“…Insights gained from these efforts, including the spread of azithromycin resistance (Beale et al, 2019) and high-resolution information on antigenic diversity (Lieberman et al, 2021), have aided our understanding of T. pallidum evolution and are invaluable to vaccine design. Although whole genome sequencing of low abundance T. pallidum DNA directly from clinical specimens is technically challenging due to the necessity of enrichment protocols such as hybrid capture with RNA or DNA baits (Pinto et al, 2016;Arora et al, 2017;Beale et al, 2019Beale et al, , 2021Lieberman et al, 2021;Taouk et al, 2022), Dpn1 enrichment (Grillová et al, 2019), whole genome amplification (Chen et al, 2021;Thurlow et al, 2022), and/or the traditional technique of passage of clinical strains through rabbits, sufficient progress has been made in development of these techniques that sequencing throughput of samples on a scale appropriate for monitoring of vaccine trials is feasible. Most genomic analyses of T. pallidum have excluded portions of the genome difficult to resolve by short-read sequencing, including the T. pallidum repeat (tpr) family of paralogous genes, the number of 60 bp tandem near-perfect repeats in the gene encoding the acidic repeat protein (arp; tp0433), and the number of 24 bp tandem repeats in the gene encoding the tetratricopeptide repeat protein TP0470 (tp0470).…”