Genomic epidemiology of Neisseria gonorrhoeae isolates from Europe, 2020

Background Regular quality-assured whole-genome sequencing (WGS) linked to antimicrobial resistance (AMR) and patient metadata is imperative to elucidate the shifting gonorrhoea epidemiology, nationally and internationally. We describe the gonococcal population in the EU/EEA in 2020 and elucidate emerging and disappearing gonococcal lineages associated with AMR and patient metadata, compare to 2013 and 2018 WGS data, to explain recent changes in gonococcal AMR and gonorrhoea epidemiology and inform national and international STI surveillance, interventions, and guidelines. Methods We performed WGS on 1932 gonococcal isolates from 21 EU/EEA countries, 2020. Molecular typing and AMR determinants were obtained from quality-checked WGS data. Association analyses identified links between genomic lineages, AMR and patient metadata. Findings The majority of azithromycin resistance (9·4%, 181/1932) was explained by the continued expansion of the NG-STAR CC63 clone (with mtr mosaic 2) and the novel NG-STAR CC1031 (semi-mosaic mtrD 13), associated with men-who-have-sex-with-men and anorectal/oropharyngeal infections. The declining cefixime resistance (0·5%, 9/1932) and negligible ceftriaxone resistance (0·05%, 1/1932) was largely because of the progressive disappearance of NG-STAR CC90 (with mosaic penA), predominant especially in 2013. Promisingly, no resistance mutations for novel antimicrobials (zoliflodacin, gepotidacin , lefamulin) were found. Interpretation Azithromycin resistance, mainly caused by mtrD mosaics/semi-mosaics, appears to be stabilising at a relatively high level in the EU/EEA. This mostly low-level azithromycin resistance may threaten the recommended ceftriaxone-azithromycin therapy, but the negligible ceftriaxone resistance is encouraging. The decreased genomic population diversity and increased clonality may be partly explained by the COVID-19-pandemic resulting in limited importation of novel strains into Europe.