{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["7(2)"],"submitter":["Pinto M"],"pubmed_abstract":["<i>Neisseria gonorrhoeae</i>, 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (<i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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."],"journal":["Microbial genomics"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC8208699"],"repository":["biostudies-literature"],"pubmed_title":["<i>Neisseria gonorrhoeae</i> clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance."],"pmcid":["PMC8208699"],"pubmed_authors":["Borges V","Borrego MJ","Gomes JP","Isidro J","Vieira L","Rodrigues JC","Pinto M"],"additional_accession":[]},"is_claimable":false,"name":"<i>Neisseria gonorrhoeae</i> clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance.","description":"<i>Neisseria gonorrhoeae</i>, 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> typing methods [i.e. MLST (multilocus sequence typing), NG-MAST (<i>N. gonorrhoeae</i> 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 <i>N. gonorrhoeae</i> 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.","dates":{"release":"2021-01-01T00:00:00Z","publication":"2021 Feb","modification":"2022-02-10T15:43:33.57Z","creation":"2022-02-10T15:43:33.57Z"},"accession":"S-EPMC8208699","cross_references":{"pubmed":["33245688"],"doi":["10.1099/mgen.0.000481"]}}