wales 2031, Australia.,School of Biotechnology and Biomolecular Science, The University of New South Wales, Sydney, New South Wales 2052
| | - Tiffany R Hogan
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, NSWHP Microbiology, Prince of Wales Hospital, Sydney, New South Wales 2031, Australia
| | - Cameron Buckley
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland 4029, Australia
| | - Ella Trembizki
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland 4029, Australia
| | - Hazel Mitchell
- School of Biotechnology and Biomolecular Science, The University of New South Wales, Sydney, New South Wales 2052
| | - Colleen L Lau
- Research School of Population Health, The Australian National University, Canberra, ACT 2600, Australia
| | - David M Whiley
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Herston, Queensland 4029, Australia.,Pathology Queensland, Microbiology Department, Herston, Queensland 4029, Australia
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, NSWHP Microbiology, Prince of Wales Hospital, Sydney, New South Wales 2031, Australia.,School of Biotechnology and Biomolecular Science, The University of New South Wales, Sydney, New South Wales 2052
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49
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Sanderson ND, Swann J, Barker L, Kavanagh J, Hoosdally S, Crook D, Street TL, Eyre DW. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing. Genome Res 2020; 30:1354-1363. [PMID: 32873606 PMCID: PMC7545138 DOI: 10.1101/gr.262865.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
The rise of antimicrobial-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near-complete N. gonorrhoeae genomes. However, disentangling the N. gonorrhoeae genome from metagenomic samples and robustly identifying antimicrobial resistance determinants from error-prone Nanopore sequencing is a substantial bioinformatics challenge. Here, we show an N. gonorrhoeae diagnostic workflow for analysis of metagenomic sequencing data obtained from clinical samples using R9.4.1 Nanopore sequencing. We compared results from simulated and clinical infections with data from known reference strains and Illumina sequencing of isolates cultured from the same patients. We evaluated three Nanopore variant callers and developed a random forest classifier to filter called SNPs. Clair was the most suitable variant caller after SNP filtering. A minimum depth of 20× reads was required to confidently identify resistant determinants over the entire genome. Our findings show that metagenomic Nanopore sequencing can provide reliable diagnostic information in N. gonorrhoeae infection.
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Affiliation(s)
- Nicholas D Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Jeremy Swann
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Leanne Barker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - James Kavanagh
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Sarah Hoosdally
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Derrick Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | | | - Teresa L Street
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - David W Eyre
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.,Big Data Institute, University of Oxford, Oxford OX3 7LF, United Kingdom
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Mortimer TD, Pathela P, Crawley A, Rakeman JL, Lin Y, Harris SR, Blank S, Schillinger JA, Grad YH. The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center. Clin Infect Dis 2020; 73:e3146-e3155. [PMID: 32829411 PMCID: PMC8563204 DOI: 10.1093/cid/ciaa1229] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Background Genomic epidemiology studies of gonorrhea in the United States have primarily focused on national surveillance for antibiotic resistance, and patterns of local transmission between demographic groups of resistant and susceptible strains are unknown. Methods We analyzed a convenience sample of genome sequences, antibiotic susceptibility, and patient data from 897 gonococcal isolates cultured at the New York City (NYC) Public Health Laboratory from NYC Department of Health and Mental Hygiene (DOHMH) Sexual Health Clinic (SHC) patients, primarily in 2012–2013. We reconstructed the gonococcal phylogeny, defined transmission clusters using a 10 nonrecombinant single nucleotide polymorphism threshold, tested for clustering of demographic groups, and placed NYC isolates in a global phylogenetic context. Results The NYC gonococcal phylogeny reflected global diversity with isolates from 22/23 of the prevalent global lineages (96%). Isolates clustered on the phylogeny by patient sexual behavior (P < .001) and race/ethnicity (P < .001). Minimum inhibitory concentrations were higher across antibiotics in isolates from men who have sex with men compared to heterosexuals (P < .001) and white heterosexuals compared to black heterosexuals (P < .01). In our dataset, all large transmission clusters (≥10 samples) of N. gonorrhoeae were susceptible to ciprofloxacin, ceftriaxone, and azithromycin, and comprised isolates from patients across demographic groups. Conclusions All large transmission clusters were susceptible to gonorrhea therapies, suggesting that resistance to empiric therapy was not a main driver of spread, even as risk for resistance varied across demographic groups. Further study of local transmission networks is needed to identify drivers of transmission.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Preeti Pathela
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Addie Crawley
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Jennifer L Rakeman
- Bureau of Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Ying Lin
- Bureau of Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Simon R Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Susan Blank
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America.,Division of STD Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, US Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Julia A Schillinger
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America.,Division of STD Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, US Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
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