Figure 2.

Phylogeny of the most closely related publicly available Neisseria gonorrhoeae genome sequences (n = 52) and the ceftriaxone-resistant, multidrug-resistant F92 gonococcal isolate from France, June 2022

CC: clonal complex; NG-STAR: Neisseria gonorrhoeae sequence typing for antimicrobial resistance; MLST: multilocus sequence typing.

Publicly available gonococcal genomes (n = 36,310) were downloaded from the European Nucleotide Archive using the search term ’Taxon:485’ (on 4 August 2022) and analysed as previously described [23]. Briefly, all genomes were characterised based on a core genome MLST (cgMLST) scheme defined by the 2016 WHO gonococcal isolates, WHO Q and WHO R using Ridom Seqsphere + (v.8.4.1). Pairwise comparisons of the cgMLST alleles (n = 2,062) were performed and subsequent neighbour-joining tree was constructed in Ridom Seqsphere + (v.8.4.1). Phylogenomic trees and subtrees were visualised in Microreact (https://microreact.org). Additionally, closely related isolates (n = 52) to F92 (black solid circle), including the closely related UK722 isolate [12] (star) with 42 SNP differences, were characterised for antimicrobial resistance determinants and typing schemes using CLC Genomics Workbench (v22.0.1) as previously described [6,23].