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Unemo M, Sánchez-Busó L, Golparian D, Jacobsson S, Shimuta K, Lan PT, Eyre DW, Cole M, Maatouk I, Wi T, Lahra MM. The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization. J Antimicrob Chemother 2024:dkae176. [PMID: 38889110 DOI: 10.1093/jac/dkae176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
OBJECTIVES MDR and XDR Neisseria gonorrhoeae strains remain major public health concerns internationally, and quality-assured global gonococcal antimicrobial resistance (AMR) surveillance is imperative. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) and WHO Enhanced GASP (EGASP), including metadata and WGS, are expanding internationally. We present the phenotypic, genetic and reference genome characteristics of the 2024 WHO gonococcal reference strains (n = 15) for quality assurance worldwide. All superseded WHO gonococcal reference strains (n = 14) were identically characterized. MATERIAL AND METHODS The 2024 WHO reference strains include 11 of the 2016 WHO reference strains, which were further characterized, and four novel strains. The superseded WHO reference strains include 11 WHO reference strains previously unpublished. All strains were characterized phenotypically and genomically (single-molecule PacBio or Oxford Nanopore and Illumina sequencing). RESULTS The 2024 WHO reference strains represent all available susceptible and resistant phenotypes and genotypes for antimicrobials currently and previously used (n = 22), or considered for future use (n = 3) in gonorrhoea treatment. The novel WHO strains include internationally spreading ceftriaxone resistance, ceftriaxone resistance due to new penA mutations, ceftriaxone plus high-level azithromycin resistance and azithromycin resistance due to mosaic MtrRCDE efflux pump. AMR, serogroup, prolyliminopeptidase, genetic AMR determinants, plasmid types, molecular epidemiological types and reference genome characteristics are presented for all strains. CONCLUSIONS The 2024 WHO gonococcal reference strains are recommended for internal and external quality assurance in laboratory examinations, especially in the WHO GASP, EGASP and other GASPs, but also in phenotypic and molecular diagnostics, AMR prediction, pharmacodynamics, epidemiology, research and as complete reference genomes in WGS analysis.
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Affiliation(s)
- Magnus Unemo
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
| | - Leonor Sánchez-Busó
- Joint Research Unit 'Infection and Public Health', FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Madrid, Spain
| | - Daniel Golparian
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Microbiology, Örebro University, Örebro, Sweden
| | - Ken Shimuta
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Pham Thi Lan
- Hanoi Medical University, National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - David W Eyre
- Big Data Institute, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Ismael Maatouk
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Monica M Lahra
- WHO Collaborating Centre for Sexually Transmitted Infections and Antimicrobial Resistance, New South Wales Health Pathology, Microbiology, Randwick, NSW, Australia
- Faculty of Medicine, The University of New South Wales, Sydney, Australia
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Kandinov I, Shaskolskiy B, Kravtsov D, Filippova M, Larkin A, Gryadunov D. Mini-Multilocus Sequence Typing Scheme for the Global Population of Neisseria gonorrhoeae. Int J Mol Sci 2024; 25:5781. [PMID: 38891969 PMCID: PMC11171571 DOI: 10.3390/ijms25115781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
The increasing problem of antimicrobial resistance in N. gonorrhoeae necessitates the development of molecular typing schemes that are suitable for rapid and mass screening. The objective of this study was to design and validate a mini-MLST scheme for N. gonorrhoeae based on global pathogen population data. Using sequences of seven housekeeping genes of 21,402 isolates with known MLSTs from the PubMLST database, we identified eighteen informative polymorphisms and obtained mini-MLST nucleotide profiles to predict MLSTs of isolates. We proposed a new MLST grouping system for N. gonorrhoeae based on mini-MLST profiles. Phylogenetic analysis revealed that MLST genogroups are a stable characteristic of the N. gonorrhoeae global population. The proposed grouping system has been shown to bring together isolates with similar antimicrobial susceptibility, as demonstrated by the characteristics of major genogroups. Established MLST prediction algorithms based on nucleotide profiles are now publicly available. The mini-MLST scheme was evaluated using a MLST detection/prediction method based on the original hydrogel DNA microarray. The results confirmed a high predictive ability up to the MLST genogroup. The proposed holistic approach to gonococcal population analysis can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.
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Affiliation(s)
- Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (B.S.); (D.K.); (M.F.); (A.L.); (D.G.)
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3
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Lyu Y, Choong A, Chow EPF, Seib KL, Marshall HS, Unemo M, de Voux A, Wang B, Miranda AE, Gottlieb SL, Mello MB, Wi T, Baggaley R, Marshall C, Abu-Raddad LJ, Abara WE, Chen XS, Ong JJ. Vaccine value profile for Neisseria gonorrhoeae. Vaccine 2023:S0264-410X(23)00086-5. [PMID: 38123397 PMCID: PMC11169088 DOI: 10.1016/j.vaccine.2023.01.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/23/2022] [Accepted: 01/23/2023] [Indexed: 12/23/2023]
Abstract
Neisseria gonorrhoeae infection (gonorrhoea) is a global public health challenge, causing substantial sexual and reproductive health consequences, such as infertility, pregnancy complications and increased acquisition or transmission of HIV. There is an urgency to controlling gonorrhoea because of increasing antimicrobial resistance to ceftriaxone, the last remaining treatment option, and the potential for gonorrhoea to become untreatable. No licensed gonococcal vaccine is available. Mounting observational evidence suggests that N. meningitidis serogroup B outer membrane vesicle-based vaccines may induce cross-protection against N. gonorrhoeae (estimated 30%-40% effectiveness using the 4CMenB vaccine). Clinical trials to determine the efficacy of the 4CMenB vaccine against N. gonorrhoeae are underway, as are Phase 1/2 studies of a new gonococcal-specific vaccine candidate. Ultimately, a gonococcal vaccine must be accessible, affordable and equitably dispensed, given that those most affected by gonorrhoea are also those who may be most disadvantaged in our societies, and most cases are in less-resourced settings. This vaccine value profile (VVP) provides a high level, holistic assessment of the current data to inform the potential public health, economic and societal value of pipeline vaccines. This was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships and multi-lateral organizations. All contributors have extensive expertise on various elements of the N. gonorrhoeae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using published data obtained from peer-reviewed journals or reports.
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Affiliation(s)
- Yiming Lyu
- University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Annabelle Choong
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia.
| | - Eric P F Chow
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia; Melbourne Sexual Health Centre, Alfred Health, 580 Swanston Street, Melbourne, Victoria 3053, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, 207 Bouverie Street, Melbourne, Victoria 3053, Australia.
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland 4222, Australia.
| | - Helen S Marshall
- The University of Adelaide, Adelaide, South Australia 5005, Australia; Women's and Children's Health Network, North Adelaide, South Australia, Australia.
| | - Magnus Unemo
- WHO CC for Gonorrhoea and Other STIs, Örebro University, Örebro, Sweden; Institute for Global Health, University College London (UCL), London, UK.
| | - Alex de Voux
- Division of Epidemiology and Biostatistics, Faculty of Health Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa.
| | - Bing Wang
- The University of Adelaide, Adelaide, South Australia 5005, Australia; Women's and Children's Health Network, North Adelaide, South Australia, Australia.
| | - Angelica E Miranda
- Department of Social Medicine, Universidade Federal do Espirito Santo, Av. Fernando Ferrari, 514 - Goiabeiras, Vitória - ES 29075-910, Brazil.
| | - Sami L Gottlieb
- Department of Sexual and Reproductive Health and Research, World Health Organization, Av. Appia 20, 1211 Genève, Switzerland.
| | - Maeve B Mello
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Av. Appia 20, 1211 Genève, Switzerland.
| | - Teodora Wi
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Av. Appia 20, 1211 Genève, Switzerland.
| | - Rachel Baggaley
- Global HIV, Hepatitis and STI Programmes, World Health Organization, Av. Appia 20, 1211 Genève, Switzerland.
| | - Caroline Marshall
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Av. Appia 20, 1211 Genève, Switzerland.
| | - Laith J Abu-Raddad
- Weill Cornell Medicine-Qatar, Qatar Foundation - Education City, Box 24144, Doha, Qatar.
| | - Winston E Abara
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30329, USA.
| | - Xiang-Sheng Chen
- National Center for STD Control of China CDC, 12 Jiangwangmiao Street, Nanjing 210042, China.
| | - Jason J Ong
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, 99 Commercial Road, Melbourne, Victoria 3004, Australia.
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Belcher T, Rollier CS, Dold C, Ross JDC, MacLennan CA. Immune responses to Neisseria gonorrhoeae and implications for vaccine development. Front Immunol 2023; 14:1248613. [PMID: 37662926 PMCID: PMC10470030 DOI: 10.3389/fimmu.2023.1248613] [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: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Neisseria gonorrheoae is the causative agent of gonorrhea, a sexually transmitted infection responsible for a major burden of disease with a high global prevalence. Protective immunity to infection is often not observed in humans, possible due to high variability of key antigens, induction of blocking antibodies, or a large number of infections being relatively superficial and not inducing a strong immune response. N. gonorrhoeae is a strictly human pathogen, however, studies using mouse models provide useful insights into the immune response to gonorrhea. In mice, N. gonorrhoea appears to avoid a protective Th1 response by inducing a less protective Th17 response. In mouse models, candidate vaccines which provoke a Th1 response can accelerate the clearance of gonococcus from the mouse female genital tract. Human studies indicate that natural infection often induces a limited immune response, with modest antibody responses, which may correlate with the clinical severity of gonococcal disease. Studies of cytokine responses to gonococcal infection in humans provide conflicting evidence as to whether infection induces an IL-17 response. However, there is evidence for limited induction of protective immunity from a study of female sex workers in Kenya. A controlled human infection model (CHIM) has been used to examine the immune response to gonococcal infection in male volunteers, but has not to date demonstrated protection against re-infection. Correlates of protection for gonorrhea are lacking, which has hampered the progress towards developing a successful vaccine. However, the finding that the Neisseria meningitidis serogroup B vaccines, elicit cross-protection against gonorrhea has invigorated the gonococcal vaccine field. More studies of infection in humans, either natural infection or CHIM studies, are needed to understand better gonococcal protective immunity.
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Affiliation(s)
- Thomas Belcher
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Christina Dold
- The Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Jonathan D. C. Ross
- Sexual Health and HIV, University Hospitals Birmingham NHS Trust, Birmingham, United Kingdom
| | - Calman A. MacLennan
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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5
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Reimche JL, Clemons AA, Chivukula VL, Joseph SJ, Schmerer MW, Pham CD, Schlanger K, St Cyr SB, Kersh EN, Gernert KM. Genomic analysis of 1710 surveillance-based Neisseria gonorrhoeae isolates from the USA in 2019 identifies predominant strain types and chromosomal antimicrobial-resistance determinants. Microb Genom 2023; 9. [PMID: 37171855 DOI: 10.1099/mgen.0.001006] [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: 05/13/2023] Open
Abstract
This study characterized high-quality whole-genome sequences of a sentinel, surveillance-based collection of 1710 Neisseria gonorrhoeae (GC) isolates from 2019 collected in the USA as part of the Gonococcal Isolate Surveillance Project (GISP). It aims to provide a detailed report of strain diversity, phylogenetic relationships and resistance determinant profiles associated with reduced susceptibilities to antibiotics of concern. The 1710 isolates represented 164 multilocus sequence types and 21 predominant phylogenetic clades. Common genomic determinants defined most strains' phenotypic, reduced susceptibility to current and historic antibiotics (e.g. bla TEM plasmid for penicillin, tetM plasmid for tetracycline, gyrA for ciprofloxacin, 23S rRNA and/or mosaic mtr operon for azithromycin, and mosaic penA for cefixime and ceftriaxone). The most predominant phylogenetic clade accounted for 21 % of the isolates, included a majority of the isolates with low-level elevated MICs to azithromycin (2.0 µg ml-1), carried a mosaic mtr operon and variants in PorB, and showed expansion with respect to data previously reported from 2018. The second largest clade predominantly carried the GyrA S91F variant, was largely ciprofloxacin resistant (MIC ≥1.0 µg ml-1), and showed significant expansion with respect to 2018. Overall, a low proportion of isolates had medium- to high-level elevated MIC to azithromycin ((≥4.0 µg ml-1), based on C2611T or A2059G 23S rRNA variants). One isolate carried the penA 60.001 allele resulting in elevated MICs to cefixime and ceftriaxone of 1.0 µg ml-1. This high-resolution snapshot of genetic profiles of 1710 GC sequences, through a comparison with 2018 data (1479 GC sequences) within the sentinel system, highlights change in proportions and expansion of select GC strains and the associated genetic mechanisms of resistance. The knowledge gained through molecular surveillance may support rapid identification of outbreaks of concern. Continued monitoring may inform public health responses to limit the development and spread of antibiotic-resistant gonorrhoea.
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Affiliation(s)
- Jennifer L Reimche
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education Research Participation and Fellowship Program, Oak Ridge, TN, USA
| | - Arvon A Clemons
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Oak Ridge Institute for Science and Education Research Participation and Fellowship Program, Oak Ridge, TN, USA
| | - Vasanta L Chivukula
- Oak Ridge Institute for Science and Education Research Participation and Fellowship Program, Oak Ridge, TN, USA
- Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sandeep J Joseph
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew W Schmerer
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cau D Pham
- Antimicrobial Resistance Coordination and Strategy Unit, Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen Schlanger
- Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sancta B St Cyr
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ellen N Kersh
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kim M Gernert
- Division of STD Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Carannante A, Vacca P, Fontana S, Dal Conte I, Ghisetti V, Cusini M, Prignano G, Vocale C, Barbui AM, Stroppiana E, Busetti M, Mencacci A, Rotondi M, De Francesco MA, Bonanno CL, Innocenti P, Latino MA, Riccobono E, Poletti F, Casonato IC, Soldato G, Ambrosio L, Boros S, Ciammaruconi A, Lista F, Stefanelli P. Seven Years of Culture Collection of Neisseria gonorrhoeae: Antimicrobial Resistance and Molecular Epidemiology. Microb Drug Resist 2023; 29:85-95. [PMID: 36757312 PMCID: PMC10024589 DOI: 10.1089/mdr.2021.0483] [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: 02/10/2023] Open
Abstract
The emergence of Neisseria gonorrhoeae isolates displaying resistance to antimicrobials, in particular to ceftriaxone monotherapy or ceftriaxone plus azithromycin, represents a global public health concern. This study aimed to analyze the trend of antimicrobial resistance in a 7-year isolate collection retrospective analysis in Italy. Molecular typing on a subsample of gonococci was also included. A total of 1,810 culture-positive gonorrhea cases, collected from 2013 to 2019, were investigated by antimicrobial susceptibility, using gradient diffusion method, and by the N. gonorrhoeae multiantigen sequence typing (NG-MAST). The majority of infections occurred among men with urogenital infections and 57.9% of male patients were men who have sex with men. Overall, the cefixime resistance remained stable during the time. An increase of azithromycin resistance was observed until 2018 (26.5%) with a slight decrease in the last year. In 2019, gonococci showing azithromycin minimum inhibitory concentration above the EUCAST epidemiological cutoff value (ECOFF) accounted for 9.9%. Ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae (PPNG) percentages increased reaching 79.1% and 18.7% in 2019, respectively. The most common sequence types identified were 5,441, 1,407, 6,360, and 5,624. The predominant genogroup (G) was the 1,407; moreover, a new genogroup G13070 was also detected. A variation in the antimicrobial resistance rates and high genetic variability were observed in this study. The main phenotypic and genotypic characteristics of N. gonorrhoeae isolates were described to monitor the spread of drug-resistant gonorrhea.
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Affiliation(s)
- Anna Carannante
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Vacca
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Fontana
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Ivano Dal Conte
- Department of Prevention, Sexual Health Center, ASL Città di Torino, Turin, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, ASL Città di Torino, Turin, Italy
| | - Marco Cusini
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Grazia Prignano
- Molecular Virology, Pathology and Microbiology, IRCCS San Gallicano Dermatological Institute, Rome, Italy
| | - Caterina Vocale
- Regional Reference Center for Microbiological Emergencies (CRREM), Unit of Microbiology, St Orsola Malpighi University Hospital, Bologna, Italy
| | - Anna Maria Barbui
- Microbiology and Virology Laboratory, Molinette Hospital, Turin, Italy
| | - Elena Stroppiana
- Department of Medical Science, Dermatology Clinic, “Città della Salute e della Scienza of Turin,” Turin, Italy
| | - Marina Busetti
- Microbiology Unit, University Hospital of Trieste, Trieste, Italy
| | - Antonella Mencacci
- Medical Microbiology, Department of Medicine, University of Perugia, Perugia, Italy
- Microbiology, Santa Maria della Misericordia Hospital, Perugia, Italy
| | - Marina Rotondi
- Clinical and Microbiological Analysis Laboratory, Marilab s.r.l., Rome, Italy
| | - Maria Antonia De Francesco
- Department of Molecular and Translational Medicine, Institute of Microbiology, University of Brescia-Spedali Civili, Brescia, Italy
| | | | - Patrizia Innocenti
- Microbiology and Virology Laboratory, “Comprensorio Sanitario,” Bolzano, Italy
| | - Maria Agnese Latino
- Unit of Bacteriology, Department of “Medicina di Laboratorio," P. O. Sant'Anna, Città della Salute e della Scienza di Torino,” Turin, Italy
| | - Eleonora Riccobono
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Federica Poletti
- Department Infectious Diseases, Castelli Hospital Verbania, Verbania, Italy
| | | | | | - Luigina Ambrosio
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Boros
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Paola Stefanelli
- Department Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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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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8
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Lin X, Chen W, Yu Y, Lan Y, Xie Q, Liao Y, Wu X, Tang S, Qin X, Zheng H. Emergence and Genomic Characterization of Neisseria gonorrhoeae Isolates with High Levels of Ceftriaxone and Azithromycin Resistance in Guangdong, China, from 2016 to 2019. Microbiol Spectr 2022; 10:e0157022. [PMID: 36377922 PMCID: PMC9769569 DOI: 10.1128/spectrum.01570-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/20/2022] [Indexed: 11/16/2022] Open
Abstract
Currently, antibiotic resistance (especially ceftriaxone and azithromycin dual resistance) in Neisseria gonorrhoeae is the main obstacle affecting the efficacy of treatment. As analysis of drug sensitivity, molecular features, and dissemination of dual-resistant strains is important for gonococcal prevention and control, MIC, genotyping, and genome analysis were conducted to reveal the molecular characteristics and phylogeny of N. gonorrhoeae isolates. During 2016 to 2019, 5 out of 4,113 strains were defined as dual-resistant clones, with ceftriaxone MICs of 0.25 to ≥1 mg/L and azithromycin MICs of 2 to ≥2,048 mg/L. In particular, two strains with a ceftriaxone MIC above 0.5 mg/L were characterized as penA-60.001 FC428-related clones, and two isolates with a high-level azithromycin MIC above 1,024 mg/L featuring a 23S rRNA mutation were identified. Furthermore, phylogenetic analysis confirmed that the dual-resistant strains were closer to the evolutionary origin of F89 in France, global FC428-related clones, and high-level dual-resistant clones in Australia and the United Kingdom. Dual-resistant strains, including FC428-related clones and high-level azithromycin-resistant clones, have circulated in Guangdong, China. The ability of laboratories to perform real-time drug susceptibility and genetic analyses should be strengthened to monitor the spread of threatening strains. IMPORTANCE Here, we report five sporadic dual-resistant isolates, including FC428-related ceftriaxone-resistant clones with MICs of ≥0.5 mg/L and high-level azithromycin resistance with MICs of ≥1,024 mg/L. This study highlights that dual-resistant clones with the same evolutionary origin as FC428, A2735, and F89 have circulated in Guangdong, China, which suggests that the capacity for antibiotic resistance testing and genome analysis should be strengthened in daily epidemiological surveillance.
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Affiliation(s)
- Xiaomian Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Wentao Chen
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Yuqi Yu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Yinyuan Lan
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Qinghui Xie
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Yiwen Liao
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Xingzhong Wu
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Sanmei Tang
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Xiaolin Qin
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
| | - Heping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory for Sexually Transmitted Disease Control, Guangzhou, Guangdong, China
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9
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Culture-Independent Genotyping Improves Surveillance of Neisseria gonorrhoeae, Especially in Oropharyngeal Samples, the Netherlands, 2017 to 2018. Pathogens 2022; 11:pathogens11111344. [DOI: 10.3390/pathogens11111344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
It is important i to monitor the transmission and antimicrobial resistance of Neisseria gonorrhoeae (NG). Current surveillance relies on culturing, which frequently fails. Previously, a culture-independent genotyping method was developed based on NG multi-antigen sequence typing (NG-MAST). To determine whether crucial sequence types (STs) are missed during culture-dependent surveillance, NG-positive NAAT samples were genotyped, and the results of the culture-positive and culture-negative samples were compared. In total, 196 NG-positive NAAT samples, from January 2017 until August 2018, which were also routinely cultured, were retrospectively included. Genotyping was successful in 152 NAAT samples (77.0%), 33 NAAT samples failed, and 11 NAAT samples showed possible mixed strain infections. Oropharyngeal samples (n = 16) showed the largest increase in typing rate from 6.3% (1/16) success in culture-dependent genotyping to 81.3% (13/16) in culture-independent genotyping. Nine genogroups (n ≥ 5 samples) were found; all included both culture-positive and culture-negative NG. However, culture-independent surveillance revealed 14 additional STs in the culture-negative samples. Overall, culture-dependent surveillance could detect all genogroups, indicating that major trends could be identified with culture-dependent surveillance. However, culture-independent surveillance provides more STs, mixed infections and more oropharyngeal samples, giving a more detailed view and could result in an earlier detection of outbreaks and transmission.
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Miura M, Shigemura K, Osawa K, Nakanishi N, Nomoto R, Onishi R, Yoshida H, Sawamura T, Fang SB, Chiang YT, Sung SY, Chen KC, Miyara T, Fujisawa M. Genetic characteristics of azithromycin-resistant Neisseria gonorrhoeae collected in Hyogo, Japan during 2015-2019. J Med Microbiol 2022; 71. [PMID: 35700110 DOI: 10.1099/jmm.0.001533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Azithromycin (AZM) is a therapeutic drug for sexually transmitted infections and is used for Neisseria gonorrhoeae when first- and second-line drugs are not available. Recently, the susceptibility of N. gonorrhoeae against AZM has been decreasing worldwide.Hypothesis/Gap Statement. Azithromycin-resistance (AZM-R) rates among N. gonorrhoeae in Japan are increasing, and the gene mutations and epidemiological characteristics of AZM-R in N. gonorrhoeae have not been fully investigated.Aim. We determined the susceptibility to AZM and its correlation with genetic characteristics of N. gonorrhoeae.Methodology. We investigated the susceptibility to AZM and genetic characteristics of N. gonorrhoeae. Mutations in domain V of the 23S rRNA gene and mtrR were examined in 93 isolates, including 13 AZM-R isolates. Spread and clonality were examined using sequence types (STs) of multi-antigen sequence typing for N. gonorrhoeae (NG-MAST), and whole genome analysis (WGA) to identify single nucleotide polymorphisms.Results. The number of AZM-R isolates increased gradually from 2015 to 2019 in Hyogo (P=0.008). C2599T mutations in 23S rRNA significantly increased in AZM-R isolates (P<0.001). NG-MAST ST4207 and ST6762 were frequently detected in AZM-R isolates, and they had higher MICs to AZM from 6 to 24 µg/ml. The phylogenic tree-based WGA showed that all isolates with ST4207 were contained in the same clade, and isolates with ST6762 were divided into two clades, AZM-S isolates and AZM-R isolates, which were different from the cluster containing ST1407.Conclusion. Our study showed yearly increases in AZM-R rates in N. gonorrhoeae. NG-MAST ST4207 and ST6762 were not detected in our previous study in 2015 and were frequently identified in isolates with higher MICs to AZM. WGA confirmed that isolates with these STs are closely related to each other. Continued surveillance is needed to detect the emergence and confirm the spread of NG-MAST ST4207 and ST6762.
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Affiliation(s)
- Makiko Miura
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan.,Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Katsumi Shigemura
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan.,Department of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kayo Osawa
- Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamichi, Chuo-ku, Kobe, 650-0046, Japan
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamichi, Chuo-ku, Kobe, 650-0046, Japan
| | - Reo Onishi
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan
| | - Hiroyuki Yoshida
- Hyogo Clinical Laboratory Corporation, 5-6-2, Aoyamanishi, Himeji, 671-2224 Japan
| | - Toru Sawamura
- Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Shiuh-Bin Fang
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, 291 Jhong Jheng Road, Jhong Ho District, New Taipei City, 23561, Taiwan, ROC.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, 250, Wu Hsing Street, Hsin Yi District, Taipei, 11031, Taiwan, ROC
| | - Yi-Te Chiang
- Department of Urology, Taipei Medical University Shuang Ho Hospital, 291, Zhongzheng Rd, Zhonghe District, Taipei, 23561, Taiwan, ROC
| | - Shian-Ying Sung
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing St., Taipei, 110, Taiwan, ROC
| | - Kuan-Cho Chen
- Department of Urology, Taipei Medical University Shuang Ho Hospital, 291, Zhongzheng Rd, Zhonghe District, Taipei, 23561, Taiwan, ROC
| | - Takayuki Miyara
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Masato Fujisawa
- Department of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
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11
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Pilkie D, Gratrix J, Sawatzky P, Martin I, Singh A, Prasad E, Naidu P, Mulvey M, Wong T, Smyczek PA. Molecular Surveillance and Prediction of Antimicrobial Resistance of Neisseria gonorrhoeae in Northern Alberta, Canada, 2015 to 2018. Sex Transm Dis 2022; 49:377-382. [PMID: 35067598 DOI: 10.1097/olq.0000000000001604] [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 The aims of this study was to describe molecular surveillance of Neisseria gonorrhoeae in the North Zone of Alberta (NZ) and to determine its value in predicting antimicrobial resistance. METHODS Sequence types (STs) and single-nucleotide polymorphism (SNP) assays were performed on nucleic acid amplification testing (NAAT) samples. Sequence types of NAATs were matched to ST of cultures from across Alberta. Antimicrobial resistance prediction of NAATs for cephalosporins, azithromycin, and ciprofloxacin using SNP was compared with matching ST culture results using agar dilution and whole-genome sequencing. RESULTS Of 2755 eligible specimens (2492 cases), 61.9% (1646 specimens) were sent for sequence typing, identifying 196 unique ST. Antimicrobial resistance data for 1307 additional cases were available using matching cultures. Decreased susceptibility (DS) to antimicrobials used for gonorrhea treatment was rare in the NZ; according to the SNP assay, none of the specimens had predicted DS to cephalosporins or azithromycin resistance. However, of the NZ NAAT samples tested in this study, 10.7% (131 of 1220) were predicted to have intermediate cephalosporin minimum inhibitory concentrations and 9.6% (115 of 1204) were resistant to ciprofloxacin. Based on cultures, the proportions of resistance in all of Alberta were as follows: DS to cephalosporins, 0.6% (20 of 3373); DS to intermediate cephalosporin, 16.9% (570 of 3373); azithromycin resistance, 1.2% (41 of 3373); and ciprofloxacin resistance, 32.2% (1087 of 3373). CONCLUSIONS Our results highlight our ability to use culture-independent methods to predict antimicrobial resistance in N. gonorrhoeae.
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Affiliation(s)
- Daralynn Pilkie
- From the Department of Health Sciences, Lakehead University, Thunder Bay, Ontario
| | | | - Pam Sawatzky
- National Microbiology Laboratory, Winnipeg, Manitoba
| | - Irene Martin
- National Microbiology Laboratory, Winnipeg, Manitoba
| | | | | | | | | | - Tom Wong
- Indigenous Services Canada, Ottawa, Canada
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12
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Raisman JC, Fiore MA, Tomin L, Adjei JKO, Aswad VX, Chu J, Domondon CJ, Donahue BA, Masciotti CA, McGrath CG, Melita J, Podbielski PA, Schreiner MR, Trumpore LJ, Wengert PC, Wrightstone EA, Hudson AO, Wadsworth CB. Evolutionary paths to macrolide resistance in a Neisseria commensal converge on ribosomal genes through short sequence duplications. PLoS One 2022; 17:e0262370. [PMID: 35025928 PMCID: PMC8758062 DOI: 10.1371/journal.pone.0262370] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/22/2021] [Indexed: 11/19/2022] Open
Abstract
Neisseria commensals are an indisputable source of resistance for their pathogenic relatives. However, the evolutionary paths commensal species take to reduced susceptibility in this genus have been relatively underexplored. Here, we leverage in vitro selection as a powerful screen to identify the genetic adaptations that produce azithromycin resistance (≥ 2 μg/mL) in the Neisseria commensal, N. elongata. Across multiple lineages (n = 7/16), we find mutations that reduce susceptibility to azithromycin converge on the locus encoding the 50S ribosomal L34 protein (rpmH) and the intergenic region proximal to the 30S ribosomal S3 protein (rpsC) through short tandem duplication events. Interestingly, one of the laboratory evolved mutations in rpmH is identical (7LKRTYQ12), and two nearly identical, to those recently reported to contribute to high-level azithromycin resistance in N. gonorrhoeae. Transformations into the ancestral N. elongata lineage confirmed the causality of both rpmH and rpsC mutations. Though most lineages inheriting duplications suffered in vitro fitness costs, one variant showed no growth defect, suggesting the possibility that it may be sustained in natural populations. Ultimately, studies like this will be critical for predicting commensal alleles that could rapidly disseminate into pathogen populations via allelic exchange across recombinogenic microbial genera.
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Affiliation(s)
- Jordan C. Raisman
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Michael A. Fiore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lucille Tomin
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Joseph K. O. Adjei
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Virginia X. Aswad
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jonathan Chu
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Christina J. Domondon
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Ben A. Donahue
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Claudia A. Masciotti
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Connor G. McGrath
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Jo Melita
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Paul A. Podbielski
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Madelyn R. Schreiner
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Lauren J. Trumpore
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Peter C. Wengert
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Emalee A. Wrightstone
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - André O. Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
| | - Crista B. Wadsworth
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, NY, United States of America
- * E-mail:
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Gaspari V, Morselli S, Foschi C, Marangoni A. Culture-free genotyping of Neisseria gonorrhoeae from urogenital samples in a high-density urban area in the North of Italy. J Eur Acad Dermatol Venereol 2021; 36:e295-e297. [PMID: 34927774 DOI: 10.1111/jdv.17882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V Gaspari
- Dermatology Unit, IRCCS S. Orsola-Malpighi Hospital, Bologna, Italy
| | - S Morselli
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - C Foschi
- Microbiology, DIMES, University of Bologna, Bologna, Italy
| | - A Marangoni
- Microbiology, DIMES, University of Bologna, Bologna, Italy
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14
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Golparian D, Unemo M. Antimicrobial resistance prediction in Neisseria gonorrhoeae: Current status and future prospects. Expert Rev Mol Diagn 2021; 22:29-48. [PMID: 34872437 DOI: 10.1080/14737159.2022.2015329] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Several nucleic acid amplification tests (NAATs), mostly real-time PCRs, to detect antimicrobial resistance (AMR) determinants and predict AMR in Neisseria gonorrhoeae are promising, and some may be ready to apply at the point-of-care (POC), but important limitations remain with most NAATs. Next-generation sequencing (NGS) can overcome many of these limitations.Areas covered: Recent advances, with main focus on publications since 2017, in the development and use of NAATs and NGS to predict gonococcal AMR for surveillance and clinical use, and pros and cons of these tests as well as future perspectives for appropriate use of molecular AMR prediction for N. gonorrhoeae.Expert Commentary: NAATs and/or NGS for AMR prediction should supplement culture-based AMR surveillance, which will remain because it detects also AMR due to unknown AMR determinants, and translation into POC tests is imperative for the end-goal of individualized treatment, sparing ceftriaxone±azithromycin. Several challenges for direct testing of clinical, especially pharyngeal, specimens and for accurate prediction of cephalosporins and azithromycin resistance, especially using NAATs, remain. The choice of AMR prediction assay needs to carefully consider the intended use of the assay; limitations intrinsic to the AMR prediction technology, algorithms and specific to chosen methodology; specimen types analyzed; and cost-effectiveness.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Mitchev N, Singh R, Allam M, Kwenda S, Ismail A, Garrett N, Ramsuran V, Niehaus AJ, Mlisana KP. Antimicrobial Resistance Mechanisms, Multilocus Sequence Typing, and NG-STAR Sequence Types of Diverse Neisseria gonorrhoeae Isolates in KwaZulu-Natal, South Africa. Antimicrob Agents Chemother 2021; 65:e0075921. [PMID: 34280016 PMCID: PMC8448096 DOI: 10.1128/aac.00759-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/13/2021] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance (AMR) is a major challenge to managing infectious diseases. Africa has the highest incidence of gonorrhoea, but there is a lack of comprehensive data from sparse surveillance programs. This study investigated the molecular epidemiology and AMR profiles of Neisseria gonorrhoeae isolates in KwaZulu-Natal province (KZN), South Africa. Repository isolates from patients attending public health care clinics for sexually transmitted infection (STI) care were used for phenotypic and genotypic analysis. An Etest was performed to determine antimicrobial susceptibility. Whole-genome sequencing (WGS) was used to determine epidemiology and to predict susceptibility by detecting resistance-associated genes and mutations. Among the 61 isolates, multiple sequence types were identified. Six isolates were novel, as determined by multilocus sequence typing. N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) determined 48 sequence types, of which 35 isolates had novel antimicrobial profiles. Two novel penA alleles and eight novel mtrR alleles were identified. Point mutations were detected in gyrA, parC, mtrR, penA, ponA, and porB1. This study revealed a high prevalence of AMR (penicillin 67%, tetracycline 89%, and ciprofloxacin 52%). However, spectinomycin, cefixime, ceftriaxone, and azithromycin remained 100% effective. This study is one of the first to comprehensively describe the epidemiology and AMR of N. gonorrhoeae in KZN, South Africa and Africa, using WGS. KZN has a wide strain diversity and most of these sequence types have been detected in multiple countries; however, more than half of our isolates have novel antimicrobial profiles. Continued surveillance is crucial to monitor the emergence of resistance to cefixime, ceftriaxone, and azithromycin.
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Affiliation(s)
- Nireshni Mitchev
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ravesh Singh
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- School of Nursing and Public Health, Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Abraham J. Niehaus
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka P. Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
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16
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [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: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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Juma M, Sankaradoss A, Ndombi R, Mwaura P, Damodar T, Nazir J, Pandit A, Khurana R, Masika M, Chirchir R, Gachie J, Krishna S, Sowdhamini R, Anzala O, Meenakshi IS. Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting. Front Microbiol 2021; 12:647565. [PMID: 34385981 PMCID: PMC8353456 DOI: 10.3389/fmicb.2021.647565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background Africa has one of the highest incidences of gonorrhea. Neisseria gonorrhoeae is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected N. gonorrhoeae isolates from Nairobi, Kenya. Methods Using WGS, the isolates were confirmed to be cases of N. gonorrhoeae (n = 9), and there were three co-occurrences of N. gonorrhoeae with Moraxella osloensis and N. meningitidis (n = 2). N. meningitidis has been implicated in sexually transmitted infections in recent years. The near-complete N. gonorrhoeae genomes (n = 10) were analyzed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature. Results We observe that ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. Mutations conferring tetracycline (rpsJ) and sulfonamide (folP) resistance and plasmids encoding beta-lactamase were seen in all the strains, and tet(M)-containing plasmids were identified in nine strains. Phylogenetic analysis clustered the 10 isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Based on homology modeling of AMR targets, we see that the mutations in GyrA and ParC disrupt the hydrogen bonding with quinolone drugs and mutations in FolP may affect interaction with the antibiotic. Conclusion Here, we demonstrate the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detection of genetic determinants of AMR. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly, and analysis, can be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis, and management of infections, especially in resource-limited settings.
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Affiliation(s)
- Meshack Juma
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Arun Sankaradoss
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Redcliff Ndombi
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Patrick Mwaura
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Tina Damodar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Junaid Nazir
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Awadhesh Pandit
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Rupsy Khurana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Moses Masika
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Ruth Chirchir
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - John Gachie
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Sudhir Krishna
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India.,School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Ponda, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
| | - Omu Anzala
- KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Iyer S Meenakshi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research (TIFR), Bengaluru, India
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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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Yang Y, Yang Y, Martin I, Dong Y, Diao N, Wang Y, Demczuk W, Gu W. NG-STAR genotypes are associated with MDR in Neisseria gonorrhoeae isolates collected in 2017 in Shanghai. J Antimicrob Chemother 2021; 75:566-570. [PMID: 31713620 PMCID: PMC7021085 DOI: 10.1093/jac/dkz471] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 12/29/2022] Open
Abstract
Objectives To determine the association of Neisseria gonorrhoeae antimicrobial resistance and genotypes using N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR). Methods We characterized 124 N. gonorrhoeae isolates for their antimicrobial susceptibility profiles and NG-STAR ST characteristics using the guidelines of CLSI and EUCAST. The NG-STAR STs of seven loci were analysed. N. gonorrhoeae multiantigen sequence typing (NG-MAST) and MLST analysis was conducted in isolates with specific NG-STAR STs. Results NG-STAR differentiated 124 N. gonorrhoeae isolates into 84 STs, of which 66 STs were novel to the NG-STAR database. NG-STAR ST-199, ST-348, ST-428, ST-497 and ST-1138 were the predominant STs. Three N. gonorrhoeae isolates with ceftriaxone and cefixime MICs ≥1.0 mg/L were grouped as NG-STAR ST-233. NG-STAR ST-202 isolates (n=4) were associated with high azithromycin MICs and had an identical NG-MAST ST. The NG-STAR ST-348 group (n=5) comprised more isolates with reduced susceptibility to cefixime (n=4) than cefixime-susceptible isolates (n=1). Conclusions NG-STAR analysis differentiated N. gonorrhoeae isolates in settings with a high prevalence of antimicrobial resistance. Specific NG-STAR STs are associated with reduced susceptibility to ceftriaxone or cefixime and resistance to azithromycin in N. gonorrhoeae.
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Affiliation(s)
- Yijing Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Yang Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Yuan Dong
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Nannan Diao
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Ying Wang
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - 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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20
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Karymbaeva S, Boiko I, Jacobsson S, Mamaeva G, Ibraeva A, Usupova D, Golparian D, Unemo M. Antimicrobial resistance and molecular epidemiological typing of Neisseria gonorrhoeae isolates from Kyrgyzstan in Central Asia, 2012 and 2017. BMC Infect Dis 2021; 21:559. [PMID: 34118893 PMCID: PMC8195719 DOI: 10.1186/s12879-021-06262-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 04/04/2023] Open
Abstract
Background Gonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are significant public health concerns globally. Nearly no gonococcal AMR data are available from Central Asia, and no data from Kyrgyzstan has been published. We examined, for the first time, AMR and molecular epidemiology of N. gonorrhoeae isolates cultured in Kyrgyzstan in 2012 and 2017, in order to inform refinements of the Kyrgyz national gonorrhoea management guidelines. Methods N. gonorrhoeae isolates cultured in 2012 (n = 84) and 2017 (n = 72) in Kyrgyzstan were examined. MICs of nine antimicrobials were determined using Etest and, where available, clinical breakpoints from the EUCAST were applied. N. gonorrhoeae multiantigen sequence typing (NG-MAST) was also performed. Results The overall resistance levels were high to ciprofloxacin (88.5%), tetracycline (56.9%), benzylpenicillin (39.1%), and kanamycin (4.7%). Resistance to cefixime (0.6%, n = 1 isolate), azithromycin (0.6%, n = 1), and gentamicin (0.6%, n = 1) was rare. No resistance to ceftriaxone or spectinomycin was found. However, the proportion of isolates with decreased susceptibility (MIC = 0.125 mg/L) to ceftriaxone and cefixime was 12.8 and 11.5%, respectively. Gonococcal isolates were assigned 69 sequence types, of which 52 (75.4%) were new. Conclusions The gonococcal population in Kyrgyzstan in 2012 and 2017 showed a high genetic diversity. Ceftriaxone, 500–1000 mg, in combination with azithromycin 2 g or doxycycline, particularly when chlamydial infection has not been excluded, should be recommended as empiric first-line treatment. Spectinomycin 2 g could be an alternative treatment, and given with azithromycin 2 g if pharyngeal gonorrhoea has not been excluded. Fluoroquinolones, aminoglycosides, benzylpenicillin, or tetracyclines should not be used for empiric treatment of gonorrhoea in Kyrgyzstan. Timely updating and high compliance to national gonorrhoea treatment guidelines based on quality-assured AMR data is imperative. Expanded and improved gonococcal AMR surveillance in Kyrgyzstan is crucial.
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Affiliation(s)
- Saliya Karymbaeva
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85, Örebro, Sweden
| | - Iryna Boiko
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85, Örebro, Sweden.,Department of Functional and Laboratory Diagnostics, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85, Örebro, Sweden
| | - Galina Mamaeva
- Republican Dermatovenerological Centre, Bishkek, Kyrgyzstan
| | | | - Dilara Usupova
- Republican Dermatovenerological Centre, Bishkek, Kyrgyzstan
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University Hospital, SE-701 85, Örebro, Sweden.
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21
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Abstract
We report on the first high-level azithromycin-resistant Neisseria gonorrhoeae isolate (minimum inhibitory concentration, ≥256 μg/mL) in North Carolina isolated from a pharyngeal swab of a 33-year-old HIV-negative man who has sex with men. In addition, the isolate was found to be susceptible to cefixime, ceftriaxone, and penicillin and resistant to tetracycline. By whole-genome sequencing, the strain was assigned as MLST ST9363, NG-MAST ST5035, and a novel NG-STAR sequence type, ST1993.
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22
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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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Kandinov I, Dementieva E, Kravtsov D, Chestkov A, Kubanov A, Solomka V, Deryabin D, Gryadunov D, Shaskolskiy B. Molecular Typing of Neisseria gonorrhoeae Clinical Isolates in Russia, 2018-2019: A Link Between penA Alleles and NG-MAST Types. Pathogens 2020; 9:pathogens9110941. [PMID: 33198126 PMCID: PMC7696878 DOI: 10.3390/pathogens9110941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/05/2023] Open
Abstract
This work aimed to study penA gene polymorphisms in clinical isolates of Neisseria gonorrhoeae collected in Russia in 2018-2019 and the contribution of the penA allele type to susceptibility to β-lactam antibiotics. A total of 182 isolates were analyzed. penA allele types were determined by sequencing, and the minimum inhibitory concentrations (MICs) of benzylpenicillin and ceftriaxone were measured. The influence of genetic factors on MICs was evaluated by regression analysis. All isolates were susceptible to ceftriaxone, and 40.1% of isolates were susceptible to penicillin. Eleven penA allele types were identified. The mosaic type XXXIV penA allele and the Gly120Lys substitution in PorB made the greatest contributions to increasing the ceftriaxone MIC; the presence of the blaTEM plasmid, Gly120Asp, Ala121Gly/Asn substitutions in PorB, and the adenine deletion in the promoter region of the mtrR gene caused an increase in the penicillin MIC. Among 61 NG-MAST types identified, the most frequent were types 228, 807, 9486, 1993, and 6226. A link between penA alleles and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) types was established. Resistance to two groups of β-lactam antibiotics was associated with non-identical changes in penA alleles. To prevent the emergence of ceftriaxone resistance in Russia, NG-MAST genotyping must be supplemented with penA allele analysis.
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Affiliation(s)
- Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Alexander Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, 107076 Moscow, Russia; (A.C.); (A.K.); (V.S.); (D.D.)
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
| | - Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (I.K.); (E.D.); (D.K.); (D.G.)
- Correspondence:
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Is there a widespread clone of Serratia marcescens producing outbreaks worldwide? J Hosp Infect 2020; 108:7-14. [PMID: 33181279 DOI: 10.1016/j.jhin.2020.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Serratia marcescens frequently causes outbreaks in healthcare settings. There are few studies using high-throughput sequencing (HTS) that analyse S. marcescens outbreaks. We present the analysis of two outbreaks in neonatal intensive care units (NICUs) in hospitals from the Comunitat Valenciana (CV, Spain) and the impact of using different reference genomes. METHODS DNA from cultured isolates was extracted and sequenced by HTS using Illumina NextSeq. Reads were mapped against two reference genomes, strains UMH9 and Db11, and the unmapped fraction of the genomes was assembled to fully genetically characterize the isolates. FINDINGS Isolates from the first outbreak were identical to the UMH9 reference, an unrelated isolate obtained three years earlier in the USA. This did not occur when the Db11 strain, a standard reference for S. marcescens, was used as the reference for mapping. To check whether UMH9 was a widely distributed clone spreading in the CV, the second outbreak isolates were mapped against this reference. They were not closely related to this strain, and this outbreak could be defined as such regardless of the reference used for mapping the reads. CONCLUSIONS The choice of the reference for genomic analysis of outbreaks is a critical decision. In the case of the first outbreak, this choice changed the interpretation of the results drastically, allowing or preventing the definition of the outbreak according to the reference used. Although HTS is a powerful tool for epidemiological analysis, it is still essential to collect microbiological and epidemiological data for the correct interpretation of the results.
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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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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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Wang F, Liu JW, Li YZ, Zhang LJ, Huang J, Chen XS, Chen SC, Yin YP. Surveillance and molecular epidemiology of Neisseria gonorrhoeae isolates in Shenzhen, China, 2010-2017. J Glob Antimicrob Resist 2020; 23:269-274. [PMID: 32889143 DOI: 10.1016/j.jgar.2020.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/16/2020] [Accepted: 08/18/2020] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES The development and emergence of antimicrobial resistance in Neisseria gonorrhoeae (NG) have become a major public-health problem worldwide. This study aimed to analyse the antimicrobial susceptibility and molecular characteristics of NG isolates in Shenzhen, China. METHODS A total of 1282 NG isolates were consecutively collected between 2010 and 2017. Patient demographic information was also collected. MICs of ceftriaxone, spectinomycin, ciprofloxacin, azithromycin and penicillin were determined by agar dilution. Isolates were genotyped using N. gonorrhoeae multi-antigen sequence typing (NG-MAST). RESULTS Among the isolates, 97.4% were resistant to ciprofloxacin and 68.2% to penicillin. Moreover, 5.0% showed decreased susceptibility to ceftriaxone (CROD) and 17.3% were resistant to azithromycin (AZM-R); 1.3% were simultaneously CROD and AZM-R. All isolates were susceptible to spectinomycin. Increasing ceftriaxone MICs were found from 2010 to 2017. A total of 427 sequence types (STs) and 68 genogroups were identified from 724 isolates. ST5061, ST3741 and ST1766 were observed across the study years. ST14638 (n = 3) was predominant among 32 CROD isolates. Prevalent STs were ST5061 (n = 6), ST1866 (n = 5) and ST11133 (n = 5) among 96 AZM-R isolates. CONCLUSIONS A high prevalence of isolates resistant to ciprofloxacin and penicillin was found in this study. Azithromycin, one antimicrobial of dual antimicrobial therapy recommended by the WHO, showed a high prevalence of resistance. The other, ceftriaxone, can be used continuously in this region owing to lower resistance levels. However, the emergence of CROD and decreasing susceptibility to ceftriaxone indicate that continuous antimicrobial resistance surveillance is essential.
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Affiliation(s)
- Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Jing-Wei Liu
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China; Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Yi-Zhun Li
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Li-Jun Zhang
- Shenzhen Maternity & Healthcare Hospital, Shenzhen, China
| | - Jing Huang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Xiang-Sheng Chen
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China; Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Shao-Chun Chen
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China; Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China.
| | - Yue-Ping Yin
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China; Institute of Dermatology and Hospital for Skin Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China.
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28
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Poncin T, Merimeche M, Braille A, Mainardis M, Bebear C, Jacquier H, Berçot B. Two cases of multidrug-resistant Neisseria gonorrhoeae related to travel in south-eastern Asia, France, June 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 31507264 PMCID: PMC6737829 DOI: 10.2807/1560-7917.es.2019.24.36.1900528] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report two cases of multidrug-resistant Neisseria gonorrhoeae urogenital infection with ceftriaxone resistance in a heterosexual couple in south-western France who were successfully treated with a single, high dose of intramuscular ceftriaxone (1 g). Whole genome sequencing of isolate F91 identified MLST13871, NG-MAST1086, NG-STAR233. Patient history revealed the isolate F91 was most likely acquired during a trip to Cambodia and belongs to the successful multidrug-resistant FC428 Asian clone.
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Affiliation(s)
- Thibaut Poncin
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Manel Merimeche
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Aymeric Braille
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Mary Mainardis
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Cécile Bebear
- Centre Hospitalier Universitaire de Bordeaux, French National Reference Centre for bacterial sexually transmitted infections, Bordeaux, France.,University of Bordeaux, USC EA 3671, Mycoplasmal and chlamydial infections in humans, Bordeaux, France
| | - Hervé Jacquier
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
| | - Béatrice Berçot
- Paris University, INSERM, IAME, Paris, France.,French National Reference Centre for bacterial sexually transmitted infections, Associated laboratory for gonococci, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France.,Infectious Agents Department, Saint Louis Hospital, Assistance Publique - Hôpitaux de Paris (APHP), Paris, France
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29
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Gianecini RA, Golparian D, Zittermann S, Litvik A, Gonzalez S, Oviedo C, Melano RG, Unemo M, Galarza P. Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16. J Antimicrob Chemother 2020; 74:1551-1559. [PMID: 30820563 DOI: 10.1093/jac/dkz054] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/20/2018] [Accepted: 01/16/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Our aim was to describe the molecular epidemiology and antimicrobial resistance determinants of isolates of Neisseria gonorrhoeae with decreased susceptibility and resistance to extended-spectrum cephalosporins (ESCs) in Argentina in 2011-16. METHODS Gonococcal isolates (n=158) with decreased susceptibility and resistance to ESCs collected in 2011-16 across Argentina were subjected to WGS and antimicrobial susceptibility testing for six antimicrobials. RESULTS In total, 50% of the isolates were resistant to cefixime, 1.9% were resistant to ceftriaxone, 37.3% were resistant to azithromycin and 63.9% of the isolates showed an MDR phenotype. Resistance and decreased susceptibility to ESCs was mainly associated with isolates possessing the mosaic penA-34.001, in combination with an mtrR promoter A deletion, and PorB1b amino acid substitutions G120K/A121N. Phylogenetic analysis revealed two main clades of circulating strains, which were associated with the N. gonorrhoeae multiantigen sequence typing (NG-MAST) ST1407 and closely related STs, and characterized by a high prevalence rate, wide geographical distribution and temporal persistence. CONCLUSIONS N. gonorrhoeae isolates with decreased susceptibility and resistance to ESCs in Argentina have emerged and rapidly spread mainly due to two clonal expansions after importation of one or two strains, which are associated with the international MDR NG-MAST ST1407 clone. The identification of the geographical dissemination and characteristics of these predominant clones may help to focus action plans and public health policies to control the spread of ESC resistance in Argentina. Dual antimicrobial therapy (ceftriaxone plus azithromycin) for gonorrhoea needs to be considered in Argentina.
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Affiliation(s)
- Ricardo A Gianecini
- National Reference Laboratory of Sexually Transmitted Diseases, National Institute of Infectious Diseases - ANLIS 'Dr Carlos G. Malbrán', Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Ana Litvik
- Rawson Infectious Diseases Hospital, Córdoba, Argentina
| | | | - Claudia Oviedo
- National Reference Laboratory of Sexually Transmitted Diseases, National Institute of Infectious Diseases - ANLIS 'Dr Carlos G. Malbrán', Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, Department of Laboratory Medicine, Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Patricia Galarza
- National Reference Laboratory of Sexually Transmitted Diseases, National Institute of Infectious Diseases - ANLIS 'Dr Carlos G. Malbrán', Ciudad Autónoma de Buenos Aires, Argentina
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30
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Boiko I, Golparian D, Jacobsson S, Krynytska I, Frankenberg A, Shevchenko T, Unemo M. Genomic epidemiology and antimicrobial resistance determinants of
Neisseria gonorrhoeae
isolates from Ukraine, 2013–2018. APMIS 2020; 128:465-475. [DOI: 10.1111/apm.13060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Iryna Boiko
- Department of Functional and Laboratory Diagnostics I. Horbachevsky Ternopil National Medical University Ternopil Ukraine
- WHO Collaborating Centre for Gonorrhoea and other STIs National Reference Laboratory for STIs Department of Laboratory Medicine Faculty of Medicine and Health Örebro University Örebro Sweden
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other STIs National Reference Laboratory for STIs Department of Laboratory Medicine Faculty of Medicine and Health Örebro University Örebro Sweden
| | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhoea and other STIs National Reference Laboratory for STIs Department of Laboratory Medicine Faculty of Medicine and Health Örebro University Örebro Sweden
| | - Inna Krynytska
- Department of Functional and Laboratory Diagnostics I. Horbachevsky Ternopil National Medical University Ternopil Ukraine
| | | | - Tetiana Shevchenko
- Department of General Medicine with a Course of Physical Therapy Faculty of Medical Technologies of Diagnostics and Rehabilitation Oles Honchar Dnipro National University Dnipro Ukraine
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other STIs National Reference Laboratory for STIs Department of Laboratory Medicine Faculty of Medicine and Health Örebro University Örebro Sweden
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31
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Shaskolskiy B, Kandinov I, Chestkov A, Solomka V, Kubanov A, Deryabin D, Gryadunov D, Dementieva E. Comparative phylogenetic analysis of Neisseria gonorrhoeae clinical isolates in Russia, European Union, and Japan. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Surveillance of multidrug-resistant infections is a priority task for contemporary epidemiology. The aim of this study was to genotype modern clinical isolates of N. gonorrhoeae using the NG-MAST technique (Neisseria gonorrhoeae multi-antigen sequence typing) and to compare the phylogeny of the gonococcal pathogens coming from Russia, European Union and Japan. We studied a total of 822 isolates collected in Russia from 2013 through 2018. We also used NG-MAST data from the following databases: PathogenWatch (European Union, 1,071 isolates) and PubMLST (Japan, 206 isolates). Russian isolates represented 301 different NG-MAST types. The most common were types 807, 228, 1993, 5714, and 9476 (8.3%, 3.3%, 3.2%, 3.2%, and 2.7%, respectively). There were only 3 isolates (0.4%) from Russia that represented the epidemiologically significant sequence type 1407 prevailing in many countries and characterized by multiple determinants of antimicrobial resistance. A phylogenetic tree for the NG-MAST types found in Russia and European countries was constructed. The cluster analysis of the proportion of isolates belonging to unique sequence types and the country population size allowed us to identify 2 clusters (significance level — 0.01): the first cluster included Russia and Japan, the second, European countries. A distribution pattern was identified for unique sequence types: the greater is the population size, the higher is their proportion. The phylogenetic analysis demonstrated a genetic distance between the most common Russian, European and Japanese sequence types, suggesting that the Russian population of N. gonorrhoeae has been evolving relatively locally.
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Affiliation(s)
- B.L. Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - I.D. Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A.V. Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - V.S. Solomka
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - A.A. Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - D.G. Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia
| | - D.A. Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E.I. Dementieva
- 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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32
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Shaskolskiy B, Dementieva E, Kandinov I, Chestkov A, Kubanov A, Deryabin D, Gryadunov D. Genetic diversity of Neisseria gonorrhoeae multi-antigen sequence types in Russia and Europe. Int J Infect Dis 2020; 93:1-8. [PMID: 31978578 DOI: 10.1016/j.ijid.2020.01.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES The goal of this work was to assess the genetic diversity of Neisseria gonorrhoeae isolates in Russia and Europe and to compare the distribution of the N. gonorrhoeae multi-antigen sequencing types (NG-MAST) of Russian isolates with that of isolates from European countries. METHODS NG-MAST typing was performed for 804 N. gonorrhoeae isolates collected in Russia in 2013-2018. For isolates from European countries, data from the https://pathogen.watch/collection/eurogasp2013 database were used. RESULTS Among the isolates from Russia, 296 NG-MAST types were found. A maximum likelihood phylogenetic tree was constructed. Phylogenetic analysis revealed seven major genogroups uniting the most frequent Russian sequence types: G807, G1993, G9476, G14942, G1152, G9486, and G12531. CONCLUSIONS The NG-MAST type distribution in Russia differed from that in European countries. Most of the Russian isolates had sequence types that were not found in Europe. Only 33% of the Russian isolates belonged to genogroups established for European countries, and the widespread European genogroup G1407 was represented by only nine isolates. Analysis of the Russian isolates belonging to phylogenetically close European genogroups indicated similarities in drug resistance, although no epidemically dangerous drug-resistant clones were found among the Russian isolates.
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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.
| | - Ekaterina Dementieva
- 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.
| | - Alexander Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Russian Ministry of Health, Moscow, Russia.
| | - Alexey Kubanov
- 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.
| | - 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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33
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Thakur SD, Levett PN, Horsman GB, Dillon JAR. Association of Neisseria gonorrhoeae genogroups and specific PBP2/MtrR/PorB mutation patterns with susceptibility to penicillin in a susceptible gonococcal population. J Antimicrob Chemother 2019; 73:2682-2686. [PMID: 29992304 DOI: 10.1093/jac/dky233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/21/2018] [Indexed: 12/25/2022] Open
Abstract
Objectives To ascertain whether the antimicrobial susceptibility of Neisseria gonorrhoeae isolates with differing susceptibilities to penicillin is associated with genogroups (GGs) and combined mutation patterns in PBP2 (penA), the multiple transfer resistance repressor (MtrR; mtrR) and porin B (PorB; porB). Methods The susceptibility of 146 clinical N. gonorrhoeae isolates to penicillin was determined using the agar dilution method and the interpretation criteria of CLSI. The DNA sequences of penA, mtrR and porB in isolates were compared with WT sequences and mutation patterns were determined. Isolates were typed by N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and STs were grouped into specific GGs. Results The isolates tested carried 9 mutation patterns in PBP2 and 12 mutation patterns in each of MtrR and PorB. Of the 146 isolates, 121 (82.9%) were grouped into 13 different GGs. Isolates with penicillin MICs of 0.03-0.06 mg/L were significantly associated with GG25 (P < 0.05) and PBP2/MtrR/PorB mutation pattern I/WT/WT (P < 0.01). Isolates with a penicillin MIC of 1.0 mg/L were associated (P < 0.05) with: (i) GG3655 and mutation pattern XXII/A-;G45D/G120K;A121N; (ii) GG921 and mutation pattern IX/G45D/G120D;A121N; and (iii) GG1109 and mutation pattern IX/G45D/WT. Sixty percent (9/15) of penicillin-resistant isolates (MIC ≥2 mg/L) were GG3654 (P < 0.0001) and carried mutation pattern IX/G45D/G120K;A121D or IX/G45D/G120D;A121D (P < 0.05). Conclusions Specific mutation patterns in PBP2/MtrR/PorB were associated with specific GGs and penicillin susceptibility. This approach of typing strains and resistance patterns is ideal for predicting antimicrobial resistance and should be used in instances in which gonococcal culture is not available but DNA can be obtained from clinical specimens.
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Affiliation(s)
- Sidharath D Thakur
- Department of Microbiology and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada.,Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), Saskatoon, Saskatchewan, Canada
| | - Paul N Levett
- Roy Romanow Provincial Laboratory (formerly the Saskatchewan Disease Control Laboratory), Regina, Saskatchewan, Canada
| | - Gregory B Horsman
- Roy Romanow Provincial Laboratory (formerly the Saskatchewan Disease Control Laboratory), Regina, Saskatchewan, Canada
| | - Jo-Anne R Dillon
- Department of Microbiology and Immunology, College of Medicine, Saskatoon, Saskatchewan, Canada.,Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), Saskatoon, Saskatchewan, Canada
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34
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Diallo K, MacLennan J, Harrison OB, Msefula C, Sow SO, Daugla DM, Johnson E, Trotter C, MacLennan CA, Parkhill J, Borrow R, Greenwood BM, Maiden MCJ. Genomic characterization of novel Neisseria species. Sci Rep 2019; 9:13742. [PMID: 31551478 PMCID: PMC6760525 DOI: 10.1038/s41598-019-50203-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/04/2019] [Indexed: 12/11/2022] Open
Abstract
Of the ten human-restricted Neisseria species two, Neisseria meningitidis, and Neisseria gonorrhoeae, cause invasive disease: the other eight are carried asymptomatically in the pharynx, possibly modulating meningococcal and gonococcal infections. Consequently, characterizing their diversity is important for understanding the microbiome in health and disease. Whole genome sequences from 181 Neisseria isolates were examined, including those of three well-defined species (N. meningitidis; N. gonorrhoeae; and Neisseria polysaccharea) and genomes of isolates unassigned to any species (Nspp). Sequence analysis of ribosomal genes, and a set of core (cgMLST) genes were used to infer phylogenetic relationships. Average Nucleotide Identity (ANI) and phenotypic data were used to define species clusters, and morphological and metabolic differences among them. Phylogenetic analyses identified two polyphyletic clusters (N. polysaccharea and Nspp.), while, cgMLST data grouped Nspp isolates into nine clusters and identified at least three N. polysaccharea clusters. ANI results classified Nspp into seven putative species, and also indicated at least three putative N. polysaccharea species. Electron microscopy identified morphological differences among these species. This genomic approach provided a consistent methodology for species characterization using distinct phylogenetic clusters. Seven putative novel Neisseria species were identified, confirming the importance of genomic studies in the characterization of the genus Neisseria.
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Affiliation(s)
- Kanny Diallo
- Centre pour les Vaccins en Développement, Bamako, Mali. .,Department of Zoology, University of Oxford, Oxford, UK.
| | | | | | - Chisomo Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Samba O Sow
- Centre pour les Vaccins en Développement, Bamako, Mali
| | | | - Errin Johnson
- Electron Microscopy Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Caroline Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Calman A MacLennan
- Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Ray Borrow
- Vaccine Evaluation Unit, Public Health England, Manchester, UK
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35
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Poncin T, Fouere S, Braille A, Camelena F, Agsous M, Bebear C, Kumanski S, Lot F, Mercier-Delarue S, Ngangro NN, Salmona M, Schnepf N, Timsit J, Unemo M, Bercot B. Multidrug-resistant Neisseria gonorrhoeae failing treatment with ceftriaxone and doxycycline in France, November 2017. ACTA ACUST UNITED AC 2019; 23. [PMID: 29845928 DOI: 10.2807/1560-7917.es.2018.23.21.1800264] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report a multidrug-resistant Neisseria gonorrhoeae urogenital and pharyngeal infection with ceftriaxone resistance and intermediate resistance to azithromycin in a heterosexual woman in her 20s in France. Treatment with ceftriaxone plus doxycycline failed for the pharyngeal localisation. Whole-genome sequencing of isolate F90 identified MLST1903, NG-MAST ST3435, NG-STAR233, and relevant resistance determinants. F90 showed phenotypic and genotypic similarities to an internationally spreading multidrug-resistant and ceftriaxone-resistant clone detected in Japan and subsequently in Australia, Canada and Denmark.
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Affiliation(s)
- Thibault Poncin
- French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Sebastien Fouere
- Dermatology Department, CeGGID (Free Information Screening and Diagnostics Centers), Saint Louis Hospital, APHP, Paris, France
| | - Aymeric Braille
- French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Francois Camelena
- Paris Diderot University, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Myriem Agsous
- French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Cecile Bebear
- University of Bordeaux, USC EA 3671 Mycoplasmal and chlamydial infections in humans; Centre Hospitalier Universitaire de Bordeaux, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Sylvain Kumanski
- French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France
| | - Florence Lot
- Santé Publique France, French National Public Health Agency, Saint-Maurice, France
| | | | | | - Maud Salmona
- Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Nathalie Schnepf
- French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
| | - Julie Timsit
- Dermatology Department, CeGGID (Free Information Screening and Diagnostics Centers), Saint Louis Hospital, APHP, Paris, France
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other STIs, National Reference Laboratory for STIs, Department of Laboratory Medicine, Faculty of Medicine and Health, Ӧrebro University, Ӧrebro, Sweden
| | - Beatrice Bercot
- Paris Diderot University, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France.,French National Reference Center for bacterial STI, Associated laboratory for gonococci, APHP, Paris, France.,Infectious Agents Department, Saint Louis Hospital, APHP, Paris, France
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Emergence and Spread of Neisseria gonorrhoeae Strains with High-Level Resistance to Azithromycin in Taiwan from 2001 to 2018. Antimicrob Agents Chemother 2019; 63:AAC.00773-19. [PMID: 31235631 DOI: 10.1128/aac.00773-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/17/2019] [Indexed: 01/17/2023] Open
Abstract
A total of 598 Neisseria gonorrhoeae isolates obtained from patients in Taiwan from 2001 to 2018 were evaluated. The MICs of ceftriaxone (CRO) and azithromycin (AZM) against the isolates were determined by the agar dilution method. N. gonorrhoeae isolates with AZM MICs of ≥1 μg/ml were identified and characterized by the presence of AZM resistance determinants. For high-level AZM-resistant (AZM-HLR) isolates (MIC ≥ 256 μg/ml), genotyping was performed using multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence typing (NG-MAST). Among the N. gonorrhoeae isolates studied, 8.7% (52/598) exhibited AZM MICs of ≥1 μg/ml. Thirteen of the 52 isolates contained A2059G (23S rRNA NG-STAR type 1) or C2611T (23S rRNA NG-STAR type 2) mutations. The prevalence of the A2059G mutation was higher in AZM-HLR isolates (P < 0.001). The -35A deletion in the promoter region of the mtrR gene did not differ between AZM-HLR isolates (100%, 10/10) and the isolates with AZM MICs of 1 μg/ml to 64 μg/ml (95.2%, 40/42) (P = 1.000). The presence of mutations in the mtrR coding region was significantly different between these two groups at 90% (9/10) and 26.2% (11/42), respectively (P < 0.001). The AZM-HLR isolates, all carrying four mutated A2059G alleles, a -35A deletion, and G45D, were classified as MLST 12039/10899 and NG-MAST 1866/16497. In conclusion, Taiwan is among the countries reporting gonococci with high-level resistance to AZM so that a single dose of 1 g ceftriaxone intramuscularly as the first choice for management of N. gonorrhoeae infection should be evaluated.
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Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case. Forensic Sci Int Genet 2019; 42:141-146. [PMID: 31319352 DOI: 10.1016/j.fsigen.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022]
Abstract
Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission episode in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods. We obtained genomes of Neisseria gonorrhoeae from the victim, the suspect, and 29 unrelated controls. The analysis of the genomes revealed that the victim and suspect isolates had identical sequences in both the bacterial chromosome and the single plasmid present in them. One of the local controls was very similar (differing in only 2 SNPs) to the case sequences, but the remaining controls were very divergent. Additional cases of identity and very high similarity among controls were observed occasionally, pointing at recent transmission cases. These results were more discriminative than the previous molecular epidemiology analyses performed at the hospital's Microbiology Service, as Multi-Locus Sequence Typing (MLST) could not distinguish between the suspect/victim and the controls isolates, and Pulse Field Gel Electrophoresis (PFGE) was not able to distinguish between the suspect/victim and one of the local controls. These results lead us to conclude that complete bacterial genome sequences obtained with HTS technologies may be a valuable tool for establishing recent transmission cases and, although more studies are needed, they have a great potential for being used in forensic analyses.
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Cobo F, Cabezas-Fernández MT, Avivar C. Typing and antimicrobial susceptibility of 134 Neisseria gonorrhoeae strains from Southern Spain. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32:114-120. [PMID: 30727713 PMCID: PMC6441978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Last guidelines have recommended the introduction of dual antimicrobial therapy in order to avoid treatment failure. In the present report, the susceptibility to some antibiotics was evaluated, and the typing of Neisseria gonorrhoeae strains was performed. METHODS Gonococcal isolates were tested for susceptibility according to the recommendations of both CLSI and EUCAST. A total of 134 isolates were typed by the NG-MAST technique. RESULTS Seventy-two different N. gonorrhoeae types were found, and the most frequent types obtained were ST 1407, ST 14958, ST 7192, ST 13251 and ST 5405. If CLSI/EUCAST criteria were applied, a ST 9807 type was found nonsusceptible to ceftriaxone and cefixime (MIC 0.5 mg/L), and a ST 12800 type was found nonsusceptible only to cefixime (MIC 0.25 mg/L). When only EUCAST breakpoints were taken into account, three strains were also resistant to cefixime (MIC 0.25 mg/L) and three isolates were resistant to ceftriaxone (MIC 0.19, 0.16 and 0.25 mg/L, respectively). The majority of strains were resistant to ciprofloxacin (68.6%), and all N. gonorrhoeae strains were susceptible to spectinomycin; 9.7% of isolates were resistant to azithromycin. CONCLUSIONS Molecular typing may be a useful tool to predict antimicrobial resistance. High rates of resistance to penicillin, tetracycline and ciprofloxacin were found in this area. It is highly recommended to carry out antimicrobial susceptibility in all gonorrhoea cases and to identify treatment failures to verify emerging resistance.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto Biosanitario de Granada. University Hospital Virgen de las Nieves. Granada, Spain
| | | | - Cristóbal Avivar
- Microbiology Section (Biotechnology Area). Hospital de Poniente. El Ejido, Almería, Spain
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Lopez-Canovas L, Martinez Benitez MB, Herrera Isidron JA, Flores Soto E. Pulsed Field Gel Electrophoresis: Past, present, and future. Anal Biochem 2019; 573:17-29. [PMID: 30826351 DOI: 10.1016/j.ab.2019.02.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/27/2022]
Abstract
Pulsed Field Gel Electrophoresis (PFGE) has been considered for many years the 'gold-standard' for characterizing many pathogenic organisms as well as for subtyping bacterial species causing infection outbreaks. This article reviews the basic principles of PFGE and it includes the main advantages and limitations of the different electrode configurations that have been used in PFGE equipment and their influence on the DNA electrophoretic separation. Remarkably, we summarize here the most relevant theoretical and practical aspects that we have learned for more than 20 years developing and using the miniaturized PFGE systems. We also discussed the theoretical aspects related to DNA migration in PFGE agarose gels. It served as the basis for simulating the DNA electrophoretic patterns in CHEF mini gels and mini-chambers during experimental design and optimization. A critical comparison between standard and miniaturized PFGE systems, as well as the enzymatic and non-enzymatic methods for intact immobilized DNA preparation, is provided throughout the review. The PFGE current applications, advantages, limitations and future challenges of the methodology are also discussed.
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Affiliation(s)
- Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | - Maximo B Martinez Benitez
- Postgraduate Program in Genomic Sciences, School of Science and Technology (CCyT), Autonomous University of Mexico City (UACM), Mexico City, Mexico.
| | | | - Eduardo Flores Soto
- Academy of Biology, School of Sciences and Humanities, UACM, Mexico City, Mexico.
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van der Veer BMJW, Wolffs PFG, Hoebe CJPA, Dukers-Muijrers NHTM, van Alphen LB. Culture-free genotyping of Neisseria gonorrhoeae revealed distinct strains at different anatomical sites in a quarter of patients, the Netherlands, 2012 to 2016. Euro Surveill 2018; 23:1800253. [PMID: 30563596 PMCID: PMC6299510 DOI: 10.2807/1560-7917.es.2018.23.50.1800253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundGenotyping of Neisseria gonorrhoeae (NG) is essential for surveillance to monitor NG transmission and dissemination of resistant strains. Current genotyping methods rely on bacterial culture which frequently fails.AimOur aim was to develop a culture-free genotyping method that is compatible with the widely used N. gonorrhoeae multi-antigen sequence typing (NG-MAST) database, which facilitates genotyping of NG detected at separate anatomical sites in individual patients.MethodsSpecific primers for both PCR targets porB and tbpB were designed and technically validated by assessing the analytical sensitivity, cross-reactivity with 32 non-gonoccocal Neisseria species, and concordance with NG-MAST. Clinical application was assessed on 205 paired samples from concurrent NG infections at different anatomical sites of 98 patients (81 men who have sex with men and 17 women) visiting our sexually transmitted infections clinic.ResultsTyping could be consistently performed on samples with a PCR quantification cycle (Cq) value <35. Furthermore, the method showed no cross-reactivity and was concordant with NG-MAST. Culture-free NG-MAST improved the typing rate from 62% (59/95) for cultured samples to 94% (89/95) compared with culture-dependent NG-MAST. Paired samples of 80 of 98 patients were genotyped, revealing distinct NG strains in separate anatomical sites in 25% (20/80) of the patients.ConclusionsThis NG-specific genotyping method can improve NG surveillance as it facilitates genotyping of non-culturable and extra-genital samples. Furthermore, 25% of patients were infected with multiple NG strains, which is missed in current culture-dependent surveillance. Including non-culturable and concurrent NG infections in surveillance informs actions on dissemination of multidrug-resistant NG strains.
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Affiliation(s)
- Brian MJW van der Veer
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Petra FG Wolffs
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
| | - Christian JPA Hoebe
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands,Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, the Netherlands
| | - Nicole HTM Dukers-Muijrers
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands,Department of Sexual Health, Infectious Diseases and Environmental Health, South Limburg Public Health Service, Heerlen, the Netherlands
| | - Lieke B van Alphen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre (MUMC+), Maastricht, the Netherlands
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Mlynarczyk-Bonikowska B, Malejczyk M, Majewski S, Unemo M. Antibiotic resistance and NG-MAST sequence types of Neisseria gonorrhoeae isolates in Poland compared to the world. Postepy Dermatol Alergol 2018; 35:346-551. [PMID: 30618519 PMCID: PMC6320495 DOI: 10.5114/ada.2018.79780] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/12/2018] [Indexed: 11/17/2022] Open
Abstract
Gonorrhoea is one of the most common sexually transmitted infections and in 2012, the World Health Organization estimated about 78 million of new global urogenital cases among adults per year. The main concern during the latest decade has been the emergence and spread of multidrug-resistant strains of Neisseria gonorrhoeae. Resistance has emerged internationally to the extended-spectrum cephalosporins, ceftriaxone and cefixime, which are the last remaining options for empiric first-line monotherapy of gonorrhoea. In Poland, the levels of resistance to ciprofloxacin, benzylpenicillin and tetracycline are high, and the prevalence of azithromycin resistance has increased. However, no resistance to ceftriaxone has been identified. The currently spread multidrug-resistant strains frequently represent epidemic clones. The present paper reviews and describes the antimicrobial resistance and N. gonorrhoeae multiantigen sequence typing (NG-MAST) sequence types of N. gonorrhoeae strains spreading in Poland compared to the world.
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Affiliation(s)
| | - Magdalena Malejczyk
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Sławomir Majewski
- Department of Diagnostics of Sexually Transmitted Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Magnus Unemo
- World Health Organization (WHO) Collaborating Centre for Gonorrhoea and other STIs, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Tanaka M, Furuya R, Kobayashi I, Kanesaka I, Ohno A, Katsuse AK. Antimicrobial resistance and molecular characterisation of Neisseria gonorrhoeae isolates in Fukuoka, Japan, 1996-2016. J Glob Antimicrob Resist 2018; 17:3-7. [PMID: 30448519 DOI: 10.1016/j.jgar.2018.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Antimicrobial resistance and molecular characteristics of Neisseria gonorrhoeae isolates obtained from 1996-2005 (n=200) and 2008-2016 (n=200) in Fukuoka, Japan, were examined. METHODS MICs were determined by agar dilution. Sequence types (STs) were examined using N. gonorrhoeae multiantigen sequence typing (NG-MAST). Sequencing of major extended-spectrum cephalosporin (ESC) resistance determinants (penA, mtrR and ponA) was performed. RESULTS Increases in the proportion of gonococci with decreased susceptibility or resistance to cefixime (from 18.0% in 1996-2005 to 46.0% in 2008-2016) and ceftriaxone (from 2.5% to 4.0%) were observed. Gonococcal isolates also showed increased resistance to ciprofloxacin and azithromycin. The four most prevalent NG-MAST STs with a multidrug-resistant phenotype were ST2958 (n=18), ST1407 (n=14), ST6798 (n=12) and ST4015 (n=10). The number of isolates belonging to these four STs rose between the first and second period. Among the 54 isolates belonging to the four major STs, 42 (77.8%) contained a penA mosaic allele and 12 (22.2%) contained a penA non-mosaic allele. The sequence pattern types in the 42 isolates with a penA mosaic allele included type X (64.3%), type XXXIV (33.3%) and a novel pattern type (2.4%). In contrast, all 12 isolates with the penA non-mosaic allele included the sequence pattern type V. CONCLUSION Neisseria gonorrhoeae isolates with decreased susceptibility or resistance to ESC have increased over the years. Four major STs with a multidrug-resistant phenotype were identified. These isolates contained a penA mosaic allele or a non-mosaic allele.
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Affiliation(s)
- Masatoshi Tanaka
- Department of Urology, Faculty of Medical, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan.
| | - Ryusaburo Furuya
- Department of Urology, Faculty of Medical, Fukuoka University, 7-45-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Intetsu Kobayashi
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, Tokyo, Japan
| | - Izumo Kanesaka
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, Tokyo, Japan
| | - Akira Ohno
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, Tokyo, Japan
| | - Akiko Kanayama Katsuse
- Department of Infection Control and Prevention, Faculty of Nursing, Toho University, Tokyo, Japan
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Rim JH, Kim H, Lee H, Yong D, Jeong SH, Lee K. Recent Increase in the Incidence of TEM-135 β-Lactamase-harboring Neisseria gonorrhoeae in Korea. Ann Lab Med 2018; 38:324-330. [PMID: 29611382 PMCID: PMC5895861 DOI: 10.3343/alm.2018.38.4.324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/30/2017] [Accepted: 02/27/2018] [Indexed: 12/04/2022] Open
Abstract
Background We investigated the molecular epidemiological characteristics and antimicrobial susceptibility pattern of penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates to monitor the change in distribution of blaTEM in Korea. Methods We collected 804 PPNG isolates from diverse hospitals and clinics mainly located in Seoul, Korea, over a period of 11 years (2005–2015). Isolate susceptibility to seven antimicrobials was determined using the agar dilution test. The molecular epidemiological characteristics of the isolates were determined by Sanger sequencing of blaTEM, N. gonorrhoeae multiantigen sequence typing (NG-MAST) and plasmid typing. Results Among 72 fully sequenced PPNG isolates, sixteen (22.2%) possessed TEM-135. All TEM-135 isolates had a common silent mutation (c.18C>T), which was previously unreported. We observed a pattern of continuous increase in the number of TEM-135 isolates since 2012. The median and 90% minimum inhibitory concentration of azithromycin were substantially lower in the TEM-135 group than in the non-PPNG and TEM-1 groups. All TEM-135 isolates showed different NG-MAST types and predominantly harbored Toronto/Rio (75%) plasmids. A comprehensive comparative analysis of PPNG with TEM-135 according to NG-MAST, plasmid type, and year of isolation revealed a wide distribution. Conclusions The proportion of TEM-135 PPNG has continuously increased since 2012, in association with clonal spread. The difference at position 18 of the TEM-135 sequence can be interpreted as the existence of multiple clonal complexes. The possibility that TEM-135 was acquired via foreign plasmids requires careful follow-up and continuous monitoring of TEM-135 to ascertain whether it constitutes a step towards evolutionary change.
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Affiliation(s)
- John Hoon Rim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.,Department of Pharmacology, Yonsei University College of Medicine, Seoul, Korea.,Department of Medicine, Physician-Scientist Program, Yonsei University Graduate School of Medicine, Seoul, Korea
| | - Hyunsoo Kim
- Department of Laboratory Medicine, The National Police Hospital, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea.
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Surveillance for Antimicrobial Resistance in Gonorrhea: The Alberta Model, 2012⁻2016. Antibiotics (Basel) 2018; 7:antibiotics7030063. [PMID: 30036946 PMCID: PMC6164219 DOI: 10.3390/antibiotics7030063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/16/2022] Open
Abstract
Alberta established a surveillance system in 2001 to monitor resistance to antibiotics used for the treatment of gonorrhea. A retrospective review of gonorrhea cases during the last five years was conducted. All cases of gonorrhea were reportable to public health by testing laboratories and clinicians. Specimens were primarily submitted for nucleic acid amplification testing (NAAT); three sentinel sites obtained specimens for culture and NAAT. The Provincial Laboratory for Public Health conducted E-tests on isolates for multiple antibiotics. A proportion of isolates and NAAT specimens were submitted to the National Microbiology Laboratory for sequence typing (ST). Data were combined and analyzed using SAS version 9.4. Between 2012 and 2016, 13,132 gonorrhea cases were reported; 22.0% (n = 2891) had isolates available for susceptibility testing. All culture positive isolates were susceptible to ceftriaxone. Decreased susceptibility (0.5 ug/mL) to cefixime was reported in four cases in 2014. Resistance to azithromycin (≥2 ug/mL) ranged between 0.4% and 1.8%. Many (n = 509) unique STs were identified; the most prevalent sequence groups (SG) were SG-7638 (n = 367), SG-5985 (n = 145), and SG-11299 (n = 127). The Alberta model for maintaining surveillance for antimicrobial resistance in gonorrhea employs culture and NAAT specimens, providing information crucial to informing provincial treatment guidelines.
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Town K, Bolt H, Croxford S, Cole M, Harris S, Field N, Hughes G. Neisseria gonorrhoeae molecular typing for understanding sexual networks and antimicrobial resistance transmission: A systematic review. J Infect 2018; 76:507-514. [PMID: 29698633 PMCID: PMC5999358 DOI: 10.1016/j.jinf.2018.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/11/2018] [Accepted: 02/19/2018] [Indexed: 11/19/2022]
Abstract
Combined molecular and epidemiological data can describe the spread of gonorrhoea. Sexual networks can be inferred from molecular clusters of infection. Gender and sexual orientation are commonly used to characterise these networks. Application of these data within gonorrhoea control interventions is limited. Future studies should focus on evaluating molecular typing data in practice.
Objectives Neisseria gonorrhoeae (NG) is a significant global public health concern due to rising diagnoses rates and antimicrobial resistance. Molecular combined with epidemiological data have been used to understand the distribution and spread of NG, as well as relationships between cases in sexual networks, but the public health value gained from these studies is unclear. We conducted a systematic review to examine how molecular epidemiological studies have informed understanding of sexual networks and NG transmission, and subsequent public health interventions. Methods Five research databases were systematically searched up to 31st March 2017 for studies that used sequence-based DNA typing methods, including whole genome sequencing, and linked molecular data to patient-level epidemiological data. Data were extracted and summarised to identify common themes. Results Of the 49 studies included, 82% used NG Multi-antigen Sequence Typing. Gender and sexual orientation were commonly used to characterise sexual networks that were inferred using molecular clusters; clusters predominantly of one patient group often contained a small number of isolates from other patient groups. Suggested public health applications included using these data to target interventions at specific populations, confirm outbreaks, and inform partner management, but these were mainly untested. Conclusions Combining molecular and epidemiological data has provided insight into sexual mixing patterns, and dissemination of NG, but few studies have applied these findings to design or evaluate public health interventions. Future studies should focus on the application of molecular epidemiology in public health practice to provide evidence for how to prevent and control NG.
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Affiliation(s)
- Katy Town
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections at University College London in partnership with Public Health England and in collaboration with the London School of Hygiene and Tropical Medicine, Mortimer Market Centre, Third Floor, Capper Street, London WC1E 6JB, UK; Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, Mortimer Market Centre, Capper Street, London WC1E 6JB, UK.
| | - Hikaru Bolt
- HIV/STI Department, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Sara Croxford
- HIV/STI Department, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Michelle Cole
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Simon Harris
- The Wellcome Trust Sanger Institute, Genome Campus, Cambridge CB10 1SA, UK
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, Mortimer Market Centre, Capper Street, London WC1E 6JB, UK
| | - Gwenda Hughes
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections at University College London in partnership with Public Health England and in collaboration with the London School of Hygiene and Tropical Medicine, Mortimer Market Centre, Third Floor, Capper Street, London WC1E 6JB, UK; HIV/STI Department, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing. Appl Microbiol Biotechnol 2018; 102:4853-4861. [PMID: 29619504 DOI: 10.1007/s00253-018-8942-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
Abstract
In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.
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Buder S, Dudareva S, Jansen K, Loenenbach A, Nikisins S, Sailer A, Guhl E, Kohl PK, Bremer V. Antimicrobial resistance of Neisseria gonorrhoeae in Germany: low levels of cephalosporin resistance, but high azithromycin resistance. BMC Infect Dis 2018; 18:44. [PMID: 29343220 PMCID: PMC5772720 DOI: 10.1186/s12879-018-2944-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 01/03/2018] [Indexed: 11/15/2022] Open
Abstract
Background The widespread antimicrobial resistance of Neisseria gonorrhoeae is a serious problem for the treatment and control of gonorrhoea. Many of the previously effective therapeutic agents are no longer viable. Because N. gonorrhoeae infections are not reportable in Germany, only limited data on disease epidemiology and antimicrobial susceptibility patterns are available. The Gonococcal Resistance Network (GORENET) is a surveillance project to monitor trends in the antimicrobial susceptibility of N. gonorrhoeae in Germany in order to guide treatment algorithms and target future prevention strategies. Methods Between April 2014 and December 2015, data on patient-related information were collected from laboratories nationwide, and susceptibility testing was performed on 537 N. gonorrhoeae isolates forwarded from the network laboratories to the Conciliar Laboratory for gonococci. Susceptibility results for cefixime, ceftriaxone, azithromycin, ciprofloxacin and penicillin were defined according to EUCAST 4.0 standards. Percentages, medians and interquartile ranges (IQR) were calculated. Results Altogether, 90% of isolates were from men. The median age was 32 (IQR 25–44) years for men and 25 (IQR 22–40) years for women (p-value < 0.001). The most frequently tested materials among men were urethral (96.1%) and rectal swabs (1.7%), and among women, it was mainly endocervical and vaginal swabs (84.3%). None of the isolates were resistant to ceftriaxone. Furthermore, 1.9% (in 2014) and 1.4% (in 2015) of the isolates were resistant to cefixime, 11.9% and 9.8% showed resistance against azithromycin, 72.0% and 58.3% were resistant to ciprofloxacin, and 29.1% and 18.8% were resistant to penicillin. Conclusions Resistance to ceftriaxone was not detected, and the percentage of isolates with resistance to cefixime was low, whereas azithromycin resistance showed high levels during the observation period. The rates of ciprofloxacin resistance and penicillin resistance were very high across Germany. Continued surveillance of antimicrobial drug susceptibilities for N. gonorrhoeae remains highly important to ensure efficient disease management.
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Affiliation(s)
- Susanne Buder
- German Consiliary Laboratory for Gonococci, Department of Dermatology and Venerology, Vivantes Hospital Berlin, Berlin, Germany.
| | - Sandra Dudareva
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany. .,Charité University Medicine Berlin, Berlin, Germany.
| | - Klaus Jansen
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Anna Loenenbach
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Sergejs Nikisins
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.,European Public Health Microbiology Training (EUPHEM) programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Andrea Sailer
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Eva Guhl
- German Consiliary Laboratory for Gonococci, Department of Dermatology and Venerology, Vivantes Hospital Berlin, Berlin, Germany
| | - Peter K Kohl
- German Consiliary Laboratory for Gonococci, Department of Dermatology and Venerology, Vivantes Hospital Berlin, Berlin, Germany
| | - Viviane Bremer
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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Hananta IPY, van Dam AP, Schim van der Loeff MF, Dierdorp M, Wind CM, Soebono H, de Vries HJC, Bruisten SM. Molecular epidemiology of Neisseria gonorrhoeae strains circulating in Indonesia using multi-locus variable number tandem repeat analysis (MLVA) and Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) techniques. BMC Infect Dis 2018; 18:7. [PMID: 29304758 PMCID: PMC5755298 DOI: 10.1186/s12879-017-2940-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/25/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Control of gonorrhea in resource-limited countries, such as Indonesia, is mostly unsuccessful. Examining Neisseria gonorrhoeae (Ng) transmission networks using strain typing might help prioritizing public health interventions. METHODS In 2014, urogenital Ng strains were isolated from clients of sexually transmitted infection clinics in three Indonesian cities. Strains were typed using Multiple-Locus Variable Number Tandem Repeat (VNTR) Analysis (MLVA) and Ng Multi-Antigen Sequence Typing (NG-MAST) at the Public Health Service, Amsterdam, the Netherlands, and compared to Dutch strains collected from 2012 to 2015. Minimum spanning trees (MSTs) were constructed using MLVA profiles incorporating demographics and NG-MAST genogroups. A cluster was defined as ≥5 strains differing in ≤1 VNTR locus. The concordance between MLVA and NG-MAST was examined with the adjusted Wallace coefficients (AW). RESULTS We collected a total of 78 Indonesian strains from Yogyakarta (n = 44), Jakarta (n = 25), and Denpasar (n = 9). Seven MLVA clusters and 16 non-clustered strains were identified. No cluster was specific for any geographic area, risk group or age group. Combined with 119 contemporary Dutch strains, 8 MLVA clusters were identified, being four clusters of Indonesian strains, two of Dutch strains, and two of both Indonesian and Dutch strains. Indonesian strains (79.5%) were more often clustered compared to Dutch strains (24.3%). The most prevalent NG-MAST genogroups among Indonesian strains was G1407 (51.3%) and among Dutch strains was G2992 (19.3%). In Indonesian strains, the AW [95% confidence interval] for MLVA to NG-MAST was 0.07 [0.00-0.27] and for NG-MAST to MLVA was 0.03 [0.00-0.12]. CONCLUSION Indonesian Ng strains are more often clustered than Dutch strains, but show no relation with geographical area, risk group, or age group, suggesting a more clonal Ng epidemic in Indonesia. Some similar Ng strains circulate in both Indonesia and the Netherlands.
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Affiliation(s)
- I Putu Yuda Hananta
- Academic Medical Center University of Amsterdam, Amsterdam, the Netherlands. .,Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands.
| | - Alje Pieter van Dam
- Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands.,Onze Lieve Vrouwe Gasthuis (OLVG) Hospital, Amsterdam, the Netherlands
| | - Maarten Franciscus Schim van der Loeff
- Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands.,Amsterdam Infection and Immunity Institute (AI&II), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Mirjam Dierdorp
- Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands
| | - Carolien Marleen Wind
- Academic Medical Center University of Amsterdam, Amsterdam, the Netherlands.,Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands
| | - Hardyanto Soebono
- Department of Dermatology and Venereology Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Henry John Christiaan de Vries
- Academic Medical Center University of Amsterdam, Amsterdam, the Netherlands.,Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands
| | - Sylvia Maria Bruisten
- Public Health Laboratory,Public Health Service (GGD) of Amsterdam, Nieuwe Achtergracht 100, 1018, WT, Amsterdam, the Netherlands.,Amsterdam Infection and Immunity Institute (AI&II), Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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Antimicrobial Susceptibility Evaluation and Multiple-Locus Variable Number Tandem Repeat Analysis of Neisseria gonorrhoeae Isolates in China in 2012. Sex Transm Dis 2017; 44:197-201. [PMID: 28282644 DOI: 10.1097/olq.0000000000000580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE This study aimed to gain information on the antimicrobial susceptibility and molecular epidemiological typing of Neisseria gonorrhoeae (NG) isolates in China in 2012. METHODS A total of 244 NG isolates were consecutively recovered from patients with uncomplicated gonorrhea attending sexually transmitted disease clinics in 3 Chinese cities-Guangzhou, Nanjing, and Tianjin-in 2012. Neisseria gonorrhoeae susceptibilities to penicillin and tetracycline were examined by detecting penicillinase-producing NG (PPNG) and high-level tetracycline-resistant NG, and NG susceptibilities to ciprofloxacin, spectinomycin, ceftriaxone, and cefixime were determined using an agar dilution method. Neisseria gonorrhoeae isolates were typed by multiple-locus variable number tandem repeat analysis. We conducted a χ analysis to compare clusters with Bonferroni correction and Kruskal-Wallis test. RESULTS Neisseria gonorrhoeae isolates gathered from the 3 cities differed significantly in the prevalence of tetracycline-resistant NG (P < 0.001) and NG treated with ceftriaxone with a minimum inhibitory concentration of 0.125 mg/L or higher (P < 0.001). The analysis of the combination of the 7 variable number of tandem repeats loci for all of the 244 isolates yielded 110 multiple-locus variable number tandem repeat analysis types falling into 5 clusters. Cluster III was associated with PPNG, whereas cluster II was associated with non-PPNG (P < 0.05) and NG treated with ceftriaxone with a minimum inhibitory concentration of 0.125 mg/L or higher (P < 0.05). CONCLUSIONS Antimicrobials that can be used with confidence to treat NG infection currently in China include ceftriaxone and spectinomycin, but not penicillin, tetracycline, ciprofloxacin, and cefixime. Moreover, some of the resulting clusters were associated with PPNG and NG with decreased ceftriaxone susceptibility.
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Costa-Lourenço APRD, Barros Dos Santos KT, Moreira BM, Fracalanzza SEL, Bonelli RR. Antimicrobial resistance in Neisseria gonorrhoeae: history, molecular mechanisms and epidemiological aspects of an emerging global threat. Braz J Microbiol 2017; 48:617-628. [PMID: 28754299 PMCID: PMC5628311 DOI: 10.1016/j.bjm.2017.06.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 06/03/2017] [Accepted: 06/05/2017] [Indexed: 12/31/2022] Open
Abstract
Neisseria gonorrhoeae is the agent of gonorrhea, a sexually transmitted infection with an estimate from The World Health Organization of 78 million new cases in people aged 15-49 worldwide during 2012. If left untreated, complications may include pelvic inflammatory disease and infertility. Antimicrobial treatment is usually effective; however, resistance has emerged successively through various molecular mechanisms for all the regularly used therapeutic agents throughout decades. Detection of antimicrobial susceptibility is currently the most critical aspect for N. gonorrhoeae surveillance, however poorly structured health systems pose difficulties. In this review, we compiled data from worldwide reports regarding epidemiology and antimicrobial resistance in N. gonorrhoeae, and highlight the relevance of the implementation of surveillance networks to establish policies for gonorrhea treatment.
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Affiliation(s)
| | | | - Beatriz Meurer Moreira
- Institute of Microbiology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Raquel Regina Bonelli
- Institute of Microbiology, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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