We used 1102 clinical gonococcal isolates collected from 2000 to 2013 by the Centers for Disease Control and Prevention’s Gonococcal Isolate Surveillance Project [Grad et al., 2016]. The datasets comprises draft genome assemblies from Illumina HiSeq reads, resistance data, and lineages inferred from sequence cluster computed using BAPS.
The N. gonorrhoeae RASE database was constructed with the CDC GISP breakpoints ([mg/L]): azithromycin (AZM): 2.0, cefixime (CFM): 0.25, ciprofloxacin (CIP): 1.0, and ceftriaxone (CRO): 0.125. Before applying the breakpoints, azithromycin MICs for strains collected before 2005 were doubled in order to correct for the known inconsistencies of the phenotyping protocol due to a change in formulation of the commercial media.
The draft assemblies and the phylogenetic tree were downloaded from Zenodo. Three prevalent types of plasmids were downloaded from GenBank, localized in the GISP database using BLAST, and removed from the dataset: the cryptic plasmid (pJD1), the beta-lactamase plasmid (pJD4), and the conjugative plasmid (pEP5289). The gonococcal ProPhyle index was constructed with the k-mer size k=18.
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