PT - JOURNAL ARTICLE AU - Leonor Sánchez-Busó AU - Corin A. Yeats AU - Benjamin Taylor AU - Richard J. Goater AU - Anthony Underwood AU - Khalil Abudahab AU - Silvia Argimón AU - Kevin C. Ma AU - Tatum D. Mortimer AU - Daniel Golparian AU - Michelle J. Cole AU - Yonatan H. Grad AU - Irene Martin AU - Brian H. Raphael AU - William M. Shafer AU - Gianfranco Spiteri AU - Katy Town AU - Teodora Wi AU - Simon R. Harris AU - Magnus Unemo AU - David M. Aanensen TI - A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of <em>Neisseria gonorrhoeae</em> at Pathogenwatch AID - 10.1101/2020.07.03.186726 DP - 2020 Jan 01 TA - bioRxiv PG - 2020.07.03.186726 4099 - http://biorxiv.org/content/early/2020/12/04/2020.07.03.186726.short 4100 - http://biorxiv.org/content/early/2020/12/04/2020.07.03.186726.full AB - 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, 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, emphasizing the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern.Conclusions The N. gonorrhoeae scheme in Pathogenwatch provides customized 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.Competing Interest StatementThe authors have declared no competing interest.List of abbreviationsAGSPAustralian Gonococcal Surveillance ProgrammeAMRAntimicrobial ResistanceAZMAzithromycinCDCCenters for Disease Control and PreventionCFMCefiximecgMLSTCore Genome Multi-Locus Sequence TypingCIPCiprofloxacinCLSIClinical Laboratory and Standards InstituteCROCeftriaxoneECOFFEpidemiological Cut-OffEGASPEnhanced Gonococcal Antimicrobial Surveillance ProgrammeENAEuropean Nucleotide ArchiveESCsExtended Spectrum CephalosporinsEUCASTEuropean Committee on Antimicrobial Susceptibility TestingEuro-GASPEuropean Gonococcal Antimicrobial Surveillance ProgrammeFNFalse NegativeFPFalse PositiveGASPGonococcal Antimicrobial Surveillance ProgrammeGISPGonococcal Isolate Surveillance ProjectGRASPGonococcal Resistance to Antimicrobials Surveillance ProgrammeHIVHuman Immunodeficiency VirusLMICsLow and Middle-Income CountriesMICMinimum Inhibitory ConcentrationMLSTMulti-Locus Sequence TypingNG-MASTN. gonorrhoeae Multi-Antigen Sequence TypingNG-STARN. gonorrhoeae Sequence Typing for Antimicrobial ResistanceNPVNegative Predictive ValuePENBenzylpenicillinPPVPositive Predictive ValueSNPsSingle Nucleotide PolymorphismsSTSequence TypeSTISexually-Transmitted InfectionTETTetracyclineTNTrue NegativeTPTrue PositiveUKUnited KingdomWGSWhole Genome SequencingWHOWorld Health Organization