Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance

Detalhes bibliográficos
Autor(a) principal: Pinto, Miguel
Data de Publicação: 2021
Outros Autores: Borges, Vítor, Isidro, Joana, Rodrigues, João Carlos, Vieira, Luís, Borrego, Maria José, Gomes, João Paulo
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/114395
Resumo: Funding information M.P. was supported by the Portuguese Science and Technology Foundation (FCT) through grant SFRH/BD/109264/2015. This work was partially funded by the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Portuguese Science and Technology Foundation (FCT).
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spelling Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistanceantimicrobial resistancemolecular epidemiologyNeisseria gonorrhoeaewhole-genome sequencingEpidemiologyMicrobiologyMolecular BiologyGeneticsSDG 3 - Good Health and Well-beingFunding information M.P. was supported by the Portuguese Science and Technology Foundation (FCT) through grant SFRH/BD/109264/2015. This work was partially funded by the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Portuguese Science and Technology Foundation (FCT).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.Centre for Toxicogenomics and Human Health (ToxOmics)NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNPinto, MiguelBorges, VítorIsidro, JoanaRodrigues, João CarlosVieira, LuísBorrego, Maria JoséGomes, João Paulo2021-03-24T23:27:40Z2021-02-012021-02-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10362/114395eng2057-5858PURE: 28725730https://doi.org/10.1099/mgen.0.000481info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T04:57:04Zoai:run.unl.pt:10362/114395Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:42:30.905923Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
title Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
spellingShingle Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
Pinto, Miguel
antimicrobial resistance
molecular epidemiology
Neisseria gonorrhoeae
whole-genome sequencing
Epidemiology
Microbiology
Molecular Biology
Genetics
SDG 3 - Good Health and Well-being
title_short Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
title_full Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
title_fullStr Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
title_full_unstemmed Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
title_sort Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance
author Pinto, Miguel
author_facet Pinto, Miguel
Borges, Vítor
Isidro, Joana
Rodrigues, João Carlos
Vieira, Luís
Borrego, Maria José
Gomes, João Paulo
author_role author
author2 Borges, Vítor
Isidro, Joana
Rodrigues, João Carlos
Vieira, Luís
Borrego, Maria José
Gomes, João Paulo
author2_role author
author
author
author
author
author
dc.contributor.none.fl_str_mv Centre for Toxicogenomics and Human Health (ToxOmics)
NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)
RUN
dc.contributor.author.fl_str_mv Pinto, Miguel
Borges, Vítor
Isidro, Joana
Rodrigues, João Carlos
Vieira, Luís
Borrego, Maria José
Gomes, João Paulo
dc.subject.por.fl_str_mv antimicrobial resistance
molecular epidemiology
Neisseria gonorrhoeae
whole-genome sequencing
Epidemiology
Microbiology
Molecular Biology
Genetics
SDG 3 - Good Health and Well-being
topic antimicrobial resistance
molecular epidemiology
Neisseria gonorrhoeae
whole-genome sequencing
Epidemiology
Microbiology
Molecular Biology
Genetics
SDG 3 - Good Health and Well-being
description Funding information M.P. was supported by the Portuguese Science and Technology Foundation (FCT) through grant SFRH/BD/109264/2015. This work was partially funded by the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by the Portuguese Science and Technology Foundation (FCT).
publishDate 2021
dc.date.none.fl_str_mv 2021-03-24T23:27:40Z
2021-02-01
2021-02-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10362/114395
url http://hdl.handle.net/10362/114395
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 2057-5858
PURE: 28725730
https://doi.org/10.1099/mgen.0.000481
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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