Figure 1.

Core phylogenomics of publicly available Neisseria gonorrhoeae genome sequences (n = 38,370) showing the ceftriaxone-resistant, multidrug-resistant SE690 isolate from Sweden, September 2022

AMR: antimicrobial resistance; CC: clonal complex; MLST: multilocus sequence typing; ST: sequence type; NG-STAR: Neisseria gonorrhoeae sequence typing for antimicrobial resistance; WHO: World Health Organization.

Panel A shows the phylogenomic relationship of the SE690 isolate and 38,370 publicly available gonococcal genomes. The tree shows SE690 in the more antimicrobial-susceptible lineage B and previously reported ceftriaxone-resistant strains harbouring mosaic penA-60.001 (underlined) or other ceftriaxone-resistance determinants (all in lineage A). WHO F [17] represents strains susceptible to most antimicrobials.

Panel B shows a subtree including SE690 (dark red circle) and the 52 most closely related isolates. Coloured bars represent country of infection when available (otherwise reporting country), year, MLST ST, NG-STAR CC, penA allele and presence of other key AMR determinants. Data or AMR determinant lacking when blank bars.

Publicly available gonococcal genomes (n = 38,370) were downloaded from the European Nucleotide Archive using the search term ‘Taxon:485’ (12 December, 2022) and analysed as described [4,6]. All genomes were characterised based on a core genome MLST (cgMLST) scheme defined by the 2016 WHO gonococcal reference strains [17], WHO Q [15] and FC428 [8] using Ridom Seqsphere+ (v.8.4.1). Pairwise comparisons of the cgMLST alleles (n = 2,062) were performed and a subsequent neighbour-joining tree was constructed in Ridom Seqsphere+ (v.8.4.1). Phylogenomic trees and subtrees were visualised in Microreact (https://microreact.org/). Isolates closely related to SE690 (n = 52) were characterised for AMR determinants and typing schemes using CLC Genomics Workbench (v22.0.1) as described [6,26].