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Clegg SR, Angell JW, Millson SH, Duncan JS, Staton GJ, Evans NJ. Multilocus sequence typing of pathogenic treponemes isolated from contagious ovine digital dermatitis stage five lesions: Implications for disease transmission dynamics. Res Vet Sci 2024; 177:105345. [PMID: 38996658 DOI: 10.1016/j.rvsc.2024.105345] [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: 03/24/2024] [Revised: 05/24/2024] [Accepted: 06/30/2024] [Indexed: 07/14/2024]
Abstract
Contagious ovine digital dermatitis (CODD) causes a severe, infectious foot disease and lameness of sheep, is common within the UK and is now also emerging in other countries. As well as causing severe animal welfare issues, huge economic losses emerge from the disease due to weight loss/lack of weight gain, and veterinary treatments. CODD lesion progress is measured, with a scoring system from 1 (early lesions) to 5 (healed). Here, using samples from an experimental flock infected by natural means, samples were taken from CODD stage 5 lesions, post treatment, and subjected to bacterial isolation and MLST using previously published methods. Sequences were compared to others from the same flock, and those from previous studies. All CODD 5 lesions produced viable Treponema spp. bacteria. High levels of variation of bacteria were seen, with 12 sequence types (STs) for T. medium phylogroup (11 new), 15 STs for T. phagedenis phylogroup (9 new) and six T. pedis STs, of which two were new. This study shows that CODD stage 5 lesions still contain viable bacteria, representing all three known pathogenic Treponema spp. phylogroups, and these may thus play a role in disease transmission and epidemiology despite appearing healed after treatment. The high level CODD treponeme variability within an infected flock where sheep were bought from different sources, as might occur in common agricultural practice, may suggest reasons as to why the bacterial disease is difficult to treat, control and eradicate, and adds further complexity to the polybacterial pathogenesis of these lesions.
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Affiliation(s)
- S R Clegg
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; School of Life and Environmental Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln, UK.
| | - J W Angell
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Wern Vets CYF, Department of Research and Innovation, Unit 11, Lon Parcwr Industrial Estate, Ruthin, Denbighshire LL15 1NJ, UK
| | - S H Millson
- School of Life and Environmental Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln, UK
| | - J S Duncan
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - G J Staton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - N J Evans
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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Caracoti VI, Caracoti CȘ, Ancuța DL, Ioniță F, Muntean AA, Bhide M, Popa GL, Popa MI, Coman C. Developing a Novel Murine Meningococcal Meningitis Model Using a Capsule-Null Bacterial Strain. Diagnostics (Basel) 2024; 14:1116. [PMID: 38893642 PMCID: PMC11172168 DOI: 10.3390/diagnostics14111116] [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: 03/18/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Neisseria meningitidis (meningococcus) is a Gram-negative bacterium that colonises the nasopharynx of about 10% of the healthy human population. Under certain conditions, it spreads into the body, causing infections with high morbidity and mortality rates. Although the capsule is the key virulence factor, unencapsulated strains have proved to possess significant clinical implications as well. Meningococcal meningitis is a primarily human infection, with limited animal models that are dependent on a variety of parameters such as bacterial virulence and mouse strain. In this study, we aimed to develop a murine Neisseria meningitidis meningitis model to be used in the study of various antimicrobial compounds. METHOD We used a capsule-deficient Neisseria meningitidis strain that was thoroughly analysed through various methods. The bacterial strain was incubated for 48 h in brain-heart infusion (BHI) broth before being concentrated and injected intracisternally to bypass the blood-brain barrier in CD-1 mice. This prolonged incubation time was a key factor in increasing the virulence of the bacterial strain. A total of three more differently prepared inoculums were tested to further solidify the importance of the protocol (a 24-h incubated inoculum, a diluted inoculum, and an inactivated inoculum). Antibiotic treatment groups were also established. The clinical parameters and number of deaths were recorded over a period of 5 days, and comatose mice with no chance of recovery were euthanised. RESULTS The bacterial strain was confirmed to have no capsule but was found to harbour a total of 56 genes coding virulence factors, and its antibiotic susceptibility was established. Meningitis was confirmed through positive tissue culture and histological evaluation, where specific lesions were observed, such as perivascular sheaths with inflammatory infiltrate. In the treatment groups, survival rates were significantly higher (up to 81.25% in one of the treatment groups compared to 18.75% in the control group). CONCLUSION We managed to successfully develop a cost-efficient murine (using simple CD-1 mice instead of expensive transgenic mice) meningococcal meningitis model using an unencapsulated strain with a novel method of preparation.
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Affiliation(s)
- Viorela-I. Caracoti
- Faculty of Medicine, Microbiology Discipline II, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-I.C.); (C.-Ș.C.); (A.-A.M.); (G.L.P.)
| | - Costin-Ș. Caracoti
- Faculty of Medicine, Microbiology Discipline II, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-I.C.); (C.-Ș.C.); (A.-A.M.); (G.L.P.)
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
| | - Diana L. Ancuța
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine, 050097 Bucharest, Romania
| | - Fabiola Ioniță
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine, 050097 Bucharest, Romania
| | - Andrei-A. Muntean
- Faculty of Medicine, Microbiology Discipline II, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-I.C.); (C.-Ș.C.); (A.-A.M.); (G.L.P.)
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
| | - Mangesh Bhide
- Faculty of Veterinary Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 73, 04181 Kosice, Slovakia;
- Institute of Neuroimmunology of Slovak Academy of Sciences, Dubravska Cesta 9, 84510 Bratislava, Slovakia
| | - Gabriela L. Popa
- Faculty of Medicine, Microbiology Discipline II, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-I.C.); (C.-Ș.C.); (A.-A.M.); (G.L.P.)
| | - Mircea I. Popa
- Faculty of Medicine, Microbiology Discipline II, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (V.-I.C.); (C.-Ș.C.); (A.-A.M.); (G.L.P.)
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
| | - Cristin Coman
- Cantacuzino National Military Medical Institute for Research and Development, Preclinical Testing Unit, 050096 Bucharest, Romania; (D.L.A.); (F.I.); (C.C.)
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine, 050097 Bucharest, Romania
- Fundeni Clinical Institute Translational Medicine Centre of Excellence, 022328 Bucharest, Romania
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Sarenje KL, van Zwetselaar M, Kumburu H, Sonda T, Mmbaga B, Ngalamika O, Maimbolwa MC, Siame A, Munsaka S, Kwenda G. Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia. BMC Genomics 2024; 25:290. [PMID: 38500064 PMCID: PMC10949682 DOI: 10.1186/s12864-024-10155-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia. METHODS A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset. RESULTS The most frequent STs with 18.4% of isolates each were ST7363, ST1921 and ST1582, followed by ST1583 (13%), novel ST17026 (7.9%), ST1588 (7.9%), ST1596 (5.3%), ST11181 (5.3%), ST11750 (2.6/%) and ST11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B, ermT, and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM (15.8%), and gonococcal genetic island (GGI) was detected in all isolates. CONCLUSION This study revealed remarkable heterogeneity of N. gonorrhoeae with blaTEM-1, tetM, ponA, gyrA, and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.
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Affiliation(s)
- Kelvin Lutambo Sarenje
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia.
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia.
| | | | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Owen Ngalamika
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia
| | - Margaret C Maimbolwa
- Department of Midwifery Child, and Women's Health, School of Nursing Sciences, University of Zambia, Lusaka, Zambia
| | - Amon Siame
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
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Klaper K, Tlapák H, Selb R, Jansen K, Heuer D. Integrated molecular, phenotypic and epidemiological surveillance of antimicrobial resistance in Neisseria gonorrhoeae in Germany. Int J Med Microbiol 2024; 314:151611. [PMID: 38309143 DOI: 10.1016/j.ijmm.2024.151611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Numbers of infections with Neisseria gonorrhoeae are among the top three sexually transmitted infections (STI) worldwide. In addition, the emergence and spread of antimicrobial resistance (AMR) in Neisseria gonorrhoeae pose an important public-health issue. The integration of genomic, phenotypic and epidemiological data to monitor Neisseria gonorrhoeae fosters our understanding of the emergence and spread of AMR in Neisseria gonorrhoeae and helps to inform therapy guidelines and intervention strategies. Thus, the Gonococcal resistance surveillance (Go-Surv-AMR) was implemented at the Robert Koch Institute in Germany in 2021 to obtain molecular, phenotypic and epidemiological data on Neisseria gonorrhoeae isolated in Germany. Here, we describe the structure and aims of Go-Surv-AMR. Furthermore, we point out future directions of Go-Surv-AMR to improve the integrated genomic surveillance of Neisseria gonorrhoeae. In this context we discuss current and prospective sequencing approaches and the information derived from their application. Moreover, we highlight the importance of combining phenotypic and WGS data to monitor the evolution of AMR in Neisseria gonorrhoeae in Germany. The implementation and constant development of techniques and tools to improve the genomic surveillance of Neisseria gonorrhoeae will be important in coming years.
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Affiliation(s)
- Kathleen Klaper
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Hana Tlapák
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Regina Selb
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Klaus Jansen
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Dagmar Heuer
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany.
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Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M. pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections. Microb Genom 2024; 10:001189. [PMID: 38288762 PMCID: PMC10868605 DOI: 10.1099/mgen.0.001189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.
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Affiliation(s)
- Leonor Sánchez-Busó
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBERESP, ISCIII, Spain
| | - Andrea Sánchez-Serrano
- Joint Research Unit ‘Infection and Public Health’, FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Department of Laboratory Medicine Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London (UCL), London, UK
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Núñez-Samudio V, Herrera M, Herrera G, Pimentel-Peralta G, Landires I. The Molecular Genetic Epidemiology and Antimicrobial Resistance of Neisseria gonorrhoeae Strains Obtained from Clinical Isolates in Central Panama. Microorganisms 2023; 11:2572. [PMID: 37894230 PMCID: PMC10608929 DOI: 10.3390/microorganisms11102572] [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: 09/25/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
We aim to analyze Neisseria gonorrhoeae isolates in central Panama, characterize the associated gonococcal antimicrobial resistance (AMR) and conduct molecular epidemiology and genetic typing. We conducted a retrospective study based on N. gonorrhoeae hospital isolates collected between 2013 and 2018. AMR was determined using dilution agar and Etest®. Molecular typing was conducted using the Multilocus Sequence Typing (ST) scheme. The isolates analyzed (n = 30) showed resistance to penicillin (38%), tetracycline (40%), and ciprofloxacin (30%), and sensitivity to extended-spectrum cephalosporins and azithromycin. We identified 11 STs, the most frequent of which was ST1901 among the strains with decreased sensitivity and resistance to three types of antibiotics. We identified eight variations for the penA gene, all non-mosaic, with type II LVG as the most frequent (50%). To the best of our knowledge, we conducted the first Central American genomic study that analyzes a collection of gonococcal isolates, which represents a benchmark for future epidemiological and molecular genetic studies. The high prevalence of ciprofloxacin, tetracycline, and penicillin resistance, in addition to the identification of the worldwide spread of multidrug-resistant clone ST1901, should prompt the continuous and reinforced surveillance of AMR, including the molecular epidemiology of N. gonorrhoeae in Panama.
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Affiliation(s)
- Virginia Núñez-Samudio
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama;
- Sección de Epidemiología, Departamento de Salud Pública, Región de Salud de Herrera, Ministry of Health, Chitré 0601, Herrera, Panama
| | - Mellissa Herrera
- Laboratorio Clínico, Hospital Luis “Chicho” Fábrega, Región de Salud Veraguas, Ministry of Health, Santiago 0923, Veraguas, Panama; (M.H.); (G.H.)
| | - Genarino Herrera
- Laboratorio Clínico, Hospital Luis “Chicho” Fábrega, Región de Salud Veraguas, Ministry of Health, Santiago 0923, Veraguas, Panama; (M.H.); (G.H.)
| | | | - Iván Landires
- Instituto de Ciencias Médicas, Las Tablas 0710, Los Santos, Panama;
- Hospital Regional Dr. Joaquín Pablo Franco Sayas, Región de Salud de Los Santos, Ministry of Health, Las Tablas 0710, Los Santos, Panama
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Kakooza F, Golparian D, Matoga M, Maseko V, Lamorde M, Krysiak R, Manabe YC, Chen JS, Kularatne R, Jacobsson S, Godreuil S, Hoffman I, Bercot B, Wi T, Unemo M. Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20. J Antimicrob Chemother 2023; 78:1982-1991. [PMID: 37352017 DOI: 10.1093/jac/dkad193] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/06/2023] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVES Global antimicrobial resistance (AMR) surveillance in Neisseria gonorrhoeae is essential. In 2017-18, only five (10.6%) countries in the WHO African Region reported to the WHO Global Gonococcal Antimicrobial Surveillance Programme (WHO GASP). Genomics enhances our understanding of gonococcal populations nationally and internationally, including AMR strain transmission; however, genomic studies from Africa are extremely scarce. We describe the gonococcal genomic lineages/sublineages, including AMR determinants, and baseline genomic diversity among strains in Uganda, Malawi and South Africa, 2015-20, and compare with sequences from Kenya and Burkina Faso. METHODS Gonococcal isolates cultured in Uganda (n = 433), Malawi (n = 154) and South Africa (n = 99) in 2015-20 were genome-sequenced. MICs were determined using ETEST. Sequences of isolates from Kenya (n = 159), Burkina Faso (n = 52) and the 2016 WHO reference strains (n = 14) were included in the analysis. RESULTS Resistance to ciprofloxacin was high in all countries (57.1%-100%). All isolates were susceptible to ceftriaxone, cefixime and spectinomycin, and 99.9% were susceptible to azithromycin. AMR determinants for ciprofloxacin, benzylpenicillin and tetracycline were common, but rare for cephalosporins and azithromycin. Most isolates belonged to the more antimicrobial-susceptible lineage B (n = 780) compared with the AMR lineage A (n = 141), and limited geographical phylogenomic signal was observed. CONCLUSIONS We report the first multi-country gonococcal genomic comparison from Africa, which will support the WHO GASP and WHO enhanced GASP (EGASP). The high prevalence of resistance to ciprofloxacin (and empirical use continues), tetracycline and benzylpenicillin, and the emerging resistance determinants for azithromycin show it is imperative to strengthen the gonococcal AMR surveillance, ideally including genomics, in African countries.
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Affiliation(s)
- Francis Kakooza
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Daniel Golparian
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
| | | | - Venessa Maseko
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Yuka C Manabe
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jane S Chen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ranmini Kularatne
- Labtests Laboratory and Head Office, Mt Wellington, Auckland, New Zealand
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
| | - Sylvain Godreuil
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Montpellier, and MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - Irving Hoffman
- UNC Project Malawi, Lilongwe, Malawi
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Beatrice Bercot
- Infectious Agents Department, French National Reference Centre for Bacterial STIs, Associated Laboratory for Gonococci, and APHP, Saint Louis Hospital, Paris, France
| | - Teodora Wi
- Department of the Global HIV, Hepatitis and STI Programmes, WHO, Geneva, Switzerland
| | - Magnus Unemo
- Department of Laboratory Medicine, Faculty of Medicine and Health, WHO Collaborating Centre for Gonorrhoea and other STIs, National Reference Laboratory for STIs, Örebro University, Örebro, Sweden
- Institute for Global Health, University College London, London, UK
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Hadjineophytou C, Anonsen JH, Svingerud T, Mortimer TD, Grad YH, Scott NE, Koomey M. Sculpting the Bacterial O-Glycoproteome: Functional Analyses of Orthologous Oligosaccharyltransferases with Diverse Targeting Specificities. mBio 2022; 13:e0379721. [PMID: 35471082 PMCID: PMC9239064 DOI: 10.1128/mbio.03797-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
Protein glycosylation systems are widely recognized in bacteria, including members of the genus Neisseria. In most bacterial species, the molecular mechanisms and evolutionary contexts underpinning target protein selection and the glycan repertoire remain poorly understood. Broad-spectrum O-linked protein glycosylation occurs in all human-associated species groups within the genus Neisseria, but knowledge of their individual glycoprotein repertoires is limited. Interestingly, PilE, the pilin subunit of the type IV pilus (Tfp) colonization factor, is glycosylated in Neisseria gonorrhoeae and Neisseria meningitidis but not in the deeply branching species N. elongata subsp. glycolytica. To examine this in more detail, we assessed PilE glycosylation status across the genus and found that PilEs of commensal clade species are not modified by the gonococcal PglO oligosaccharyltransferase. Experiments using PglO oligosaccharyltransferases from across the genus expressed in N. gonorrhoeae showed that although all were capable of broad-spectrum protein glycosylation, those from a deep-branching group of commensals were unable to support resident PilE glycosylation. Further glycoproteomic analyses of these strains using immunoblotting and mass spectrometry revealed other proteins differentially targeted by otherwise remarkably similar oligosaccharyltransferases. Finally, we generated pglO allelic chimeras that begin to localize PglO protein domains associated with unique substrate targeting activities. These findings reveal previously unappreciated differences within the protein glycosylation systems of highly related bacterial species. We propose that the natural diversity manifest in the neisserial protein substrates and oligosaccharyltransferases has significant potential to inform the structure-function relationships operating in these and related bacterial protein glycosylation systems. IMPORTANCE Although general protein glycosylation systems have been well recognized in prokaryotes, the processes governing their distribution, function, and evolution remain poorly understood. Here, we have begun to address these gaps in knowledge by comparative analyses of broad-spectrum O-linked protein glycosylation manifest in species within the genus Neisseria that strictly colonize humans. Using N. gonorrhoeae as a well-defined model organism in conjunction with comparative genomics, intraspecies gene complementation, and glycoprotein phenotyping, we discovered clear differences in both glycosylation susceptibilities and enzymatic targeting activities of otherwise largely conserved proteins. These findings reveal previously unappreciated differences within the protein glycosylation systems of highly related bacterial species. We propose that the natural diversity manifest within Neisseria species has significant potential to elucidate the structure-function relationships operating in these and related systems and to inform novel approaches to applied glycoengineering strategies.
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Affiliation(s)
- Chris Hadjineophytou
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Jan Haug Anonsen
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Tina Svingerud
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | - Tatum D. Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Michael Koomey
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
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9
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In Vitro Analysis of Matched Isolates from Localized and Disseminated Gonococcal Infections Suggests That Opa Expression Impacts Clinical Outcome. Pathogens 2022; 11:pathogens11020217. [PMID: 35215160 PMCID: PMC8880309 DOI: 10.3390/pathogens11020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 12/04/2022] Open
Abstract
Gonorrhea is the second most common sexually transmitted infection, which is primarily localized but can be disseminated systemically. The mechanisms by which a localized infection becomes a disseminated infection are unknown. We used five pairs of Neisseria gonorrhoeae isolates from the cervix/urethra (localized) and the blood (disseminated) of patients with disseminated gonococcal infection to examine the mechanisms that confine gonococci to the genital tract or enable them to disseminate to the blood. Multilocus sequence analysis found that the local and disseminated isolates from the same patients were isogenic. When culturing in vitro, disseminated isolates aggregated significantly less and transmigrated across a polarized epithelial monolayer more efficiently than localized isolates. While localized cervical isolates transmigrated across epithelial monolayers inefficiently, those transmigrated bacteria self-aggregated less and transmigrated more than cervical isolates but comparably to disseminating isolates. The local cervical isolates recruited the host receptors of gonococcal Opa proteins carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) on epithelial cells. However, the transmigrated cervical isolate and the disseminated blood isolates recruit CEACAMs significantly less often. Our results collectively suggest that switching off the expression of CEACAM-binding Opa(s), which reduces self-aggregation, promotes gonococcal dissemination.
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10
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Harrison OB, Maiden MCJ. Recent advances in understanding and combatting Neisseria gonorrhoeae: a genomic perspective. Fac Rev 2021; 10:65. [PMID: 34557869 PMCID: PMC8442004 DOI: 10.12703/r/10-65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The sexually transmitted infection (STI) gonorrhoea remains a major global public health concern. The World Health Organization (WHO) estimates that 87 million new cases in individuals who were 15 to 49 years of age occurred in 2016. The growing number of gonorrhoea cases is concerning given the rise in gonococci developing antimicrobial resistance (AMR). Therefore, a global action plan is needed to facilitate surveillance. Indeed, the WHO has made surveillance leading to the elimination of STIs (including gonorrhoea) a global health priority. The availability of whole genome sequence data offers new opportunities to combat gonorrhoea. This can be through (i) enhanced surveillance of the global prevalence of AMR, (ii) improved understanding of the population biology of the gonococcus, and (iii) opportunities to mine sequence data in the search for vaccine candidates. Here, we review the current status in Neisseria gonorrhoeae genomics. In particular, we explore how genomics continues to advance our understanding of this complex pathogen.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
| | - Martin CJ Maiden
- Department of Zoology, University of Oxford, The Peter Medawar Building, Oxford, UK
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11
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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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12
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Symptomatic Female Genital Tract Infections Due to Neisseria meningitidis in Athens, Greece. Diagnostics (Basel) 2021; 11:diagnostics11071265. [PMID: 34359348 PMCID: PMC8305777 DOI: 10.3390/diagnostics11071265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/02/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
Neisseria meningitidis is considered as an obligate human pathogen and can cause life-threatening diseases like meningitis and/or septicaemia. Occasionally, it can be recovered from infections outside the bloodstream or central nervous system, like respiratory, ocular, joint, urogenital or other unusual sites. Herein, we present two rare cases of female genital infections due to N. meningitidis within a two-year period (2019-2020), identified as serogroup B (MenB) and Y (MenY), respectively. Genotypic analysis for PorA, FetA and MLST revealed the following characteristics: MenB: 7-12, 14, F5-36, 1572cc and MenY: 5-1,10-1, F4-5, 23cc, respectively. Such unusual presentations should alert the clinicians and microbiologists not to exclude N. meningitidis from routine diagnosis and the need of early detection. This is the first report in Greece, and, to our knowledge, in Europe since 2005 describing meningococcal female genital infections.
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13
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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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14
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Typing of Neisseria Gonorrhoeae isolates in Shenzhen, China from 2014-2018 reveals the shift of genotypes associated with antimicrobial resistance. Antimicrob Agents Chemother 2021; 65:AAC.02311-20. [PMID: 33593843 PMCID: PMC8092899 DOI: 10.1128/aac.02311-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The growing antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a serious global threat to gonococcal therapy. Molecular typing is an ideal tool to reveal the association between specific genotype and resistance phenotype that provides effective data for tracking the transmission of resistant clones of N. gonorrhoeae In our study, we aimed to describe the molecular epidemiology of AMR and the distribution of resistance-associated genotypes in Shenzhen during 2014-2018. In total, 909 isolates were collected from Shenzhen from 2014-2018. Two typing schemes, multilocus sequence typing (MLST) and N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR), were performed for all isolates. The distribution of resistance-associated genotypes was described using goeBURST analysis combined with data of logistic regression. Among 909 isolates, ST8123, ST7363, ST1901, ST7365, and ST7360 were most the common MLST sequence types (STs), and ST348, ST2473, ST497, and ST199 were the most prevalent NG-STAR STs. The logistic regression analysis showed that NG-STARST497, MLSTST7365, and MLSTST7360 were typically associated with decreased susceptibility to ceftriaxone. Furthermore, the internationally spreading ESC-resistant clone MLSTST1901 has been prevalent at least in 2014 in Shenzhen and showed a significant increase during 2014-2018. Additionally, MLSTST7363 owns the potential to become the next internationally spreading ceftriaxone-resistant ST. In conclusions, we performed a comprehensive epidemiological study to explore the correlation between AMR and specific STs, which provided important data for future studies of the molecular epidemiology of AMR in N. gonorrhoeae Besides, these findings provide insight for adjusting surveillance strategies and therapy management in Shenzhen.
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15
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Kahler CM. Neisseria species and their complicated relationships with human health. MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Neisseria spp. are a transient low abundance member of the human microbiome. This species contains the very well described pathogens, Neisseria gonorrhoeae and N. meningitidis. Recent advances in molecular typing have revealed that this genus is more diverse than previously thought and that commensal species may have important roles in inhibiting the growth the pathogens. This short review summates these new findings and examines the evidence that the relatively under-reported Neisseria commensal species maybe beneficial to human health.
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16
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Harrison OB, Cehovin A, Skett J, Jolley KA, Massari P, Genco CA, Tang CM, Maiden MCJ. Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance. J Infect Dis 2020; 222:1816-1825. [PMID: 32163580 PMCID: PMC7653085 DOI: 10.1093/infdis/jiaa002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods. METHODS In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes. RESULTS A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups. CONCLUSIONS Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.
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Affiliation(s)
- Odile B Harrison
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Ana Cehovin
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Jessica Skett
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
| | - Paola Massari
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Caroline Attardo Genco
- Department of Immunology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Christoph M Tang
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Martin C J Maiden
- Department of Zoology, The Peter Medawar Building for Pathogen Research, South Parks Road, University of Oxford, Oxford, United Kingdom
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17
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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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18
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Oh S, Kim SH, Baek JY, Huh K, Cho SY, Kang CI, Chung DR, Huh HJ, Lee NY, Peck KR. A case of gonococcal meningitis caused by Neisseria gonorrhoeae MLST ST7363 in a healthy young adult. J Infect Chemother 2020; 26:995-998. [PMID: 32402736 DOI: 10.1016/j.jiac.2020.04.002] [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: 02/17/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 11/26/2022]
Abstract
A 37-year-old healthy man was admitted with fever, skin rash, migratory arthralgia, and headache without preceding urogenital symptoms. Sexual contact history and positive CSF culture for Neisseria gonorrhoeae using BacT/Alert blood culture bottles were diagnostic for gonococcal meningitis. Multilocus sequence typing of this isolate showed sequence type (ST) 7363, the most predominant ST among ceftriaxone-resistant strains. The isolate from this case remained susceptible to ceftriaxone although it was resistant to penicillin, tetracycline, and ciprofloxacin. With the high selective pressure of ceftriaxone for treatment of plasmid-mediated β-lactamase producing N. gonorrhoeae, resistance to ceftriaxone and molecular characteristics should be monitored.
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Affiliation(s)
- Suhyun Oh
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Si-Ho Kim
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Yang Baek
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Asia Pacific Foundation for Infectious Diseases (APFID), Seoul, Republic of Korea
| | - Kyungmin Huh
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sun Young Cho
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Cheol-In Kang
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Doo Ryeon Chung
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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19
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Kahler CM. The Goldilocks Zone: Searching for a Phylogenetic Approach for the Recombinogenic Neisseria gonorrhoeae. J Infect Dis 2020; 222:1762-1763. [DOI: 10.1093/infdis/jiaa079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/21/2020] [Indexed: 01/02/2023] Open
Affiliation(s)
- Charlene M Kahler
- The Marshall Center for Infectious Diseases Research and Training, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
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20
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Abstract
The bacterium Neisseria gonorrhoeae causes the sexually transmitted infection (STI) gonorrhoea, which has an estimated global annual incidence of 86.9 million adults. Gonorrhoea can present as urethritis in men, cervicitis or urethritis in women, and in extragenital sites (pharynx, rectum, conjunctiva and, rarely, systemically) in both sexes. Confirmation of diagnosis requires microscopy of Gram-stained samples, bacterial culture or nucleic acid amplification tests. As no gonococcal vaccine is available, prevention relies on promoting safe sexual behaviours and reducing STI-associated stigma, which hinders timely diagnosis and treatment thereby increasing transmission. Single-dose systemic therapy (usually injectable ceftriaxone plus oral azithromycin) is the recommended first-line treatment. However, a major public health concern globally is that N. gonorrhoeae is evolving high levels of antimicrobial resistance (AMR), which threatens the effectiveness of the available gonorrhoea treatments. Improved global surveillance of the emergence, evolution, fitness, and geographical and temporal spread of AMR in N. gonorrhoeae, and improved understanding of the pharmacokinetics and pharmacodynamics for current and future antimicrobials in the treatment of urogenital and extragenital gonorrhoea, are essential to inform treatment guidelines. Key priorities for gonorrhoea control include strengthening prevention, early diagnosis, and treatment of patients and their partners; decreasing stigma; expanding surveillance of AMR and treatment failures; and promoting responsible antimicrobial use and stewardship. To achieve these goals, the development of rapid and affordable point-of-care diagnostic tests that can simultaneously detect AMR, novel therapeutic antimicrobials and gonococcal vaccine(s) in particular is crucial.
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21
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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] [Key Words] [MESH Headings] [Grants] [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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22
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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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23
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Vigué L, Eyre-Walker A. The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae. PeerJ 2019; 7:e7216. [PMID: 31293838 PMCID: PMC6599670 DOI: 10.7717/peerj.7216] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/30/2019] [Indexed: 12/31/2022] Open
Abstract
Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.
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24
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Carannante A, Ciammaruconi A, Vacca P, Anselmo A, Fillo S, Palozzi AM, Fortunato A, Lista F, Stefanelli P. Genomic Characterization of Gonococci from Different Anatomic Sites, Italy, 2007-2014. Microb Drug Resist 2019; 25:1316-1324. [PMID: 31219400 DOI: 10.1089/mdr.2018.0371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In recent decades, Neisseria gonorrhoeae has developed resistance to several antimicrobial classes. Molecular epidemiology approaches are useful for detecting emerging, often resistant, gonococcal clones. In this study, 67 N. gonorrhoeae isolates from different anatomic sites, collected over 8 years in Italy, were analyzed by whole genome sequencing (WGS). WGS was performed using the Illumina NextSeq 500 platform. Phylogenetic analysis was based on core single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST). N. gonorrhoeae multi-antigen sequence typing (NG-MAST), MLST, and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) were carried out in silico using WGS data. Antimicrobial susceptibility against a four-drug panel was evaluated using a gradient diffusion method. Overall, gonococci clustered in accordance with NG-MAST, MLST, NG-STAR, and antimicrobials susceptibility profiles, but not with the site of isolation, HIV status, and patient sexual orientation. Phylogenetic analysis identified nine clades: two of them were the predominant and including gonococci of G1407 and G2400 genogroups.
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Affiliation(s)
- Anna Carannante
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Paola Vacca
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Anselmo
- Scientific Department, Army Medical Center, Rome, Italy
| | - Silvia Fillo
- Scientific Department, Army Medical Center, Rome, Italy
| | | | | | | | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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25
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Whittles LK, White PJ, Paul J, Didelot X. Epidemiological Trends of Antibiotic Resistant Gonorrhoea in the United Kingdom. Antibiotics (Basel) 2018; 7:antibiotics7030060. [PMID: 30011825 PMCID: PMC6165062 DOI: 10.3390/antibiotics7030060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/06/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022] Open
Abstract
Gonorrhoea is one of the most common sexually-transmitted bacterial infections, globally and in the United Kingdom. The levels of antibiotic resistance in gonorrhoea reported in recent years represent a critical public health issue. From penicillins to cefixime, the gonococcus has become resistant to all antibiotics that have been previously used against it, in each case only a matter of years after introduction as a first-line therapy. After each instance of resistance emergence, the treatment recommendations have required revision, to the point that only a few antibiotics can reliably be prescribed to treat infected individuals. Most countries, including the UK, now recommend that gonorrhoea be treated with a dual therapy combining ceftriaxone and azithromycin. While this treatment is still currently effective for the vast majority of cases, there are concerning signs that this will not always remain the case, and there is no readily apparent alternative. Here, we review the use of antibiotics and epidemiological trends of antibiotic resistance in gonorrhoea from surveillance data over the past 15 years in the UK and describe how surveillance could be improved.
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Affiliation(s)
- Lilith K Whittles
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
| | - Peter J White
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
- MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, London W2 1PG, UK.
- NIHR Health Protection Research Unit in Modelling Methodology, School of Public Health, Imperial College London, London W2 1PG, UK.
- Modelling and Economics Unit, National Infection Service, Public Health England, London NW9 5EQ, UK.
| | - John Paul
- Department of Microbiology, Public Health England Collaborative Centre, Royal Sussex County Hospital, Brighton BN2 5BE, UK.
- Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PH, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London W2 1PG, UK.
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26
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Mortimer TD, Grad YH. Applications of genomics to slow the spread of multidrug-resistant Neisseria gonorrhoeae. Ann N Y Acad Sci 2018; 1435:93-109. [PMID: 29876934 DOI: 10.1111/nyas.13871] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Infections with Neisseria gonorrhoeae, a sexually transmitted pathogen that causes urethritis, cervicitis, and more severe complications, are increasing. Gonorrhea is typically treated with antibiotics; however, N. gonorrhoeae has rapidly acquired resistance to many antibiotic classes, and lineages with reduced susceptibility to the currently recommended therapies are emerging worldwide. In this review, we discuss the contributions of whole genome sequencing (WGS) to our understanding of resistant N. gonorrhoeae. Genomics has illuminated the evolutionary origins and population structure of N. gonorrhoeae and the magnitude of horizontal gene transfer within and between Neisseria species. WGS can be used to predict the susceptibility of N. gonorrhoeae based on known resistance determinants, track the spread of these determinants throughout the N. gonorrhoeae population, and identify novel loci contributing to resistance. WGS has also allowed more detailed epidemiological analysis of transmission of N. gonorrhoeae between individuals and populations than previously used typing methods. Ongoing N. gonorrhoeae genomics will complement other laboratory techniques to understand the biology and evolution of the pathogen, improve diagnostics and treatment in the clinic, and inform public health policies to limit the impact of antibiotic resistance.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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27
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Wan C, Li Y, Le WJ, Liu YR, Li S, Wang BX, Rice PA, Su XH. Increasing Resistance to Azithromycin in Neisseria gonorrhoeae in Eastern Chinese Cities: Resistance Mechanisms and Genetic Diversity among Isolates from Nanjing. Antimicrob Agents Chemother 2018; 62:e02499-17. [PMID: 29530847 PMCID: PMC5923098 DOI: 10.1128/aac.02499-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Azithromycin resistance (AZM-R) of Neisseria gonorrhoeae is emerging as a clinical and public health challenge. We determined molecular characteristics of recent AZM-R Nanjing gonococcal isolates and tracked the emergence of AZM-R isolates in eastern Chinese cities in recent years. A total of 384 N. gonorrhoeae isolates from Nanjing collected from 2013 to 2014 were tested for susceptibility to AZM and six additional antibiotics; all AZM-R strains were characterized genetically for resistance determinants by sequencing and were genotyped using N. gonorrhoeae multiantigen sequence typing (NG-MAST). Among the 384 isolates, 124 (32.3%) were AZM-R. High-level resistance (MIC, ≥256 mg/liter) was present in 10.4% (40/384) of isolates, all of which possessed the A2143G mutation in all four 23S rRNA alleles. Low- to mid-level resistance (MIC, 1 to 64 mg/liter) was present in 21.9% (84/384) of isolates, 59.5% of which possessed the C2599T mutation in all four 23S rRNA alleles. The 124 AZM-R isolates were distributed in 71 different NG-MAST sequence types (STs). ST1866 was the most prevalent type in high-level AZM-R (HL-AZM-R) isolates (45% [18/40]). This study, together with previous reports, revealed that the prevalence of AZM-R in N. gonorrhoeae isolates in certain eastern Chinese cities has risen >4-fold (7% to 32%) from 2008 to 2014. The principal mechanisms of AZM resistance in recent Nanjing isolates were A2143G mutations (high-level resistance) and C2599T mutations (low- to mid-level resistance) in the 23S rRNA alleles. Characterization of NG-MAST STs and phylogenetic analysis indicated the genetic diversity of N. gonorrhoeae in Nanjing; however, ST1866 was the dominant genotype associated with HL-AZM-R isolates.
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Affiliation(s)
- Chuan Wan
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Yang Li
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Wen-Jing Le
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Yu-Rong Liu
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Sai Li
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Bao-Xi Wang
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| | - Peter A Rice
- Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Xiao-Hong Su
- STD Clinic, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
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28
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Retchless AC, Kretz CB, Chang HY, Bazan JA, Abrams AJ, Norris Turner A, Jenkins LT, Trees DL, Tzeng YL, Stephens DS, MacNeil JR, Wang X. Expansion of a urethritis-associated Neisseria meningitidis clade in the United States with concurrent acquisition of N. gonorrhoeae alleles. BMC Genomics 2018; 19:176. [PMID: 29499642 PMCID: PMC5834837 DOI: 10.1186/s12864-018-4560-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/20/2018] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Increased reports of Neisseria meningitidis urethritis in multiple U.S. cities during 2015 have been attributed to the emergence of a novel clade of nongroupable N. meningitidis within the ST-11 clonal complex, the "U.S. NmNG urethritis clade". Genetic recombination with N. gonorrhoeae has been proposed to enable efficient sexual transmission by this clade. To understand the evolutionary origin and diversification of the U.S. NmNG urethritis clade, whole-genome phylogenetic analysis was performed to identify its members among the N. meningitidis strain collection from the Centers for Disease Control and Prevention, including 209 urogenital and rectal N. meningitidis isolates submitted by U.S. public health departments in eleven states starting in 2015. RESULTS The earliest representatives of the U.S. NmNG urethritis clade were identified from cases of invasive disease that occurred in 2013. Among 209 urogenital and rectal isolates submitted from January 2015 to September 2016, the clade accounted for 189/198 male urogenital isolates, 3/4 female urogenital isolates, and 1/7 rectal isolates. In total, members of the clade were isolated in thirteen states between 2013 and 2016, which evolved from a common ancestor that likely existed during 2011. The ancestor contained N. gonorrhoeae-like alleles in three regions of its genome, two of which may facilitate nitrite-dependent anaerobic growth during colonization of urogenital sites. Additional gonococcal-like alleles were acquired as the clade diversified. Notably, one isolate contained a sequence associated with azithromycin resistance in N. gonorrhoeae, but no other gonococcal antimicrobial resistance determinants were detected. CONCLUSIONS Interspecies genetic recombination contributed to the early evolution and subsequent diversification of the U.S. NmNG urethritis clade. Ongoing acquisition of N. gonorrhoeae alleles by the U.S. NmNG urethritis clade may facilitate the expansion of its ecological niche while also increasing the frequency with which it causes urethritis.
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Affiliation(s)
- Adam C. Retchless
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Cécilia B. Kretz
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
- Present address: Division of Scientific Education and Professional Development, Center for Surveillance, Epidemiology and Laboratory Services, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - How-Yi Chang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Jose A. Bazan
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH USA
- Sexual Health Clinic, Columbus Public Health, Columbus, OH USA
| | - A. Jeanine Abrams
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Abigail Norris Turner
- Division of Infectious Diseases, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH USA
| | - Laurel T. Jenkins
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - David L. Trees
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Yih-Ling Tzeng
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA USA
| | - Jessica R. MacNeil
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
| | - Xin Wang
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA USA
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29
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Kwong JC, Chow EPF, Stevens K, Stinear TP, Seemann T, Fairley CK, Chen MY, Howden BP. Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study. Sex Transm Infect 2017; 94:151-157. [PMID: 29247013 PMCID: PMC5870456 DOI: 10.1136/sextrans-2017-053287] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/10/2017] [Accepted: 11/25/2017] [Indexed: 01/03/2023] Open
Abstract
Objectives Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level. Methods 458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST. Results For 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual. These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons. Conclusions These data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.
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Affiliation(s)
- Jason C Kwong
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia
| | - Eric P F Chow
- Melbourne Sexual Health Centre, Alfred Health, Carlton, Victoria, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Carlton, Victoria, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Carlton, Victoria, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia
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Abrams AJ, Trees DL. Genomic sequencing of Neisseria gonorrhoeae to respond to the urgent threat of antimicrobial-resistant gonorrhea. Pathog Dis 2017; 75:3106325. [PMID: 28387837 PMCID: PMC6956991 DOI: 10.1093/femspd/ftx041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/04/2017] [Indexed: 01/02/2023] Open
Abstract
The development of resistance of Neisseria gonorrhoeae to available first-line antibiotics, including penicillins, tetracyclines, fluoroquinolones and cephalosporins, has led to the circulation of multidrug-resistant gonorrhea at a global scale. Advancements in high-throughput whole-genome sequencing (WGS) provide useful tools that can be used to enhance gonococcal detection, treatment and management capabilities, which will ultimately aid in the control of antimicrobial resistant gonorrhea worldwide. In this minireview, we discuss the application of WGS of N. gonorrhoeae to strain typing, phylogenomic, molecular surveillance and transmission studies. We also examine the application of WGS analyses to the public health sector as well as the potential usage of WGS-based transcriptomic and epigenetic methods to identify novel gonococcal resistance mechanisms.
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Affiliation(s)
- A. Jeanine Abrams
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA 30333, USA
| | - David L. Trees
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA 30333, USA
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31
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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Hill SA, Masters TL, Wachter J. Gonorrhea - an evolving disease of the new millennium. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:371-389. [PMID: 28357376 PMCID: PMC5354566 DOI: 10.15698/mic2016.09.524] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/30/2016] [Indexed: 12/21/2022]
Abstract
Etiology, transmission and protection: Neisseria gonorrhoeae (the gonococcus) is the etiological agent for the strictly human sexually transmitted disease gonorrhea. Infections lead to limited immunity, therefore individuals can become repeatedly infected. Pathology/symptomatology: Gonorrhea is generally a non-complicated mucosal infection with a pustular discharge. More severe sequellae include salpingitis and pelvic inflammatory disease which may lead to sterility and/or ectopic pregnancy. Occasionally, the organism can disseminate as a bloodstream infection. Epidemiology, incidence and prevalence: Gonorrhea is a global disease infecting approximately 60 million people annually. In the United States there are approximately 300, 000 cases each year, with an incidence of approximately 100 cases per 100,000 population. Treatment and curability: Gonorrhea is susceptible to an array of antibiotics. Antibiotic resistance is becoming a major problem and there are fears that the gonococcus will become the next "superbug" as the antibiotic arsenal diminishes. Currently, third generation extended-spectrum cephalosporins are being prescribed. Molecular mechanisms of infection: Gonococci elaborate numerous strategies to thwart the immune system. The organism engages in extensive phase (on/off switching) and antigenic variation of several surface antigens. The organism expresses IgA protease which cleaves mucosal antibody. The organism can become serum resistant due to its ability to sialylate lipooligosaccharide in conjunction with its ability to subvert complement activation. The gonococcus can survive within neutrophils as well as in several other lymphocytic cells. The organism manipulates the immune response such that no immune memory is generated which leads to a lack of protective immunity.
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Affiliation(s)
- Stuart A. Hill
- Department of Epidemiology, Gillings School of Global Public Health,
University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7435
| | - Thao L. Masters
- Department of Epidemiology, Gillings School of Global Public Health,
University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7435
| | - Jenny Wachter
- Department of Epidemiology, Gillings School of Global Public Health,
University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7435
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33
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Belkacem A, Jacquier H, Goubard A, Mougari F, La Ruche G, Patey O, Micaëlo M, Semaille C, Cambau E, Bercot B. Molecular epidemiology and mechanisms of resistance of azithromycin-resistant Neisseria gonorrhoeae isolated in France during 2013-14. J Antimicrob Chemother 2016; 71:2471-8. [PMID: 27301565 DOI: 10.1093/jac/dkw182] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/21/2016] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to determine the prevalence and mechanisms of azithromycin resistance of Neisseria gonorrhoeae French isolates from 2013 to 2014. METHODS N. gonorrhoeae samples isolated in a network of laboratories were tested for susceptibility to azithromycin between April 2013 and March 2014. Fifty-four isolates that were non-susceptible to azithromycin and 18 susceptible isolates were characterized for molecular mechanisms of resistance by PCR/sequencing and genotyped using N. gonorrhoeae multiantigen sequence typing (NG-MAST). RESULTS Among the 970 N. gonorrhoeae isolates, 54 (5.56%) were non-susceptible to azithromycin, 9 (1%) were resistant and 45 (4.6%) showed intermediate resistance. Azithromycin-non-susceptible isolates harboured a C2599T mutation in the rrl gene encoding the 23S rRNA alleles (5.5%), a C substitution in the mtrR promoter (5.5%), an A deletion in the mtrR promoter (53.7%) and mutations in the L4 ribosomal protein (14.8%) and in the MtrR repressor (25.9%). No isolates showed an L22 mutation or carried an erm, ere, mef(A)/(E) or mphA gene. Thirty different STs were highlighted using the NG-MAST technique. The predominant genogroups non-susceptible to azithromycin were G21 (31%), G1407 (20%) and G2400 (15%). Genogroup G2400 (15%) was revealed to be a novel cluster prevalent in the south of France and resistant to azithromycin, ciprofloxacin and tetracycline. CONCLUSIONS Our study highlights that the prevalence of resistance of N. gonorrhoeae to azithromycin in France is low and essentially due to multiple genetic mutations. Its dissemination occurs through three major genogroups including a novel one in France (G2400).
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Affiliation(s)
- Anna Belkacem
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France Department of Tropical and Infectious Diseases, CHI, Villeneuve Saint Georges, France
| | - Hervé Jacquier
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France INSERM, IAME, UMR 1137, F-75018 Paris, France University Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Agathe Goubard
- Alfred Fournier Institute, National Reference Centre for Gonococci, F-75014 Paris, France
| | - Faiza Mougari
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France INSERM, IAME, UMR 1137, F-75018 Paris, France University Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Guy La Ruche
- French Institute for Public Health Surveillance (InVS), Department of Infectious Diseases, Saint-Maurice, France
| | - Olivier Patey
- Department of Tropical and Infectious Diseases, CHI, Villeneuve Saint Georges, France
| | - Maïté Micaëlo
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France INSERM, IAME, UMR 1137, F-75018 Paris, France University Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Caroline Semaille
- French Institute for Public Health Surveillance (InVS), Department of Infectious Diseases, Saint-Maurice, France
| | - Emmanuelle Cambau
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France INSERM, IAME, UMR 1137, F-75018 Paris, France University Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Béatrice Bercot
- APHP, Lariboisière-Fernand Widal Hospital, Laboratory of Bacteriology and Associated Laboratory for the National Reference Centre for Gonococci, F-75010 Paris, France INSERM, IAME, UMR 1137, F-75018 Paris, France University Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
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Abstract
Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. Here, investigations of the genus Neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of WGS data. Using the gene and its link to phenotype as a starting point, the BIGSdb database, which powers the PubMLST databases, enables the assembly of large open-access collections of annotated genomes that provide insight into the evolution of the Neisseria, the epidemiology of meningococcal and gonococcal disease, and mechanisms of Neisseria pathogenicity.
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Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MCJ, Sheppard SK, Falush D. The Landscape of Realized Homologous Recombination in Pathogenic Bacteria. Mol Biol Evol 2016; 33:456-71. [PMID: 26516092 PMCID: PMC4866539 DOI: 10.1093/molbev/msv237] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Recombination enhances the adaptive potential of organisms by allowing genetic variants to be tested on multiple genomic backgrounds. Its distribution in the genome can provide insight into the evolutionary forces that underlie traits, such as the emergence of pathogenicity. Here, we examined landscapes of realized homologous recombination of 500 genomes from ten bacterial species and found all species have "hot" regions with elevated rates relative to the genome average. We examined the size, gene content, and chromosomal features associated with these regions and the correlations between closely related species. The recombination landscape is variable and evolves rapidly. For example in Salmonella, only short regions of around 1 kb in length are hot whereas in the closely related species Escherichia coli, some hot regions exceed 100 kb, spanning many genes. Only Streptococcus pyogenes shows evidence for the positive correlation between GC content and recombination that has been reported for several eukaryotes. Genes with function related to the cell surface/membrane are often found in recombination hot regions but E. coli is the only species where genes annotated as "virulence associated" are consistently hotter. There is also evidence that some genes with "housekeeping" functions tend to be overrepresented in cold regions. For example, ribosomal proteins showed low recombination in all of the species. Among specific genes, transferrin-binding proteins are recombination hot in all three of the species in which they were found, and are subject to interspecies recombination.
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Affiliation(s)
- Koji Yahara
- Biostatistics Center, Kurume University, Kurume, Fukuoka, Japan College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ichizo Kobayashi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | | | - Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Daniel Falush
- College of Medicine, Institute of Life Science, Swansea University, Swansea, United Kingdom Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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36
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Abstract
The three species Neisseria meningitidis, Neisseria gonorrheae, and Neisseria lactamica are often regarded as highly recombining bacteria. N. meningitidis has been considered a paradigmatic case of the "semiclonal model" or of "epidemic clonality," demonstrating occasional bouts of clonal propagation in an otherwise recombining species. In this model, occasional clonality generates linkage disequilibrium in the short term. In the long run, however, the effects of clonality are countered by recombination. We show that many data are at odds with this proposal and that N. meningitidis fits the criteria that we have proposed for predominant clonal evolution (PCE). We point out that (i) the proposed way to distinguish epidemic clonality from PCE may be faulty and (ii) the evidence of deep phylogenies by microarrays and whole-genome sequencing is at odds with the predictions of the semiclonal model. Last, we revisit the species status of N. meningitidis, N. gonorrheae, and N. lactamica in the light of the PCE model.
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37
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Lynagh Y, Mac Aogáin M, Walsh A, Rogers TR, Unemo M, Crowley B. Detailed characterization of the first high-level azithromycin-resistantNeisseria gonorrhoeaecases in Ireland: Table 1. J Antimicrob Chemother 2015; 70:2411-3. [DOI: 10.1093/jac/dkv106] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Bercot B, Belkacem A, Goubard A, Mougari F, Sednaoui P, La Ruche G, Cambau E. High-level azithromycin-resistant Neisseria gonorrhoeae clinical isolate in France, March 2014. ACTA ACUST UNITED AC 2014; 19. [PMID: 25394255 DOI: 10.2807/1560-7917.es2014.19.44.20951] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the first case in France of a high-level azithromycin-resistant Neisseria gonorrhoeae (minimum inhibitory concentration (MIC) = 96 mg/L) assigned to MLST7363 (NG-MAST ST6360), also resistant to ciprofloxacin and tetracycline but susceptible to ceftriaxone. The patient was a 51 year-old heterosexual man who returned following 1g azithromycin monotherapy. Mechanisms of azithromycin resistance were a C2599T mutation in the four copies of the rrl gene and a novel mutation in the promoter of the mtrR gene.
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Affiliation(s)
- B Bercot
- APHP, Lariboisiere-St Louis-Fernand Widal Hospital, Laboratory of Bacteriology-Virology, Associated Laboratory for the National Reference Centre for gonococci, Paris, France
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Contrasting within- and between-host immune selection shapes Neisseria Opa repertoires. Sci Rep 2014; 4:6554. [PMID: 25296566 PMCID: PMC4894414 DOI: 10.1038/srep06554] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 09/08/2014] [Indexed: 11/30/2022] Open
Abstract
Pathogen evolution is influenced strongly by the host immune response. Previous studies of the effects of herd immunity on the population structure of directly transmitted, short-lived pathogens have primarily focused on the impact of competition for hosts. In contrast, for long-lived infections like HIV, theoretical work has focused on the mechanisms promoting antigenic variation within the host. In reality, successful transmission requires that pathogens balance both within- and between-host immune selection. The Opa adhesins in the bacterial Neisseria genus provide a unique system to study the evolution of the same antigens across two major pathogens: while N. meningitidis is an airborne, respiratory pathogen colonising the nasopharynx relatively transiently, N. gonorrhoeae can cause sexually transmitted, long-lived infections. We use a simple mathematical model and genomic data to show that trade-offs between immune selection pressures within- and between-hosts can explain the contrasting Opa repertoires observed in meningococci and gonococci.
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40
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41
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A genome-wide identification of genes undergoing recombination and positive selection in Neisseria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:815672. [PMID: 25180194 PMCID: PMC4142384 DOI: 10.1155/2014/815672] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 01/01/2023]
Abstract
Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria. Neisseria is a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic species N. meningitidis and N. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18 Neisseria genomes (14 N. meningitidis, 3 N. gonorrhoeae and 1 commensal N. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution of Neisseria genomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution in Neisseria.
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42
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Bennett JS, Watkins ER, Jolley KA, Harrison OB, Maiden MCJ. Identifying Neisseria species by use of the 50S ribosomal protein L6 (rplF) gene. J Clin Microbiol 2014; 52:1375-81. [PMID: 24523465 PMCID: PMC3993661 DOI: 10.1128/jcm.03529-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/03/2014] [Indexed: 02/05/2023] Open
Abstract
The comparison of 16S rRNA gene sequences is widely used to differentiate bacteria; however, this gene can lack resolution among closely related but distinct members of the same genus. This is a problem in clinical situations in those genera, such as Neisseria, where some species are associated with disease while others are not. Here, we identified and validated an alternative genetic target common to all Neisseria species which can be readily sequenced to provide an assay that rapidly and accurately discriminates among members of the genus. Ribosomal multilocus sequence typing (rMLST) using ribosomal protein genes has been shown to unambiguously identify these bacteria. The PubMLST Neisseria database (http://pubmlst.org/neisseria/) was queried to extract the 53 ribosomal protein gene sequences from 44 genomes from diverse species. Phylogenies reconstructed from these genes were examined, and a single 413-bp fragment of the 50S ribosomal protein L6 (rplF) gene was identified which produced a phylogeny that was congruent with the phylogeny reconstructed from concatenated ribosomal protein genes. Primers that enabled the amplification and direct sequencing of the rplF gene fragment were designed to validate the assay in vitro and in silico. Allele sequences were defined for the gene fragment, associated with particular species names, and stored on the PubMLST Neisseria database, providing a curated electronic resource. This approach provides an alternative to 16S rRNA gene sequencing, which can be readily replicated for other organisms for which more resolution is required, and it has potential applications in high-resolution metagenomic studies.
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Affiliation(s)
- Julia S Bennett
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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43
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Trembizki E, Lahra M, Stevens K, Freeman K, Hogan T, Hogg G, Lawrence A, Limnios A, Pearson J, Smith H, Nissen M, Sloots T, Whiley D. A national quality assurance survey of Neisseria gonorrhoeae testing. J Med Microbiol 2014; 63:45-49. [DOI: 10.1099/jmm.0.065094-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aims of this study were to (1) conduct a national survey of Neisseria gonorrhoeae identification by National Neisseria Network (NNN) reference laboratories contributing data to the Australian Gonococcal Surveillance Programme and (2) determine the prevalence in Australia of strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays for confirmation of gonococcal nucleic acid amplification tests. Gonococcal clinical isolates referred to NNN laboratories for the first half of 2012 were screened using in-house real-time PCR assays targeting multicopy opa, porA pseudogene and cppB genes. There were 2455 clinical gonococcal isolates received in the study period; 98.6 % (2420/2455) of isolates harboured all three gene targets, 0.12 % (3/2455) were porA-negative, 0.04 % (1/2455) opa-negative and 1.14 % (28/2455) cppB-negative by PCR. Notably, no isolates were simultaneously negative for two targets. However, three isolates failed to be amplified by all three PCR methods, one isolate of which was shown to be a commensal Neisseria strain by 16S rRNA sequencing. Using PCR as the reference standard the results showed that (1) identification of N. gonorrhoeae isolates by NNN laboratories was highly specific (99.96 %) and (2) strains of N. gonorrhoeae lacking gene sequences commonly targeted by in-house PCR assays are present but not widespread throughout Australia at this point in time.
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Affiliation(s)
- Ella Trembizki
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - Monica Lahra
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Kevin Freeman
- Microbiology Laboratory, Pathology Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Tiffany Hogan
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Lawrence
- Microbiology and Infectious Diseases Department, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Athena Limnios
- WHO Collaborating Centre for STD, Microbiology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Sydney, New South Wales, Australia
| | - Julie Pearson
- PathWest Laboratory Medicine-WA, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Helen Smith
- Public Health Microbiology, Communicable Disease, Queensland Health Forensic and Scientific Services, Archerfield, Queensland, Australia
| | - Michael Nissen
- Microbiology Division, Pathology Queensland Central, Royal Brisbane and Women’s Hospital Campus, Queensland, Australia
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - Theo Sloots
- Microbiology Division, Pathology Queensland Central, Royal Brisbane and Women’s Hospital Campus, Queensland, Australia
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
| | - David Whiley
- Queensland Children’s Medical Research Institute, University of Queensland, Queensland, Australia
- Queensland Paediatric Infectious Diseases Laboratory, Queensland Children’s Health Services, Queensland, Australia
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44
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Cody AJ, Bennett JS, Maiden MC. Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation. J Microbiol Methods 2014. [DOI: 10.1016/bs.mim.2014.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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45
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Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. BMC Evol Biol 2013; 13:184. [PMID: 24007216 PMCID: PMC3848584 DOI: 10.1186/1471-2148-13-184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/28/2013] [Indexed: 02/03/2023] Open
Abstract
Background Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organism’s pathogenicity within its host. Previously we introduced a tool called S-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. Utilizing S-plot and new functionality developed here, we examined 18 publicly available Neisseria genomes, including strains of both pathogenic and non-pathogenic species, in order to identify regions of unusual compositional properties (RUCPs) using both a sliding window as well as a gene-by-gene approach. Results Numerous GEIs and PAIs were identified including virulence genes previously found within the pathogenic Neisseria species. While some genes were conserved amongst all species, only pathogenic species, or an individual species, a number of genes were detected that are unique to an individual strain. While the majority of such genes have an origin unknown, a number of putative sources including pathogenic and capsule-containing bacteria were determined, indicative of gene exchange between Neisseria spp. and other bacteria within their microhabitat. Furthermore, we uncovered evidence that both N. meningitidis and N. gonorrhoeae have separately acquired DNA from their human host. Data suggests that all three Neisseria species have received horizontally transferred elements post-speciation. Conclusions Using this approach, we were able to not only find previously identified regions of virulence but also new regions which may be contributing to the virulence of the species. This comparative analysis provides a means for tracing the evolutionary history of the acquisition of foreign DNA within this genus. Looking specifically at the RUCPs present within the 18 genomes considered, a stronger similarity between N. meningitidis and N. lactamica is observed, suggesting that N. meningitidis arose before N. gonorrhoeae.
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Affiliation(s)
- Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W, Sheridan Rd, Chicago, IL 60660, USA.
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Description of an unusual Neisseria meningitidis isolate containing and expressing Neisseria gonorrhoeae-Specific 16S rRNA gene sequences. J Clin Microbiol 2013; 51:3199-206. [PMID: 23863567 DOI: 10.1128/jcm.00309-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An apparently rare Neisseria meningitidis isolate containing one copy of a Neisseria gonorrhoeae 16S rRNA gene is described herein. This isolate was identified as N. meningitidis by biochemical identification methods but generated a positive signal with Gen-Probe Aptima assays for the detection of Neisseria gonorrhoeae. Direct 16S rRNA gene sequencing of the purified isolate revealed mixed bases in signature regions that allow for discrimination between N. meningitidis and N. gonorrhoeae. The mixed bases were resolved by sequencing individually PCR-amplified single copies of the genomic 16S rRNA gene. A total of 121 discrete sequences were obtained; 92 (76%) were N. meningitidis sequences, and 29 (24%) were N. gonorrhoeae sequences. Based on the ratio of species-specific sequences, the N. meningitidis strain seems to have replaced one of its four intrinsic 16S rRNA genes with the gonococcal gene. Fluorescence in situ hybridization (FISH) probes specific for meningococcal and gonococcal rRNA were used to demonstrate the expression of the rRNA genes. Interestingly, the clinical isolate described here expresses both N. meningitidis and N. gonorrhoeae 16S rRNA genes, as shown by positive FISH signals with both probes. This explains why the probes for N. gonorrhoeae in the Gen-Probe Aptima assays cross-react with this N. meningitidis isolate. The N. meningitidis isolate described must have obtained N. gonorrhoeae-specific DNA through interspecies recombination.
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Molecular Epidemiology of β-Lactamase–Producing Neisseria gonorrhoeae Strains in Manaus, AM, Brazil. Sex Transm Dis 2013; 40:469-72. [DOI: 10.1097/olq.0b013e318286d2ce] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Weyand NJ, Wertheimer AM, Hobbs TR, Sisko JL, Taku NA, Gregston LD, Clary S, Higashi DL, Biais N, Brown LM, Planer SL, Legasse AW, Axthelm MK, Wong SW, So M. Neisseria infection of rhesus macaques as a model to study colonization, transmission, persistence, and horizontal gene transfer. Proc Natl Acad Sci U S A 2013; 110:3059-64. [PMID: 23382234 PMCID: PMC3581930 DOI: 10.1073/pnas.1217420110] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The strict tropism of many pathogens for man hampers the development of animal models that recapitulate important microbe-host interactions. We developed a rhesus macaque model for studying Neisseria-host interactions using Neisseria species indigenous to the animal. We report that Neisseria are common inhabitants of the rhesus macaque. Neisseria isolated from the rhesus macaque recolonize animals after laboratory passage, persist in the animals for at least 72 d, and are transmitted between animals. Neisseria are naturally competent and acquire genetic markers from each other in vivo, in the absence of selection, within 44 d after colonization. Neisseria macacae encodes orthologs of known or presumed virulence factors of human-adapted Neisseria, as well as current or candidate vaccine antigens. We conclude that the rhesus macaque model will allow studies of the molecular mechanisms of Neisseria colonization, transmission, persistence, and horizontal gene transfer. The model can potentially be developed further for preclinical testing of vaccine candidates.
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Affiliation(s)
- Nathan J Weyand
- BIO5 Institute and Department of Immunobiology, University of Arizona, Tucson, AZ 85721, USA.
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Read PJ, Limnios EA, McNulty A, Whiley D, Lahra MM. One confirmed and one suspected case of pharyngeal gonorrhoea treatment failure following 500mg ceftriaxone in Sydney, Australia. Sex Health 2013; 10:460-2. [DOI: 10.1071/sh13077] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/03/2013] [Indexed: 11/23/2022]
Abstract
Emerging antimicrobial resistance within Neisseria gonorrhoeae (NG) is a significant global public health threat. Detection and investigation of treatment failures is a crucial component of the World Health Organisation’s response to this challenge. We report the cases of two homosexual men, both treated for pharyngeal NG with 500 mg intramuscular ceftriaxone, in whom a test of cure 1 week after treatment showed persisting infection. Both men denied further sexual activity. In the first case, treatment failure was confirmed, since the isolates before and after treatment were identical by auxotype, antibiogram, multilocus sequence type (MLST) and multi-antigen sequence type (NG-MAST). In the second case, the MLSTs before and after treatment were identical, but NG-MAST results were similar but not indistinguishable. These cases underline the importance of test-of-cure and molecular investigations in identifying treatment failure, but also highlight the complexity of distinguishing treatment failure from reinfection when relying on highly variable molecular targets that may be subject to drug pressure.
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Vidovic S, Thakur SD, Horsman GB, Levett PN, Anvari V, Dillon JAR. Longitudinal analysis of the evolution and dissemination of Neisseria gonorrhoeae strains (Saskatchewan, Canada, 2005 to 2008) reveals three major circulating strains and convergent evolution of ciprofloxacin and azithromycin resistance. J Clin Microbiol 2012; 50:3823-30. [PMID: 22972828 PMCID: PMC3502962 DOI: 10.1128/jcm.01402-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/30/2012] [Indexed: 12/28/2022] Open
Abstract
A longitudinal study combining multilocus sequence typing with molecular evolutionary analysis determined the distribution, population structure, and evolution of antibiotic resistance in Neisseria gonorrhoeae isolates in Saskatchewan that were collected between 2005 and 2008. Of 195 gonococcal isolates examined, 29 sequence types (STs) were identified with 3 major circulating strains (ST-1 through ST-3) comprising 52% of all gonococcal isolates studied. The prevalences, persistence, distribution patterns, and clonalities of these isolates strongly suggest that gonorrhea endemicity within this broad geographic region was driven by these 3 circulating strains. ST-1 exhibited a significantly (P = 0.001) higher prevalence throughout the study than did the others, accounting for ∼25% of the tested isolates each year. The spatial distributions of the gonococcal strains indicated that ST-1 in 2007 entered a linear component of the sexual network, reaching the remote north and resulting in the further spread and maintenance of infection. Ciprofloxacin and azithromycin resistances were observed in distantly related gonococcal lineages, clearly indicating the convergent acquisition of these antibiotic-resistant phenotypes. In addition, all ciprofloxacin- and azithromycin-resistant lineages were found at the edges of the minimum spanning tree, far from the major lineages, suggesting that these antibiotic phenotypes were most likely introduced into the province. In contrast, resistance to penicillin was found mostly in the endemic gonococcal lineages, suggesting that penicillin resistance was probably acquired in Saskatchewan as a result of spontaneous mutations in already-established lineages. Tetracycline resistance was present in all STs except one, indicating its ubiquitous nature in the gonococcal population studied.
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Affiliation(s)
- Sinisa Vidovic
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
| | - Sidharath D. Thakur
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
| | - Greg B. Horsman
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | - Paul N. Levett
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | | | - Jo-Anne R. Dillon
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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