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Martin SL, Mortimer TD, Grad YH. Machine learning models for Neisseria gonorrhoeae antimicrobial susceptibility tests. Ann N Y Acad Sci 2023; 1520:74-88. [PMID: 36573759 PMCID: PMC9974846 DOI: 10.1111/nyas.14549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Neisseria gonorrhoeae is an urgent public health threat due to the emergence of antibiotic resistance. As most isolates in the United States are susceptible to at least one antibiotic, rapid molecular antimicrobial susceptibility tests (ASTs) would offer the opportunity to tailor antibiotic therapy, thereby expanding treatment options. With genome sequence and antibiotic resistance phenotype data for nearly 20,000 clinical N. gonorrhoeae isolates now available, there is an opportunity to use statistical methods to develop sequence-based diagnostics that predict antibiotic susceptibility from genotype. N. gonorrhoeae, therefore, provides a useful example illustrating how to apply machine learning models to aid in the design of sequence-based ASTs. We present an overview of this framework, which begins with establishing the assay technology, the performance criteria, the population in which the diagnostic will be used, and the clinical goals, and extends to the choices that must be made to arrive at a set of features with the desired properties for predicting susceptibility phenotype from genotype. While we focus on the example of N. gonorrhoeae, the framework generalizes to other organisms for which large-scale genotype and antibiotic resistance data can be combined to aid in diagnostics development.
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Affiliation(s)
- Skylar L. Martin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Tatum D. Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Lu Z, Tadi DA, Fu J, Azizian K, Kouhsari E. Global status of Azithromycin and Erythromycin Resistance Rates in Neisseria gonorrhoeae: A Systematic Review and Meta-analysis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:465-478. [PMID: 36568835 PMCID: PMC9765340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background: The widespread development of antibiotic resistance or decreased susceptibility in Neisseria gonorrhoeae (NG) infection is a global and significant human public health issue. Objectives: Therefore, this meta-analysis aimed to estimate worldwide resistance rates of NG to the azithromycin and erythromycin according to years, regions, and antimicrobial susceptibility testing (AST). Methods: We systematically searched the published studies in PubMed, Scopus, and Embase from 1988 to 2021. All analyses were conducted using Stata software. Results: The 134 reports included in the meta-analysis were performed in 51 countries and examined 165,172 NG isolates. Most of the included studies were from Asia (50 studies) and Europe (46 studies). In the metadata, the global prevalence over the past 30 years were 6% for azithromycin and 48% for erythromycin. There was substantial change in the prevalence of macrolides NG resistance over time (P <0.01). In this metadata, among 58 countries reporting resistance data for azithromycin, 17 (29.3%) countries reported that >5% of specimens had azithromycin resistance. Conclusions: The implications of this study emphasize the rigorous or improved antimicrobial stewardship, early diagnosis, contact tracing, and enhanced intensive global surveillance system are crucial for control of further spreading of gonococcal emergence of antimicrobial resistance (AMR).
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Affiliation(s)
- Zhiwei Lu
- Graduate School, Zhejiang Chinese Medical University,
Hangzhou, Zhejiang, China,Hangzhou Heyunjia Hospital, Hangzhou, Zhejiang,
China
| | - Danyal Abbasi Tadi
- Department of Veterinary, Azad University of Shahr-e
Kord, Shahr-e Kord, Iran
| | - Jinchao Fu
- Department of General Practice, Shulan (Hangzhou)
Hospital Affiliated to Zhejiang Shuren University Shulan International Medical
College, Hangzhou, Zhejiang, China,To whom all correspondence should be addressed:
Jinchao Fu, ; Ebrahim Kouhsari,
; ORCID:
https://www.orcid.org/0000-0001-5893-6483
| | - Khalil Azizian
- Department of Microbiology, Faculty of Medicine,
Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan
University of Medical Sciences, Gorgan, Iran,Department of Laboratory Sciences, Faculty of
Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran,To whom all correspondence should be addressed:
Jinchao Fu, ; Ebrahim Kouhsari,
; ORCID:
https://www.orcid.org/0000-0001-5893-6483
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3
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Schaeffer J, Lippert K, Pleininger S, Stöger A, Hasenberger P, Stadlbauer S, Heger F, Eigentler A, Geusau A, Indra A, Allerberger F, Ruppitsch W. Association of Phylogenomic Relatedness among Neisseria gonorrhoeae Strains with Antimicrobial Resistance, Austria, 2016-2020. Emerg Infect Dis 2022; 28:1694-1698. [PMID: 35876744 PMCID: PMC9328923 DOI: 10.3201/eid2808.220071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated genomic determinants of antimicrobial resistance in 1,318 Neisseria gonorrhoeae strains isolated in Austria during 2016–2020. Sequence type (ST) 9363 and ST11422 isolates had high rates of azithromycin resistance, and ST7363 isolates correlated with cephalosporin resistance. These results underline the benefit of genomic surveillance for antimicrobial resistance monitoring.
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Miura M, Shigemura K, Osawa K, Nakanishi N, Nomoto R, Onishi R, Yoshida H, Sawamura T, Fang SB, Chiang YT, Sung SY, Chen KC, Miyara T, Fujisawa M. Genetic characteristics of azithromycin-resistant Neisseria gonorrhoeae collected in Hyogo, Japan during 2015-2019. J Med Microbiol 2022; 71. [PMID: 35700110 DOI: 10.1099/jmm.0.001533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Azithromycin (AZM) is a therapeutic drug for sexually transmitted infections and is used for Neisseria gonorrhoeae when first- and second-line drugs are not available. Recently, the susceptibility of N. gonorrhoeae against AZM has been decreasing worldwide.Hypothesis/Gap Statement. Azithromycin-resistance (AZM-R) rates among N. gonorrhoeae in Japan are increasing, and the gene mutations and epidemiological characteristics of AZM-R in N. gonorrhoeae have not been fully investigated.Aim. We determined the susceptibility to AZM and its correlation with genetic characteristics of N. gonorrhoeae.Methodology. We investigated the susceptibility to AZM and genetic characteristics of N. gonorrhoeae. Mutations in domain V of the 23S rRNA gene and mtrR were examined in 93 isolates, including 13 AZM-R isolates. Spread and clonality were examined using sequence types (STs) of multi-antigen sequence typing for N. gonorrhoeae (NG-MAST), and whole genome analysis (WGA) to identify single nucleotide polymorphisms.Results. The number of AZM-R isolates increased gradually from 2015 to 2019 in Hyogo (P=0.008). C2599T mutations in 23S rRNA significantly increased in AZM-R isolates (P<0.001). NG-MAST ST4207 and ST6762 were frequently detected in AZM-R isolates, and they had higher MICs to AZM from 6 to 24 µg/ml. The phylogenic tree-based WGA showed that all isolates with ST4207 were contained in the same clade, and isolates with ST6762 were divided into two clades, AZM-S isolates and AZM-R isolates, which were different from the cluster containing ST1407.Conclusion. Our study showed yearly increases in AZM-R rates in N. gonorrhoeae. NG-MAST ST4207 and ST6762 were not detected in our previous study in 2015 and were frequently identified in isolates with higher MICs to AZM. WGA confirmed that isolates with these STs are closely related to each other. Continued surveillance is needed to detect the emergence and confirm the spread of NG-MAST ST4207 and ST6762.
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Affiliation(s)
- Makiko Miura
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan.,Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Katsumi Shigemura
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan.,Department of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Kayo Osawa
- Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamichi, Chuo-ku, Kobe, 650-0046, Japan
| | - Ryohei Nomoto
- Department of Infectious Diseases, Kobe Institute of Health, 4-6-5 Minatojima-nakamichi, Chuo-ku, Kobe, 650-0046, Japan
| | - Reo Onishi
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka Suma-ku, Kobe, 654-0142, Japan
| | - Hiroyuki Yoshida
- Hyogo Clinical Laboratory Corporation, 5-6-2, Aoyamanishi, Himeji, 671-2224 Japan
| | - Toru Sawamura
- Department of Medical Technology, Faculty of Health Sciences, Kobe Tokiwa University, 2-6-2 Otani-cho, Nagata-ku, Kobe, 653-0838, Japan
| | - Shiuh-Bin Fang
- Division of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Shuang Ho Hospital, Taipei Medical University, 291 Jhong Jheng Road, Jhong Ho District, New Taipei City, 23561, Taiwan, ROC.,Department of Pediatrics, School of Medicine, College of Medicine, Taipei Medical University, 250, Wu Hsing Street, Hsin Yi District, Taipei, 11031, Taiwan, ROC
| | - Yi-Te Chiang
- Department of Urology, Taipei Medical University Shuang Ho Hospital, 291, Zhongzheng Rd, Zhonghe District, Taipei, 23561, Taiwan, ROC
| | - Shian-Ying Sung
- Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing St., Taipei, 110, Taiwan, ROC
| | - Kuan-Cho Chen
- Department of Urology, Taipei Medical University Shuang Ho Hospital, 291, Zhongzheng Rd, Zhonghe District, Taipei, 23561, Taiwan, ROC
| | - Takayuki Miyara
- Department of Infection Control and Prevention, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Masato Fujisawa
- Department of Urology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
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Yasir M, Mustafa Karim A, Kausar Malik S, Bajaffer AA, Azhar EI. Prediction of Antimicrobial Minimal Inhibitory Concentrations for Neisseria gonorrhoeae using Machine Learning Models. Saudi J Biol Sci 2022; 29:3687-3693. [PMID: 35844400 PMCID: PMC9280306 DOI: 10.1016/j.sjbs.2022.02.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/12/2022] [Accepted: 02/27/2022] [Indexed: 11/26/2022] Open
Abstract
The lowest concentration of an antimicrobial agent that can inhibit the visible growth of a microorganism after overnight incubation is called as minimum inhibitory concentration (MIC) and the drug prescriptions are made on the basis of MIC data to ensure successful treatment outcomes. Therefore, reliable antimicrobial susceptibility data is crucial, and it will help clinicians about which drug to prescribe. Although few prediction studies based on strategies have been conducted, however, no single machine learning (ML) modelling has been carried out to predict MICs in N. gonorrhoeae. In this study, we propose a ML based approach that can predict MICs of a specific antibiotic using unitigs sequences data. We retrieved N. gonorrhoeae genomes from European Nucleotide Archive and NCBI and analysed them combined with their respective MIC data for cefixime, ciprofloxacin, and azithromycin and then we constructed unitigs by using de Brujin graphs. We built and compared 35 different ML regression models to predict MICs. Our results demonstrate that RandomForest and CATBoost models showed best performance in predicting MICs of the three antibiotics. The coefficient of determination, R2, (a statistical measure of how well the regression predictions approximate the real data points) for cefixime, ciprofloxacin, and azithromycin was 0.75787, 0.77241, and 0.79009 respectively using RandomForest. For CATBoost model, the R2 value was 0.74570, 0.77393, and 0.79317 for cefixime, ciprofloxacin, and azithromycin respectively. Lastly, using feature importance, we explore the important genomic regions identified by the models for predicting MICs. The major mutations which are responsible for resistance against these three antibiotics were chosen by ML models as a top feature in case of each antibiotics. CATBoost, DecisionTree, GradientBoosting, and RandomForest regression models chose the same unitigs which are responsible for resistance. This unitigs-based strategy for developing models for MIC prediction, clinical diagnostics, and surveillance can be applicable for other critical bacterial pathogens.
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Decano AG, Pettigrew K, Sabiiti W, Sloan DJ, Neema S, Bazira J, Kiiru J, Onyango H, Asiimwe B, Holden MTG. Pan-Resistome Characterization of Uropathogenic Escherichia coli and Klebsiella pneumoniae Strains Circulating in Uganda and Kenya, Isolated from 2017-2018. Antibiotics (Basel) 2021; 10:antibiotics10121547. [PMID: 34943759 PMCID: PMC8698711 DOI: 10.3390/antibiotics10121547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 01/24/2023] Open
Abstract
Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017–2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure, and performed comparative analysis their pangenome contents. We found 55 Escherichia coli and 19 Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI virulence genes including fimH, iutA, feoA/B/C, mrkD, and foc. We identified 18 different sequence types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli sequence types were ST131 (26%), ST335/1193 (10%), and ST10 (6%). Diverse plasmid types were observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups. Pangenome analysis of each set revealed a total of 2862 and 3464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively. Among these are acquired AMR determinants including fluoroquinolone resistance-conferring genes aac(3)-Ib-cr and other significant genes: aad, tet, sul1, sul2, and cat, which are associated with aminoglycoside, tetracycline, sulfonamide, and chloramphenicol resistance, respectively. Accessory genomes of both species collections were detected several β-lactamase genes, blaCTX-M, blaTEM and blaOXA, or blaNDM. Overall, 93% are multi-drug resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are associated with resistance to three or more antibiotic classes. Our findings illustrate the abundant acquired resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae, which are mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial epidemiology of these important AMR pathogens.
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Affiliation(s)
- Arun Gonzales Decano
- School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK; (K.P.); (W.S.); (D.J.S.); (M.T.G.H.)
- Correspondence:
| | - Kerry Pettigrew
- School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK; (K.P.); (W.S.); (D.J.S.); (M.T.G.H.)
| | - Wilber Sabiiti
- School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK; (K.P.); (W.S.); (D.J.S.); (M.T.G.H.)
| | - Derek J. Sloan
- School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK; (K.P.); (W.S.); (D.J.S.); (M.T.G.H.)
| | - Stella Neema
- Department of Sociology and Anthropology, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Joel Bazira
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara P.O. Box 410, Uganda;
| | - John Kiiru
- Centre of Microbiology Research, Kenya Medical Research Institute, Off Raila Odinga Way, Nairobi P.O. Box 54840 00200, Kenya;
| | - Hellen Onyango
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62 000, Kenya;
| | - Benon Asiimwe
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala P.O. Box 7062, Uganda;
| | - Matthew T. G. Holden
- School of Medicine, University of St Andrews, St Andrews KY16 8BQ, UK; (K.P.); (W.S.); (D.J.S.); (M.T.G.H.)
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Straub C, Thirkell C, Tiong A, Woodhouse R, Szeto J, Dyet KH. The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission. Microb Genom 2021; 7:000701. [PMID: 34755593 PMCID: PMC8743534 DOI: 10.1099/mgen.0.000701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/30/2021] [Indexed: 11/18/2022] Open
Abstract
The increasing use of culture independent diagnostic testing for the diagnosis of Neisseria gonorrhoeae infection has led to gaps in surveillance of antimicrobial resistance (AMR) rates due to limited availability of cultures. Our study reports the findings of a second national survey of N. gonorrhoeae in New Zealand, utilizing whole-genome sequencing (WGS) to study the population structure, prevalence of AMR, epidemiology and transmission of gonorrhoea isolates. We analysed 314 isolates and found a strong correlation between carriage of acquired resistance genes or chromosomal point mutations and phenotypic susceptibility testing results. Overall, the New Zealand rates of azithromycin resistance and decreased susceptibility to ceftriaxone remain lower than in most countries, which are part of the World Health Organization (WHO) Global Gonococcal Antimicrobial Surveillance Programme (GASP). The phylogeny provides evidence of a diverse population significantly associated with sexual behaviour groups. Transmission clustering with a ten single nucleotide polymorphism (SNP) cut-off identified 49 clusters, of which ten were solely associated with men who have sex with men (MSM), whereas remaining clusters included heterosexual patients, as well as MSM, suggesting that bridging of sexual networks is occurring. Utilizing pairwise SNP differences between isolates of the same sequence types we determined genetic variation for the three typing schemes used in this study [Multi locus sequence typing (MLST), multi-antigen sequence typing (NG-MAST), and sequence typing for antimicrobial resistance (NG-STAR)]. A median of 0.0 to 52.5 pairwise SNP differences within a single NG-STAR sequence type underlines previous findings of the superiority of the NG-STAR typing scheme in terms of genomic inherency. With our analysis incorporating epidemiological and genomic data, we were able to show a comprehensive overview of the N. gonorrhoeae population circulating in New Zealand, focussing on AMR and transmission within sexual networks. Regular surveillance studies to understand the origin, evolution and spread of AMR for gonorrhoea remain necessary to make informed decisions about public health guidelines, as the internationally rising rates of ceftriaxone and azithromycin resistance have already led to adaptation of current treatment guidelines in the UK and the USA, highlighting the importance of regular surveillance in individual countries.
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Affiliation(s)
- Christina Straub
- The Institute of Environmental Science and Research, Auckland 1025, New Zealand
- Genomics Aotearoa, New Zealand
| | - Callum Thirkell
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Audrey Tiong
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Rosemary Woodhouse
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Jenny Szeto
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
| | - Kristin H. Dyet
- The Institute of Environmental Science and Research, Porirua 5022, New Zealand
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Shaskolskiy B, Kandinov I, Kravtsov D, Filippova M, Chestkov A, Solomka V, Kubanov A, Deryabin D, Dementieva E, Gryadunov D. Prediction of ceftriaxone MIC in Neisseria gonorrhoeae using DNA microarray technology and regression analysis. J Antimicrob Chemother 2021; 76:3151-3158. [PMID: 34458918 DOI: 10.1093/jac/dkab308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/26/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Decreased susceptibility of Neisseria gonorrhoeae to extended-spectrum cephalosporins is a major concern. Elucidation of the phenotypic and genetic characteristics of such isolates is a priority task. METHODS We developed a method for predicting the N. gonorrhoeae ceftriaxone susceptibility level (MICcro) by identifying genetic determinants of resistance using low-density hydrogel microarrays and a regression equation. A training dataset, containing 5631 isolates from the Pathogenwatch database and 181 isolates obtained in the Russian Federation during 2018-19, was used to build a regression model. The regression equation was tested on 14 WHO reference strains. Ceftriaxone resistance determinants for the 448 evaluated clinical isolates collected in Russia were identified using microarray analysis, and MICcro values were calculated using the regression equation and compared with those measured by the serial dilution method. RESULTS The regression equation for calculating MICcro values included 20 chromosomal resistance determinants. The greatest contributions to the increase in MICcro were shown to be PBP2: Ala-501→Pro, Ala-311→Val, Gly-545→Ser substitutions, Asp(345-346) insertion; and PorB: Gly-120→Arg substitution. The substitutions PBP2: Ala-501→Thr/Val, PorB: Gly-120→Asn/Asp/Lys and PBP1: Leu-421→Pro had weaker effects. For 94.4% of the isolates in the evaluation set, the predicted MICcro was within one doubling dilution of the experimentally determined MICcro. No ceftriaxone-resistant isolates were identified in the analysed samples from Russia, and no interpretative errors were detected in the MICcro calculations. CONCLUSIONS The developed strategy for predicting ceftriaxone MIC can be used for the continuous surveillance of known and emerging resistant N. gonorrhoeae isolates.
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Affiliation(s)
- Boris Shaskolskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Ilya Kandinov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Dmitry Kravtsov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Marina Filippova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Alexander Chestkov
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Victoria Solomka
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Alexey Kubanov
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Dmitry Deryabin
- State Research Center of Dermatovenerology and Cosmetology, Ministry of Health of the Russian Federation, Korolenko str. 3/1, 107076 Moscow, Russia
| | - Ekaterina Dementieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
| | - Dmitry Gryadunov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov str., 119991 Moscow, Russia
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9
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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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10
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The Accuracy of Molecular Detection Targeting the Mutation C2611T for Detecting Moderate-Level Azithromycin Resistance in Neisseria gonorrhoeae: A Systematic Review and Meta-Analysis. Antibiotics (Basel) 2021; 10:antibiotics10091027. [PMID: 34572609 PMCID: PMC8471969 DOI: 10.3390/antibiotics10091027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (N. gonorrhoeae) is now recognized as a commonly reported sexually transmitted pathogen, and the increasing drug resistance of N. gonorrhoeae has become a serious public health problem. The accuracy of molecular detection for detecting moderate-level azithromycin resistance is not well-established. We summarized the data from studies of the N. gonorrhoeae 23S rRNA mutation at position 2611 with azithromycin resistance to determine the relationship between the mutation and resistance. METHODS AND FINDINGS In this systematic review and meta-analysis, two researchers independently searched six databases for studies with data for the azithromycin minimum inhibitory concentrations (MICs) and the 23S rRNA mutation C2611T of each N. gonorrhoeae isolate. Since the breakpoint of moderate-level resistance to azithromycin (ML-AzmR) was not determined, we divided the moderate level into two groups according to the range of MICs (moderate resistance limited to 2-128 mg/L or 4-128 mg/L) for data extraction. A random-effects model was used to calculate the pooled sensitivity rate, the specificity rate, the pooled positive likelihood ratio (PLR), the negative likelihood ratio (NLR), and the diagnostic odds ratio (DOR). Meta-regression analyses by detection method, isolates sampling (a random sample or not), location, and sample size were performed to explore the possible causes of heterogeneity. The potential publication bias of the included studies was conducted by the Deeks' test. We included 20 studies in our study: 20 studies have data of N. gonorrhoeae with MICs between 2 and 128 mg/L with mutation or without mutation at position 2611(4759 samples), and 14 studies have data of N. gonorrhoeae with MICs between 4 and 128 mg/L (3367 samples). In the group with the moderate level of 2-128 mg/L, the pooled sensitivity rate of the molecular assays was determined to be 71.9% (95% CI, 67.6-74%), the pooled specificity rate was 98.7% (95% CI, 98.2-99.0%), and the DOR ranged from 55.0 to 351.3 (mean, 139.1). In the 4-128 mg/L group, the pooled sensitivity rate was 91.9% (95% CI, 88.9-94.2%), the pooled specificity rate was 95.9% (95% CI, 95.1-96.6%), and the DOR ranged from 41.9 to 364.1 (mean, 123.6). CONCLUSION Through this meta-analysis, we found that the C2611T mutation of 23S rRNA is valuable for the molecular diagnostic of moderate-level azithromycin resistance (ML-AzmR) in N. gonorrhoeae, especially when the moderate level is set at 4-128 mg/L. This rapid molecular detection method can be used for the rapid identification of ML-AzmR isolates in the clinic.
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Singh R, Kusalik A, Dillon JAR. Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review. Brief Funct Genomics 2021; 21:78-89. [PMID: 34170311 DOI: 10.1093/bfgp/elab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/02/2023] Open
Abstract
Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.
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Affiliation(s)
- Reema Singh
- Department of Biochemistry, Microbiology and Immunology
| | - Anthony Kusalik
- Department of Computer Science at the University of Saskatchewan
| | - Jo-Anne R Dillon
- Department of Biochemistry Microbiology and Immunology, College of Medicine, c/o Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N5E3, Canada
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12
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Manoharan-Basil SS, Laumen JGE, Van Dijck C, De Block T, De Baetselier I, Kenyon C. Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae. Front Microbiol 2021; 12:683901. [PMID: 34177869 PMCID: PMC8222677 DOI: 10.3389/fmicb.2021.683901] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/27/2021] [Indexed: 11/25/2022] Open
Abstract
Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.
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Affiliation(s)
| | - Jolein Gyonne Elise Laumen
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christophe Van Dijck
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Tessa De Block
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Irith De Baetselier
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Chris Kenyon
- Department of Clinical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Medicine, University of Cape Town, Cape Town, South Africa
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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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Osnes MN, van Dorp L, Brynildsrud OB, Alfsnes K, Schneiders T, Templeton KE, Yahara K, Balloux F, Caugant DA, Eldholm V. Antibiotic Treatment Regimes as a Driver of the Global Population Dynamics of a Major Gonorrhea Lineage. Mol Biol Evol 2021; 38:1249-1261. [PMID: 33432328 PMCID: PMC8042733 DOI: 10.1093/molbev/msaa282] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Neisseria gonorrhoeae multilocus sequence type (ST) 1901 is among the lineages most commonly associated with treatment failure. Here, we analyze a global collection of ST-1901 genomes to shed light on the emergence and spread of alleles associated with reduced susceptibility to extended-spectrum cephalosporins (ESCs). The genetic diversity of ST-1901 falls into a minor and a major clade, both of which were inferred to have originated in East Asia. The dispersal of the major clade from Asia happened in two separate waves expanding from ∼1987 and 1996, respectively. Both waves first reached North America, and from there spread to Europe and Oceania, with multiple secondary reintroductions to Asia. The ancestor of the second wave acquired the penA 34.001 allele, which significantly reduces susceptibility to ESCs. Our results suggest that the acquisition of this allele granted the second wave a fitness advantage at a time when ESCs became the key drug class used to treat gonorrhea. Following its establishment globally, the lineage has served as a reservoir for the repeated emergence of clones fully resistant to the ESC ceftriaxone, an essential drug for effective treatment of gonorrhea. We infer that the effective population sizes of both clades went into decline as treatment schemes shifted from fluoroquinolones via ESC monotherapy to dual therapy with ceftriaxone and azithromycin in Europe and the United States. Despite the inferred recent population size decline, the short evolutionary path from the penA 34.001 allele to alleles providing full ceftriaxone resistance is a cause of concern.
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Affiliation(s)
- Magnus N Osnes
- Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Ola B Brynildsrud
- Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristian Alfsnes
- Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Thamarai Schneiders
- Division of Infection Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Kate E Templeton
- Department of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Francois Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Dominique A Caugant
- Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Vegard Eldholm
- Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
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15
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Yahara K, Ma KC, Mortimer TD, Shimuta K, Nakayama SI, Hirabayashi A, Suzuki M, Jinnai M, Ohya H, Kuroki T, Watanabe Y, Yasuda M, Deguchi T, Eldholm V, Harrison OB, Maiden MCJ, Grad YH, Ohnishi M. Emergence and evolution of antimicrobial resistance genes and mutations in Neisseria gonorrhoeae. Genome Med 2021; 13:51. [PMID: 33785063 PMCID: PMC8008663 DOI: 10.1186/s13073-021-00860-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/24/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance in Neisseria gonorrhoeae is a global health concern. Strains from two internationally circulating sequence types, ST-7363 and ST-1901, have acquired resistance to third-generation cephalosporins, mainly due to mosaic penA alleles. These two STs were first detected in Japan; however, the timeline, mechanism, and process of emergence and spread of these mosaic penA alleles to other countries remain unknown. METHODS We studied the evolution of penA alleles by obtaining the complete genomes from three Japanese ST-1901 clinical isolates harboring mosaic penA allele 34 (penA-34) dating from 2005 and generating a phylogenetic representation of 1075 strains sampled from 35 countries. We also sequenced the genomes of 103 Japanese ST-7363 N. gonorrhoeae isolates from 1996 to 2005 and reconstructed a phylogeny including 88 previously sequenced genomes. RESULTS Based on an estimate of the time-of-emergence of ST-1901 (harboring mosaic penA-34) and ST-7363 (harboring mosaic penA-10), and > 300 additional genome sequences of Japanese strains representing multiple STs isolated in 1996-2015, we suggest that penA-34 in ST-1901 was generated from penA-10 via recombination with another Neisseria species, followed by recombination with a gonococcal strain harboring wildtype penA-1. Following the acquisition of penA-10 in ST-7363, a dominant sub-lineage rapidly acquired fluoroquinolone resistance mutations at GyrA 95 and ParC 87-88, by independent mutations rather than horizontal gene transfer. Data in the literature suggest that the emergence of these resistance determinants may reflect selection from the standard treatment regimens in Japan at that time. CONCLUSIONS Our findings highlight how antibiotic use and recombination across and within Neisseria species intersect in driving the emergence and spread of drug-resistant gonorrhea.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - 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
| | - Ken Shimuta
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shu-Ichi Nakayama
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Michio Jinnai
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Hitomi Ohya
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Toshiro Kuroki
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
- Present address: Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoinooka, Imabari, Ehime, 794-8555, Japan
| | - Yuko Watanabe
- Department of Microbiology, Kanagawa Prefectural Institute of Public Health, Chigasaki, Kanagawa, Japan
| | - Mitsuru Yasuda
- Center for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Japan
| | - Takashi Deguchi
- Department of Urology, Kizawa Memorial Hospital, Gifu, Japan
| | - Vegard Eldholm
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
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16
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Pinto M, Borges V, Isidro J, Rodrigues JC, Vieira L, Borrego MJ, Gomes JP. Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance. Microb Genom 2021; 7:000481. [PMID: 33245688 PMCID: PMC8208699 DOI: 10.1099/mgen.0.000481] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted disease gonorrhoea, has shown an extraordinary ability to develop antimicrobial resistance (AMR) to multiple classes of antimicrobials. With no available vaccine, managing N. gonorrhoeae infections demands effective preventive measures, antibiotic treatment and epidemiological surveillance. The latter two are progressively being supported by the generation of whole-genome sequencing (WGS) data on behalf of national and international surveillance programmes. In this context, this study aims to perform N. gonorrhoeae clustering into genogroups based on WGS data, for enhanced prospective laboratory surveillance. Particularly, it aims to identify the major circulating WGS-genogroups in Europe and to establish a relationship between these and AMR. Ultimately, it enriches public databases by contributing with WGS data from Portuguese isolates spanning 15 years of surveillance. A total of 3791 carefully inspected N. gonorrhoeae genomes from isolates collected across Europe were analysed using a gene-by-gene approach (i.e. using cgMLST). Analysis of cluster composition and stability allowed the classification of isolates into a two-step hierarchical genogroup level determined by two allelic distance thresholds revealing cluster stability. Genogroup clustering in general agreed with available N. gonorrhoeae typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (N. gonorrhoeae multi-antigen sequence typing) and PubMLST core-genome groups], highlighting the predominant genogroups circulating in Europe, and revealed that the vast majority of the genogroups present a dominant AMR profile. Additionally, a non-static gene-by-gene approach combined with a more discriminatory threshold for potential epidemiological linkage enabled us to match data with previous reports on outbreaks or transmission chains. In conclusion, this genogroup assignment allows a comprehensive analysis of N. gonorrhoeae genetic diversity and the identification of the WGS-based genogroups circulating in Europe, while facilitating the assessment (and continuous monitoring) of their frequency, geographical dispersion and potential association with specific AMR signatures. This strategy may benefit public-health actions through the prioritization of genogroups to be controlled, the identification of emerging resistance carriage, and the potential facilitation of data sharing and communication.
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Affiliation(s)
- Miguel Pinto
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Carlos Rodrigues
- Laboratory of Microbiology, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, Nova Medical School/Faculty of Medical Sciences, New University of Lisbon, Lisbon, Portugal
| | - Maria José Borrego
- Reference Laboratory of Bacterial Sexually Transmitted Infections, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, 1649-016 Lisbon, Portugal
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Al Suwayyid BA, Rankine-Wilson L, Speers DJ, Wise MJ, Coombs GW, Kahler CM. Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species. Genome Biol Evol 2020; 12:3938-3950. [PMID: 32031617 PMCID: PMC7058167 DOI: 10.1093/gbe/evaa023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.
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Affiliation(s)
- Barakat A Al Suwayyid
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Ministry of Education, Riyadh, Saudi Arabia
| | - Leah Rankine-Wilson
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,Computer Science and Software Engineering, The University of Western Australia, Crawley, Australia
| | - Geoffrey W Coombs
- Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary Life Sciences, Murdoch University, Australia
| | - Charlene M Kahler
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
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Forster RF, Smith M, Cooper G, Brokenshire M, Roberts SA, McAuliffe GN. Demographic and behavioural factors associated with antimicrobial susceptibility to azithromycin and ceftriaxone in Neisseria gonorrhoeae. Int J STD AIDS 2020; 32:67-74. [PMID: 33198606 DOI: 10.1177/0956462420959171] [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] [Indexed: 11/17/2022]
Abstract
Antimicrobial resistance of Neisseria gonorrhoeae (NG) is of global public health concern. The aim of this study was to explore demographic and behavioural factors associated with antimicrobial susceptibility of NG to ceftriaxone and azithromycin. Gonococcal isolates (n = 391) from clients attending the Auckland Sexual Health Service, New Zealand, from July 2014 - June 2015 (n = 206), and July 2017 - June 2018 (n = 185), were tested for susceptibility to ceftriaxone and azithromycin. Laboratory data were linked with behavioural and demographic data. Geometric mean azithromycin MICs increased across the two time periods (0.239 mg/L in 2014/15 to 0.347 mg/L in 2017/18, p < 0.001), and ceftriaxone MICs decreased (0.007 mg/L in 2014/15 to 0.005 mg/L in 2017/18, p < 0.001). Demographic and behavioural factors were not associated with differences in ceftriaxone MICs; however azithromycin MICs were higher in men who have sex with men (0.356 mg/L) compared with the heterosexual study population (0.192 mg/L, p < 0.001) and were lower in Pacific peoples (0.201 mg/L, p < 0.001) and Māori (0.244 mg/L, p = 0.05) compared with those of European ethnicity (0.321 mg/L). Our findings show that azithromycin MICs increased in our region between 2014 and 2018; associations were seen with sexual orientation and ethnicity.
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Affiliation(s)
- Rose F Forster
- Auckland Sexual Health Service, Greenlane Clinical Centre, Auckland, New Zealand
| | - Marian Smith
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Gavin Cooper
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Mike Brokenshire
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Sally A Roberts
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Gary N McAuliffe
- Microbiology Department, LabPLUS, Auckland City Hospital, Auckland, New Zealand
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19
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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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20
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Dong Y, Yang Y, Wang Y, Martin I, Demczuk W, Gu W. Shanghai Neisseria gonorrhoeae Isolates Exhibit Resistance to Extended-Spectrum Cephalosporins and Clonal Distribution. Front Microbiol 2020; 11:580399. [PMID: 33123111 PMCID: PMC7573285 DOI: 10.3389/fmicb.2020.580399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022] Open
Abstract
The emergence of Neisseria gonorrhoeae strains with resistance (R) to extended-spectrum cephalosporins (ESCsR) represents a public health threat of untreatable gonococcal infections. This study was designed to determine the prevalence and molecular mechanisms of ESCR of Shanghai N. gonorrhoeae isolates. A total of 366 N. gonorrhoeae isolates were collected in 2017 in Shanghai. Susceptibility to ceftriaxone (CRO), cefixime (CFM), azithromycin (AZM), ciprofloxacin (CIP), spectinomycin, penicillin, and tetracycline was determined using the agar dilution method. A subset of 124 isolates was subjected to phylogenetic analysis for nine antimicrobial resistance-associated genes, i.e., penA, porB, ponA, mtrR, 23S rRNA, gyrA, parC, 16S rRNA, and rpsE. Approximately 20.0% of the isolates exhibited CFMR [minimum inhibitory concentration (MIC) >0.125 mg/L], and 5.5% were CROR (MIC > 0.125 mg/L). In total, 72.7% of ESCR isolates were clonal and associated with mosaic penA 10 and 60 alleles. Non-mosaic penA 18 allele and substitutions of PenA A501T, G542S, and PorB1b G213S/Y were observed in non-clonal ESCR. Approximately 6.8% of the isolates showed AZM MIC above the epidemiological cutoff (ECOFF, 1 mg/L), were associated with 23S rRNA A2059G mutation, and did not exhibit clonal distribution. Almost all isolates were CIPR (resistance to ciprofloxacin) and associated with GyrA-91/92 and ParC-85/86/87/88/89/91 alterations. Isolates with ParC S88P substitution were clustered into the ESCR clade. The Shanghai isolates exhibited a high level of ESCR and distinct resistant patterns.
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Affiliation(s)
- Yuan Dong
- Shanghai Skin Disease Hospital, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yang Yang
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Ying Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Irene Martin
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Walter Demczuk
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, MB, Canada
| | - Weiming Gu
- Shanghai Skin Disease Hospital, Shanghai, China
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21
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Mortimer TD, Pathela P, Crawley A, Rakeman JL, Lin Y, Harris SR, Blank S, Schillinger JA, Grad YH. The distribution and spread of susceptible and resistant Neisseria gonorrhoeae across demographic groups in a major metropolitan center. Clin Infect Dis 2020; 73:e3146-e3155. [PMID: 32829411 PMCID: PMC8563204 DOI: 10.1093/cid/ciaa1229] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Background Genomic epidemiology studies of gonorrhea in the United States have primarily focused on national surveillance for antibiotic resistance, and patterns of local transmission between demographic groups of resistant and susceptible strains are unknown. Methods We analyzed a convenience sample of genome sequences, antibiotic susceptibility, and patient data from 897 gonococcal isolates cultured at the New York City (NYC) Public Health Laboratory from NYC Department of Health and Mental Hygiene (DOHMH) Sexual Health Clinic (SHC) patients, primarily in 2012–2013. We reconstructed the gonococcal phylogeny, defined transmission clusters using a 10 nonrecombinant single nucleotide polymorphism threshold, tested for clustering of demographic groups, and placed NYC isolates in a global phylogenetic context. Results The NYC gonococcal phylogeny reflected global diversity with isolates from 22/23 of the prevalent global lineages (96%). Isolates clustered on the phylogeny by patient sexual behavior (P < .001) and race/ethnicity (P < .001). Minimum inhibitory concentrations were higher across antibiotics in isolates from men who have sex with men compared to heterosexuals (P < .001) and white heterosexuals compared to black heterosexuals (P < .01). In our dataset, all large transmission clusters (≥10 samples) of N. gonorrhoeae were susceptible to ciprofloxacin, ceftriaxone, and azithromycin, and comprised isolates from patients across demographic groups. Conclusions All large transmission clusters were susceptible to gonorrhea therapies, suggesting that resistance to empiric therapy was not a main driver of spread, even as risk for resistance varied across demographic groups. Further study of local transmission networks is needed to identify drivers of transmission.
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Affiliation(s)
- Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America
| | - Preeti Pathela
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Addie Crawley
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Jennifer L Rakeman
- Bureau of Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Ying Lin
- Bureau of Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York City, United States of America
| | - Simon R Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Susan Blank
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America.,Division of STD Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, US Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Julia A Schillinger
- Bureau of Sexually Transmitted Infections, New York City Department of Health and Mental Hygiene, New York City, United States of America.,Division of STD Prevention, National Center for HIV, Hepatitis, STD, and TB Prevention, US Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States of America.,Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States of America
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22
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Hicks AL, Kissler SM, Mortimer TD, Ma KC, Taiaroa G, Ashcroft M, Williamson DA, Lipsitch M, Grad YH. Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants. eLife 2020; 9:e56367. [PMID: 32602459 PMCID: PMC7326491 DOI: 10.7554/elife.56367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/17/2020] [Indexed: 12/14/2022] Open
Abstract
Genotype-based diagnostics for antibiotic resistance represent a promising alternative to empiric therapy, reducing inappropriate antibiotic use. However, because such assays infer resistance based on known genetic markers, their utility will wane with the emergence of novel resistance. Maintenance of these diagnostics will therefore require surveillance to ensure early detection of novel resistance variants, but efficient strategies to do so remain undefined. We evaluate the efficiency of targeted sampling approaches informed by patient and pathogen characteristics in detecting antibiotic resistance and diagnostic escape variants in Neisseria gonorrhoeae, a pathogen associated with a high burden of disease and antibiotic resistance and the development of genotype-based diagnostics. We show that patient characteristic-informed sampling is not a reliable strategy for efficient variant detection. In contrast, sampling informed by pathogen characteristics, such as genomic diversity and genomic background, is significantly more efficient than random sampling in identifying genetic variants associated with resistance and diagnostic escape.
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Affiliation(s)
- Allison L Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Stephen M Kissler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Kevin C Ma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Melinda Ashcroft
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Marc Lipsitch
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
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23
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Gen2EpiGUI: User-Friendly Pipeline for Analyzing Whole-Genome Sequencing Data for Epidemiological Studies of Neisseria gonorrhoeae. Sex Transm Dis 2020; 47:e42-e44. [DOI: 10.1097/olq.0000000000001206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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24
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Town K, Field N, Harris SR, Sánchez-Busó L, Cole MJ, Pitt R, Fifer H, Mohammed H, Hughes G. Phylogenomic analysis of Neisseria gonorrhoeae transmission to assess sexual mixing and HIV transmission risk in England: a cross-sectional, observational, whole-genome sequencing study. THE LANCET. INFECTIOUS DISEASES 2020; 20:478-486. [PMID: 31978353 PMCID: PMC7099395 DOI: 10.1016/s1473-3099(19)30610-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/21/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Characterising sexual networks with transmission of sexually transmitted infections might allow identification of individuals at increased risk of infection. We aimed to investigate sexual mixing in Neisseria gonorrhoeae transmission networks between women, heterosexual men, and men who report sex with men (MSM), and between people with and without HIV. METHODS In this cross-sectional observational study, we whole-genome sequenced N gonorrhoeae isolates from the archive of the Gonococcal Resistance to Antimicrobials Surveillance Programme (GRASP).w Isolates that varied by five single nucleotide polymorphisms or fewer were grouped into clusters that represented sexual networks with N gonorrhoeae transmission. Clusters were described by gender, sexual risk group, and HIV status. FINDINGS We sequenced 1277 N gonorrhoeae isolates with linked clinical and sociodemographic data that were collected in five clinics in England during 2013-16 (July 1 to Sept 30 in 2013-15; July 1 to Sept 9 in 2016). The isolates grouped into 213 clusters. 30 (14%) clusters contained isolates from heterosexual men and MSM but no women and three (1%) clusters contained isolates from only women and MSM. 146 (69%) clusters comprised solely people with negative or unknown HIV status and seven (3%) comprised only HIV-positive people. 60 (28%) clusters comprised MSM with positive and negative or unknown HIV status. INTERPRETATION N gonorrhoeae molecular data can provide information indicating risk of HIV or other sexually transmitted infections for some individuals for whom such risk might not be known from clinical history. These findings have implications for sexual health care, including offering testing, prevention advice, and preventive treatment, such as HIV pre-exposure prophylaxis. FUNDING National Institute for Health Research Health Protection Research Unit; Wellcome; Public Health England.
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Affiliation(s)
- Katy Town
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, University College London, London, UK; Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK; National Infection Service, Public Health England, London, UK.
| | - Nigel Field
- Centre for Molecular Epidemiology and Translational Research, Institute for Global Health, University College London, London, UK
| | | | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Hinxton, UK; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Rachel Pitt
- National Infection Service, Public Health England, London, UK
| | - Helen Fifer
- National Infection Service, Public Health England, London, UK
| | - Hamish Mohammed
- National Infection Service, Public Health England, London, UK
| | - Gwenda Hughes
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, University College London, London, UK; National Infection Service, Public Health England, London, UK
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25
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Arnold B, Sohail M, Wadsworth C, Corander J, Hanage WP, Sunyaev S, Grad YH. Fine-Scale Haplotype Structure Reveals Strong Signatures of Positive Selection in a Recombining Bacterial Pathogen. Mol Biol Evol 2020; 37:417-428. [PMID: 31589312 PMCID: PMC6993868 DOI: 10.1093/molbev/msz225] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Identifying genetic variation in bacteria that has been shaped by ecological differences remains an important challenge. For recombining bacteria, the sign and strength of linkage provide a unique lens into ongoing selection. We show that derived alleles <300 bp apart in Neisseria gonorrhoeae exhibit more coupling linkage than repulsion linkage, a pattern that cannot be explained by limited recombination or neutrality as these couplings are significantly stronger for nonsynonymous alleles than synonymous alleles. This general pattern is driven by a small fraction of highly diverse genes, many of which exhibit evidence of interspecies horizontal gene transfer and an excess of intermediate frequency alleles. Extensive simulations show that two distinct forms of positive selection can create these patterns of genetic variation: directional selection on horizontally transferred alleles or balancing selection that maintains distinct haplotypes in the presence of recombination. Our results establish a framework for identifying patterns of selection in fine-scale haplotype structure that indicate specific ecological processes in species that recombine with distantly related lineages or possess coexisting adaptive haplotypes.
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Affiliation(s)
- Brian Arnold
- Division of Informatics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Mashaal Sohail
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Crista Wadsworth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Shamil Sunyaev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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26
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Indriatmi W, Prayogo RL, Nilasari H, Suseno LS. Antimicrobial resistance of Neisseria gonorrhoeae in Jakarta, Indonesia: a cross-sectional study. Sex Health 2019; 17:9-14. [PMID: 31837714 DOI: 10.1071/sh19140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/28/2019] [Indexed: 11/23/2022]
Abstract
Background Neisseria gonorrhoeae has developed resistance to various antimicrobials. At least 10 countries have reported treatment failures with extended-spectrum cephalosporins. Periodic surveillance is essential to determine local treatment guidelines. This study was conducted to determine the resistance of N. gonorrhoeae to penicillin, tetracycline, levofloxacin, cefixime and ceftriaxone among the high-risk population for acquiring STIs in Jakarta and to identify factors associated with resistance. METHODS A cross-sectional study was conducted in Jakarta, Indonesia, from September to November 2018. In all, 98 high-risk males and females who fulfilled the study criteria were included. Specimens were collected from urethral or endocervical swabs, put into Amies transport medium and then transported to the Laboratory of Clinical Microbiology, Universitas Indonesia for culture and identification. Proven gonococcal isolates were examined for susceptibility to various antimicrobials using the disk diffusion method according to Clinical and Laboratory Standard Institute guidelines. RESULTS Of the 98 specimens, 35 were confirmed to be N. gonorrhoeae. The proportion of N. gonorrhoeae specimens resistant to penicillin, tetracycline, levofloxacin, cefixime and ceftriaxone among the high-risk population was 97.1%, 97.1%, 34.3%, 0% and 0% respectively. The possible factors associated with resistance could only be analysed for levofloxacin. Age, sexual orientation and a history of orogenital sexual activity during the past month were not associated with N. gonorrhoeae resistance to levofloxacin. CONCLUSION This study detected no resistance of N. gonorrhoeae to cefixime and ceftriaxone. Further studies with larger samples are needed to obtain more representative results of N. gonorrhoeae resistance and the possible factors associated with resistance.
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Affiliation(s)
- Wresti Indriatmi
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta; and Dr Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta
| | - Rizky Lendl Prayogo
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta; and Dr Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta; and Corresponding author.
| | - Hanny Nilasari
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta; and Dr Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta
| | - Lis Surachmiati Suseno
- Department of Dermatology and Venereology, Faculty of Medicine, Universitas Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta; and Dr Cipto Mangunkusumo National General Hospital, Jakarta, Indonesia, Jalan Pangeran Diponegoro No. 71, RW 05, Kelurahan Kenari, Kecamatan Senen, Kota Jakarta Pusat, 10430, DKI Jakarta
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27
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Variability in Azithromycin Susceptibility Results for Neisseria gonorrhoeae Obtained Using Gradient MIC Strip and Agar Dilution Techniques. J Clin Microbiol 2019; 57:JCM.01353-19. [PMID: 31578264 DOI: 10.1128/jcm.01353-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/29/2019] [Indexed: 12/29/2022] Open
Abstract
Azithromycin is a component of empirical treatment regimens for Neisseria gonorrhoeae infections, but antimicrobial susceptibility testing for this agent is technically challenging. We compared the intertest variability, MIC values, and CLSI/EUCAST categorization of clinical and reference isolates of N. gonorrhoeae treated with azithromycin by testing 107 clinical isolates and nine reference isolates by agar dilution and in duplicates using MIC test strips (Liofilchem, Italy) and Etests (bioMérieux, France). Replicate isolate agreement within 1 log2 between duplicate tests was 87% for MIC test strips and 100% for Etests (P < 0.001). Essential agreement with the agar dilution method was higher for Etests (91%) than for MIC test strips (44%, P < 0.001). The geometric mean MIC was highest for MIC test strips (0.8 mg/liter) and significantly higher than both Etest (0.47 mg/liter, P < 0.001) and agar dilution (0.26 mg/liter, P < 0.001) methods. Etest MICs were higher than those obtained with agar dilution (P < 0.001). Agar dilution, MIC test strip, and Etest methods categorized 96%, 85%, and 95% (P = 0.003) of clinical isolates, respectively, as susceptible/wild type according to CLSI/EUCAST criteria. Our results illustrate the difficulties underlying azithromycin susceptibility testing for N. gonorrhoeae and demonstrate that results can vary using different methods. This variability could influence antimicrobial resistance reporting between laboratories involved in N. gonorrhoeae surveillance programs.
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28
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Fletcher-Lartey S, Dronavalli M, Alexander K, Ghosh S, Boonwaat L, Thomas J, Robinson A, Patel Z, Forssman B, Pal N. Trends in Antimicrobial Resistance Patterns in Neisseria Gonorrhoeae in Australia and New Zealand: A Meta-analysis and Systematic Review. Antibiotics (Basel) 2019; 8:E191. [PMID: 31652729 PMCID: PMC6963718 DOI: 10.3390/antibiotics8040191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/14/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
(1) Background: The widespread development of resistance among Neisseria gonorrhoeae (NG) clinical isolates has been reported by surveillance systems around the world. This meta-analysis estimated the changes in susceptibility patterns among antibiotics under surveillance in Australia and New Zealand. (2) Methods: Articles published in English from 1980-2018, from Australia or New Zealand, that met the selection criteria were included. The meta-analysis was carried out using the R statistical software. (3) Results: In Australia, there has been decreasing susceptibility of gonococcal isolates to selected antimicrobials over time. Azithromycin (Odds Ratio (OR): 0.73; 95% Confidence Interval (CI) 0.64-0.82) and ceftriaxone (OR: 0.69; 95% CI 0.59-0.80) showed decreasing levels of susceptibility each year. Western Australia (OR: 0.76; 95% CI 0.60-0.96) and Victoria (OR: 0.74; 95% CI 0.60-0.90) also had decreasing levels of susceptibility to ceftriaxone over time compared with other states and territories. (4) Conclusions: The results highlight the need for the development of new approaches for managing cases of gonorrhoea. Improved antimicrobial stewardship, enhanced surveillance and contact tracing are needed to identify and respond to changes in antibiotic resistance in a timely manner. Increasing awareness and public health follow-up of cases can help to interrupt the cycle of infection and limit transmission.
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Affiliation(s)
| | - Mithilesh Dronavalli
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
| | - Kate Alexander
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
| | - Sayontonee Ghosh
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
| | - Leng Boonwaat
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
| | - Jane Thomas
- Public Health Unit, Nepean Blue Mountains Local Health District, Penrith, NSW 2750, Australia.
| | - Amanda Robinson
- Public Health Unit, Nepean Blue Mountains Local Health District, Penrith, NSW 2750, Australia.
| | - Zeel Patel
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
| | - Bradley Forssman
- Public Health Unit, Nepean Blue Mountains Local Health District, Penrith, NSW 2750, Australia.
| | - Naru Pal
- Public Health Unit, South Western Sydney Local Health District, Liverpool, NSW 2170, Australia.
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Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era. Nat Commun 2019; 10:3988. [PMID: 31488838 PMCID: PMC6728426 DOI: 10.1038/s41467-019-12053-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/19/2019] [Indexed: 11/08/2022] Open
Abstract
Whole genome sequencing (WGS) has been used to investigate transmission of Neisseria gonorrhoeae, but to date, most studies have not combined genomic data with detailed information on sexual behaviour to define the extent of transmission across population risk groups (bridging). Here, through combined epidemiological and genomic analysis of 2,186N. gonorrhoeae isolates from Australia, we show widespread transmission of N. gonorrhoeae within and between population groups. We describe distinct transmission clusters associated with men who have sex with men (MSM) and heterosexuals, and men who have sex with men and women (MSMW) are identified as a possible bridging population between these groups. Further, the study identifies transmission of N. gonorrhoeae between HIV-positive and HIV-negative individuals receiving pre-exposure prophylaxis (PrEP). Our data highlight several groups that can be targeted for interventions aimed at improving gonorrhoea control, including returning travellers, sex workers, and PrEP users. Here, Williamson et al. combine epidemiological and genomic analysis of 2,186 Neisseria gonorrhoeae isolates from Australia and show that men who have sex with men and women are a possible ‘bridging’ population between men who have sex with men and heterosexuals.
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Hicks AL, Wheeler N, Sánchez-Busó L, Rakeman JL, Harris SR, Grad YH. Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data. PLoS Comput Biol 2019; 15:e1007349. [PMID: 31479500 PMCID: PMC6743791 DOI: 10.1371/journal.pcbi.1007349] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 09/13/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022] Open
Abstract
Prediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics. However, there has been no systematic evaluation of factors that may influence performance of such models, how they might apply to and vary across clinical populations, and what the implications might be in the clinical setting. Here, we performed a meta-analysis of seven large Neisseria gonorrhoeae datasets, as well as Klebsiella pneumoniae and Acinetobacter baumannii datasets, with whole genome sequence data and antibiotic susceptibility phenotypes using set covering machine classification, random forest classification, and random forest regression models to predict resistance phenotypes from genotype. We demonstrate how model performance varies by drug, dataset, resistance metric, and species, reflecting the complexities of generating clinically relevant conclusions from machine learning-derived models. Our findings underscore the importance of incorporating relevant biological and epidemiological knowledge into model design and assessment and suggest that doing so can inform tailored modeling for individual drugs, pathogens, and clinical populations. We further suggest that continued comprehensive sampling and incorporation of up-to-date whole genome sequence data, resistance phenotypes, and treatment outcome data into model training will be crucial to the clinical utility and sustainability of machine learning-based molecular diagnostics.
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Affiliation(s)
- Allison L. Hicks
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
| | - Nicole Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Leonor Sánchez-Busó
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer L. Rakeman
- Public Health Laboratory, Division of Disease Control, New York City Department of Health and Mental Hygiene, New York, New York, United States of America
| | - Simon R. Harris
- Microbiotica Ltd, Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Yonatan H. Grad
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (ALH); (YHG)
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de Laat MM, Wind CM, Bruisten SM, Dierdorp M, de Vries HJC, Schim van der Loeff MF, van Dam AP. Ceftriaxone Reduced Susceptible Neisseria gonorrhoeae in the Netherlands, 2009 to 2017: From PenA Mosaicism to A501T/V Nonmosaicism. Sex Transm Dis 2019; 46:594-601. [PMID: 31415041 DOI: 10.1097/olq.0000000000001031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
OBJECTIVES To compare molecular and epidemiological differences between ceftriaxone-reduced susceptible (CRO-RS) and ceftriaxone-susceptible (CRO-S) N. gonorrhoeae (Ng) and to study the genetic relatedness of CRO-RS isolates. METHODS Demographic and clinical data and samples for cultures were routinely collected from gonorrhoea patients visiting the Amsterdam STI clinic in 2009 to 2017. Ng multiantigen sequence typing (NG-MAST) and penA types were compared between CRO-RS and CRO-S Ng (frequency matched on year of isolation and sexual risk group). Minimum spanning trees were produced based on multilocus variable number of tandem repeats analysis for Ng (NG-MLVA) genotypes. RESULTS We selected 174 CRO-RS isolates (minimum inhibitory concentration, ≥0.064 mg/L) and 174 CRO-S isolates (minimum inhibitory concentration, ≤0.016 mg/L). Demographic and clinical characteristics of patients were overall comparable between those infected with CRO-RS Ng and CRO-S Ng. However, CRO-RS isolates were more often collected from the pharyngeal site (odds ratios [OR], 3.64; P < 0.001), and patients with CRO-RS Ng were less often human immunodeficiency virus (HIV) and syphilis positive (OR, 0.63; P = 0.041 and OR, 0.58; P = 0.028, respectively). We identified 12 clusters based on NG-MLVA genotypes, including 3 large (>25 isolates) clusters predominantly containing CRO-RS isolates. Those from cluster 1 (n = 32) were mostly from 2009 to 2012 (n = 24; 75.0%), with a mosaic penA XXXIV pattern (n = 27; 84.4%) and belonging to NG-MAST genogroup G1407 (n = 24; 75.0%). Isolates from cluster 2 (n = 29) were mostly from 2013 to 2015 (n = 24; 82.7%), had a nonmosaic penA IX + A501T mutation (n = 22; 75.9%) and NG-MAST G2400 (n = 14; 48.3%). Most isolates from cluster 3 (n = 37) were from 2015 to 2017 (n = 26; 70.2%), had a nonmosaic penA IV + A501V mutation (n = 24; 64.9%) and NG-MAST G2318 (n = 22; 59.5%). CONCLUSIONS We observed a shift in the predominant penA (from mosaic toward nonmosaic plus A501T/V mutation), NG-MAST and NG-MLVA types among CRO-RS Ng over time. This indicates a successive spread of different CRO-RS Ng clones.
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Affiliation(s)
- Myrthe M de Laat
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Carolien M Wind
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sylvia M Bruisten
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mirjam Dierdorp
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
| | - Henry J C de Vries
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Maarten F Schim van der Loeff
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Alje P van Dam
- From the Department of Infectious Diseases, Public Health Service Amsterdam, Amsterdam, the Netherlands
- Amsterdam Infection & Immunity Institute (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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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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Agricultural Origins of a Highly Persistent Lineage of Vancomycin-Resistant Enterococcus faecalis in New Zealand. Appl Environ Microbiol 2019; 85:AEM.00137-19. [PMID: 31028029 PMCID: PMC6581176 DOI: 10.1128/aem.00137-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/22/2019] [Indexed: 11/26/2022] Open
Abstract
Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence. Enterococcus faecalis and Enterococcus faecium are human and animal gut commensals. Vancomycin-resistant enterococci (VRE) are important opportunistic pathogens with limited treatment options. Historically, the glycopeptide antibiotics vancomycin and avoparcin selected for the emergence of vancomycin resistance in human and animal isolates, respectively, resulting in global cessation of avoparcin use between 1997 and 2000. To better understand human- and animal-associated VRE strains in the postavoparcin era, we sequenced the genomes of 231 VRE isolates from New Zealand (NZ; 75 human clinical, 156 poultry) cultured between 1998 and 2009. E. faecium lineages and their antibiotic resistance carriage patterns strictly delineated between agricultural and human reservoirs, with bacitracin resistance ubiquitous in poultry but absent in clinical E. faecium strains. In contrast, one E. faecalis lineage (ST108) predominated in both poultry and human isolates in the 3 years following avoparcin discontinuation. Both phylogenetic and antimicrobial susceptibility (i.e., ubiquitous bacitracin resistance in both poultry and clinical ST108 isolates) analyses suggest an agricultural origin for the ST108 lineage. VRE isolate resistomes were carried on multiple, heterogeneous plasmids. In some isolate genomes, bacitracin, erythromycin, and vancomycin resistance elements were colocalized, indicating multiple potentially linked selection mechanisms. IMPORTANCE Historical antimicrobial use in NZ agriculture has driven the evolution of ST108, a VRE lineage carrying a range of clinically relevant antimicrobial resistances. The persistence of this lineage in NZ for over a decade indicates that coselection may be an important stabilizing mechanism for its persistence.
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Fajardo-Lubián A, Ben Zakour NL, Agyekum A, Qi Q, Iredell JR. Host adaptation and convergent evolution increases antibiotic resistance without loss of virulence in a major human pathogen. PLoS Pathog 2019; 15:e1007218. [PMID: 30875398 PMCID: PMC6436753 DOI: 10.1371/journal.ppat.1007218] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 03/27/2019] [Accepted: 01/16/2019] [Indexed: 12/19/2022] Open
Abstract
As human population density and antibiotic exposure increase, specialised bacterial subtypes have begun to emerge. Arising among species that are common commensals and infrequent pathogens, antibiotic-resistant 'high-risk clones' have evolved to better survive in the modern human. Here, we show that the major matrix porin (OmpK35) of Klebsiella pneumoniae is not required in the mammalian host for colonisation, pathogenesis, nor for antibiotic resistance, and that it is commonly absent in pathogenic isolates. This is found in association with, but apparently independent of, a highly specific change in the co-regulated partner porin, the osmoporin (OmpK36), which provides enhanced antibiotic resistance without significant loss of fitness in the mammalian host. These features are common in well-described 'high-risk clones' of K. pneumoniae, as well as in unrelated members of this species and similar adaptations are found in other members of the Enterobacteriaceae that share this lifestyle. Available sequence data indicate evolutionary convergence, with implications for the spread of lethal antibiotic-resistant pathogens in humans.
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Affiliation(s)
- Alicia Fajardo-Lubián
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
- * E-mail: (AFL); (JRI)
| | - Nouri L. Ben Zakour
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Alex Agyekum
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Qin Qi
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
- * E-mail: (AFL); (JRI)
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Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae. BMC Genomics 2019; 20:165. [PMID: 30832565 PMCID: PMC6398234 DOI: 10.1186/s12864-019-5542-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/18/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes. RESULTS We present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. Gen2Epi is a command-line tool integrating third-party software and tailored specifically for N. gonorrhoeae. For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. The assemblies were generated using raw as well as trimmed short reads. The median genome coverage of full-length scaffolds and "N" statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Molecular antimicrobial resistant (AMR) determinants identified by Gen2Epi reproduced information for the 1484 samples as previously reported, including NG-MLST, NG-MAST, and NG-STAR molecular sequence types. CONCLUSIONS Gen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. Gen2Epi is publicly available under "CC BY-NC 2.0 CA" Creative Commons licensing as a VirtualBox image containing the constituent software components running on the LINUX operating system (CentOS 7). The image and associated documentation are available via anonymous FTP at ftp://www.cs.usask.ca/pub/combi or ftp://ftp.cs.usask.ca/pub/combi.
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Sánchez-Busó L, Harris SR. Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae. Microb Genom 2019; 5:e000239. [PMID: 30698520 PMCID: PMC6421347 DOI: 10.1099/mgen.0.000239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 11/16/2018] [Indexed: 12/22/2022] Open
Abstract
Gonorrhoea infections are on the increase and strains that are resistant to all antimicrobials used to treat the disease have been found worldwide. These observations encouraged the World Health Organization to include Neisseria gonorrhoeae on their list of high-priority organisms in need of new treatments. Fortunately, concurrent resistance to both antimicrobials used in dual therapy is still rare. The fight against antimicrobial resistance (AMR) must begin from an understanding of how it evolves and spreads in sexual networks. Genome-based analyses have allowed the study of the gonococcal population dynamics and transmission, giving a novel perspective on AMR gonorrhoea. Here, we will review past, present and future treatment options for gonorrhoea and explain how genomics is helping to increase our understanding of the changing AMR and transmission landscape. This article contains data hosted by Microreact.
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Affiliation(s)
- Leonor Sánchez-Busó
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Simon R. Harris
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
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Paynter J, Goodyear-Smith F, Morgan J, Saxton P, Black S, Petousis-Harris H. Effectiveness of a Group B Outer Membrane Vesicle Meningococcal Vaccine in Preventing Hospitalization from Gonorrhea in New Zealand: A Retrospective Cohort Study. Vaccines (Basel) 2019; 7:5. [PMID: 30621260 PMCID: PMC6466174 DOI: 10.3390/vaccines7010005 10.3390/vaccines7010031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 09/11/2023] Open
Abstract
Gonorrhea is a major global public health problem with emergence of multiple drug-resistant strains with no effective vaccine. This retrospective cohort study aimed to estimate the effectiveness of the New Zealand meningococcal B vaccine against gonorrhea-associated hospitalization. The cohort consisted of individuals born from 1984 to 1999 residing in New Zealand. Therefore, it was eligible for meningococcal B vaccination from 2004 to 2008. Administrative datasets of demographics, customs, hospitalization, education, income tax, and immunization were linked using the national Integrated Data Infrastructure. The primary outcome was hospitalization with a primary diagnosis of gonorrhea. Cox's proportional hazards models were applied with a Firth correction for rare outcomes to generate estimates of hazard ratios. Vaccine effectiveness estimates were calculated as 1-Hazard Ratio expressed as a percentage. There were 1,143,897 eligible cohort members with 135 missing information on gender, 16,245 missing ethnicity, and 197,502 missing deprivation. Therefore, only 935,496 cohort members were included in the analysis. After adjustment for gender, ethnicity, and deprivation, vaccine effectiveness (MeNZB™) against hospitalization caused by gonorrhea was estimated to be 24% (95% CI 1⁻42%). In conclusion, the data suggests vaccination with MeNZB™ significantly reduced the rate of hospitalization from gonorrhea. This supports prior research indicating possible cross protection of this vaccine against gonorrhea acquisition and disease in the outpatient setting.
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Affiliation(s)
- Janine Paynter
- Department of General Practice and Primary Health, University of Auckland, Auckland 1142, New Zealand.
| | - Felicity Goodyear-Smith
- Department of General Practice and Primary Health, University of Auckland, Auckland 1142, New Zealand.
| | - Jane Morgan
- Sexual Health Services Waikato District Health Board and Honorary Senior Lecturer, School of Medicine, University of Auckland, Auckland 1142, New Zealand.
| | - Peter Saxton
- Department of Social and Community Health, University of Auckland, Auckland 1142, New Zealand.
| | - Steven Black
- Department of Pediatrics, Cincinnati Children's Hospital, Cincinnati, OH 45229-3039, USA.
| | - Helen Petousis-Harris
- Immunisation Advisory Centre, Department of General Practice and Primary Health Care, University of Auckland, Auckland 1142, New Zealand.
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Effectiveness of a Group B Outer Membrane Vesicle Meningococcal Vaccine in Preventing Hospitalization from Gonorrhea in New Zealand: A Retrospective Cohort Study. Vaccines (Basel) 2019; 7:vaccines7010005. [PMID: 30621260 PMCID: PMC6466174 DOI: 10.3390/vaccines7010005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 12/22/2022] Open
Abstract
Gonorrhea is a major global public health problem with emergence of multiple drug-resistant strains with no effective vaccine. This retrospective cohort study aimed to estimate the effectiveness of the New Zealand meningococcal B vaccine against gonorrhea-associated hospitalization. The cohort consisted of individuals born from 1984 to 1999 residing in New Zealand. Therefore, it was eligible for meningococcal B vaccination from 2004 to 2008. Administrative datasets of demographics, customs, hospitalization, education, income tax, and immunization were linked using the national Integrated Data Infrastructure. The primary outcome was hospitalization with a primary diagnosis of gonorrhea. Cox’s proportional hazards models were applied with a Firth correction for rare outcomes to generate estimates of hazard ratios. Vaccine effectiveness estimates were calculated as 1-Hazard Ratio expressed as a percentage. There were 1,143,897 eligible cohort members with 135 missing information on gender, 16,245 missing ethnicity, and 197,502 missing deprivation. Therefore, only 935,496 cohort members were included in the analysis. After adjustment for gender, ethnicity, and deprivation, vaccine effectiveness (MeNZB™) against hospitalization caused by gonorrhea was estimated to be 24% (95% CI 1–42%). In conclusion, the data suggests vaccination with MeNZB™ significantly reduced the rate of hospitalization from gonorrhea. This supports prior research indicating possible cross protection of this vaccine against gonorrhea acquisition and disease in the outpatient setting.
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Peng JP, Yin YP, Chen SC, Yang J, Dai XQ, Zheng HP, Gu WM, Zhu BY, Yong G, Zhong N, Hu LH, Cao WL, Zheng ZJ, Wang F, Zhi Q, Zhang C, Xiu LS, Liu B, Dong J, Sun LL, Zhu YF, Chen XS, Jin Q. A Whole-genome Sequencing Analysis of Neisseria gonorrhoeae Isolates in China: An Observational Study. EClinicalMedicine 2019; 7:47-54. [PMID: 31193648 PMCID: PMC6537553 DOI: 10.1016/j.eclinm.2019.01.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/06/2018] [Accepted: 01/22/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tracking the spread of the Neisseria gonorrhoeae strains with decreased susceptibility or resistance to cephalosporins is a major priority for global surveillance programmes. Whole-genome sequencing (WGS) has been widely used by increasing countries in North America, Europe, and Pacific to determine the decreased susceptible or resistance determinants of Neisseria gonorrhoeae, track the spread of these determinants throughout the gonococcal population at national or regional level. However, no studies to date have examined the genomic epidemiology of gonorrhea in Asia where the antimicrobial resistant strains of Neisseria gonorrhoeae appears to have emerged before disseminating the strains globally. METHODS We obtained clinical isolates and data from the China Gonococcal Resistance Surveillance Programme (China-GRSP) from 2012 to 2013. We sequenced the genomes of 435 clinical isolates of Neisseria gonorrhoeae, including 112 (25.6%) isolates with decreased susceptibility to ceftriaxone (Cfx-DS). We assessed the association between antimicrobial resistance genotype and phenotype. We also compared our data with the whole genome data of the isolates from the USA and the UK in the GenBank. FINDINGS The most prevalent MLST STs in our gonococcal population were MLST ST7827 (n = 74), followed by ST7365 (n = 58), ST1600 (n = 38), ST7367 (n = 35), and ST7363 (n = 29). MLST ST1901 which was reported as the predominant ST in the US was not found in our population. A total of 2512 strains, including additional 2077 published NG strains, were further included for phylogenetic analysis. It generated two distinct lineages - lineage 1 and lineage 2. Analysis of MLST ST1901 in the database indicate that most of MLST ST1901 isolates in the lineage2.6 were Cfx-DS isolates while all isolates in the lineage 2.1 were sensitive to ceftriaxone (77/110 vs. 0/13; p < 0.001). ST1901/lineage 2.6 is a ceftriaxone resistant clone which cannot distinguished by MLST genotyping. In the isolates from our study, the MICs of ceftriaxone for ST7363/lineage 2.6 isolates ranged from 0.008-0.125 mg/L (mean ± SD; 0.054 ± 0.043 mg/L) while those for ST7363/lineage 2.8 isolates ranged from 0.032-0.250 mg/L (0.134 ± 0.085 mg/L). All ST7363/lineage 2.8 isolates contained penA mosaic alleles. INTERPRETATION To our knowledge, current study is the first WGS-based analysis of gonococcal population at national level in Asia. China harbors the different predominant clones associated with decreased susceptibility to ceftriaxone from those clones circulated in other regions. The findings from the study can be not only used as baseline data for future studies in China but also contributable to our understanding on spread of N. gonorrhoeae and its resistant strains at regional and global levels. FUNDING The Chinese Academy Medical Sciences (CAMS) Initiative for Innovative Medicine.
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Affiliation(s)
- Jun-Ping Peng
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yue-Ping Yin
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China
| | - Shao-Chun Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China
| | - Jian Yang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiu-Qin Dai
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China
| | - He-Ping Zheng
- Dermatology Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Dermatology Hospital, Guangzhou, China
| | - Wei-Ming Gu
- Shanghai Skin Disease Hospital, Shanghai, China
| | - Bang-Yong Zhu
- Institute of Dermatology, Guangxi Autonomous Region, Nanning, China
| | - Gang Yong
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Na Zhong
- Hainan Provincial Center for STD/Skin Disease Control and Prevention, Haikou, China
| | - Li-Hua Hu
- Zhejiang Provincial Institute of Dermatology, Deqing, China
| | - Wen-Ling Cao
- Guangzhou Institute of Dermatology, Guangzhou, China
| | - Zhong-Jie Zheng
- Tianjin Center for Disease Control and Prevention, Tianjin, China
| | - Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qi Zhi
- Xinjiang Center for Disease Control and Prevention, Urumqi, China
| | - Chi Zhang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Le-Shan Xiu
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Bo Liu
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Dong
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Li-Lian Sun
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ya-Fang Zhu
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiang-Sheng Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- National Center for STD Control, Chinese Center for Disease Control and Prevention, Nanjing, China
- Correspondence to: X.-S. Chen, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, 12 Jiangwangmiao Street, Nanjing 210042, China.
| | - Qi Jin
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- Corresponding author.
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Day MJ, Spiteri G, Jacobsson S, Woodford N, Amato-Gauci AJ, Cole MJ, Unemo M. Stably high azithromycin resistance and decreasing ceftriaxone susceptibility in Neisseria gonorrhoeae in 25 European countries, 2016. BMC Infect Dis 2018; 18:609. [PMID: 30509194 PMCID: PMC6276195 DOI: 10.1186/s12879-018-3528-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/19/2018] [Indexed: 11/22/2022] Open
Abstract
Background The European Gonococcal Antimicrobial Surveillance Programme (Euro-GASP) performs annual sentinel surveillance of Neisseria gonorrhoeae susceptibility to therapeutically relevant antimicrobials across the European Union/European Economic Area (EU/EEA). We present the Euro-GASP results from 2016 (25 countries), linked to patient epidemiological data, and compared with data from previous years. Methods Agar dilution and minimum inhibitory concentration (MIC) gradient strip methodologies were used to determine the antimicrobial susceptibility (using EUCAST breakpoints) of 2660 N. gonorrhoeae isolates from 25 countries across the EU/EEA. Significance of differences compared with Euro-GASP results in previous years was analysed using Z-tests. Results No isolates with resistance to ceftriaxone (MIC > 0.125 mg/L) were detected in 2016 (one in 2015). However, the proportion of isolates with decreased susceptibility to ceftriaxone (MICs from 0.03 mg/L to 0.125 mg/L) increased significantly (p = 0.01) from 2015 to 2016. There were 14 (0.5%) isolates with ceftriaxone MICs 0.125 mg/L (on the resistance breakpoint), of which one isolate was resistant to azithromycin and four showed intermediate susceptibility to azithromycin. Cefixime resistance was detected in 2.1% of isolates in 2016 compared with 1.7% in 2015 (p = 0.26) and azithromycin resistance in 7.5% in 2016 compared with 7.1% in 2015 (p = 0.74). Seven (0.3%) isolates from five countries displayed high-level azithromycin resistance (MIC≥256 mg/L) in 2016 compared with five (0.2%) isolates in 2015. Resistance rate to ciprofloxacin was 46.5% compared with 49.4% in 2015 (p = 0.06). No isolates were resistant to spectinomycin and the MICs of gentamicin remained stable compared with previous years. Conclusions Overall AMR rates in gonococci in EU/EEA remained stable from 2015 to 2016. However, the ceftriaxone MIC distribution shifted away from the most susceptible (≤0.016 mg/L) and the proportion of isolates with decreased susceptibility to ceftriaxone increased significantly. This development is of concern as current European gonorrhoea management guideline recommends ceftriaxone 500 mg plus azithromycin 2 g as first-line therapy. With azithromycin resistance at 7.5%, the increasing ceftriaxone MICs might soon threaten the effectiveness of this therapeutic regimen and requires close monitoring.
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Affiliation(s)
- Michaela J Day
- National Infection Service, Public Health England, London, UK.
| | | | - Susanne Jacobsson
- WHO Collaborating Centre for Gonorrhea and other STIs, Örebro University, Örebro, Sweden
| | - Neil Woodford
- National Infection Service, Public Health England, London, UK
| | | | - Michelle J Cole
- National Infection Service, Public Health England, London, UK
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhea and other STIs, Örebro University, Örebro, Sweden
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Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory. J Clin Microbiol 2018; 56:JCM.00813-18. [PMID: 29950328 DOI: 10.1128/jcm.00813-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Whole-genome sequencing of bacterial isolates is increasingly being used to predict antibacterial susceptibility and resistance. Mason and coauthors describe the phenotypic susceptibility interpretations of more than 1,300 Staphylococcus aureus isolates tested against a dozen antistaphylococcal agents, and they compared these findings to susceptibility predictions made by analyzing whole-genome sequence data (J Clin Microbiol 56:e01815-17, 2018, https://doi.org/10.1128/JCM.01815-17). The genotype-phenotype susceptibility interpretations correlated in 96.3% (2,720/2,825) of resistant findings and 98.8% (11,504/11,639) of susceptible findings. This work by Mason and colleagues is helping to lower the barriers to using whole-genome sequencing of S. aureus in clinical microbiology practice.
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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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