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

2020-11-27Journal article Open access
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dc.contributor.authorPinto, Miguel
dc.contributor.authorBorges, Vítor
dc.contributor.authorIsidro, Joana
dc.contributor.authorRodrigues, João Carlos
dc.contributor.authorVieira, Luís
dc.contributor.authorBorrego, Maria José
dc.contributor.authorGomes, João Paulo
dc.date.accessioned2021-05-06T17:28:37Z
dc.date.available2021-05-06T17:28:37Z
dc.date.issued2020-11-27
dc.description.abstractNeisseria 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.pt_PT
dc.description.sponsorshipM.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).pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMicrob Genom. 2021 Feb;7(2):000481. Epub 2020 Nov 27. doi: 10.1099/mgen.0.000481pt_PT
dc.identifier.doi10.1099/mgen.0.000481pt_PT
dc.identifier.issn2057-5858
dc.identifier.urihttp://hdl.handle.net/10400.18/7721
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherMicrobiology Societypt_PT
dc.relationGenomePTpt_PT
dc.relationGenomics of Neisseria gonorrhoeae tropism and antimicrobial resistance
dc.relation.publisherversionhttps://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000481pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/pt_PT
dc.subjectNeisseria gonorrhoeaept_PT
dc.subjectAntimicrobial Resistancept_PT
dc.subjectMolecular Epidemiologypt_PT
dc.subjectWhole-Genome Sequencingpt_PT
dc.subjectEuropept_PT
dc.subjectInfecções Sexualmente Transmissíveispt_PT
dc.titleNeisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistancept_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleGenomics of Neisseria gonorrhoeae tropism and antimicrobial resistance
oaire.awardURIinfo:eu-repo/grantAgreement/FCT//SFRH%2FBD%2F109264%2F2015/PT
oaire.citation.issue2pt_PT
oaire.citation.startPage000481pt_PT
oaire.citation.titleMicrobial Genomicspt_PT
oaire.citation.volume7pt_PT
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.embargofctAcesso de acordo com politica editorial da revistas.pt_PT
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublication7141a4e8-2eac-4b0a-99c8-2bcde418f692
relation.isProjectOfPublication.latestForDiscovery7141a4e8-2eac-4b0a-99c8-2bcde418f692

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