The presence of AMR genes was scanned in the genomic assemblies of the outbreak strains clade using AMRFinderPlus v3.10.16 [49 (link)]. To assess penicillin susceptibility, the protein sequences of the penicillin binding proteins (PBPs) were extracted and screened for amino acid substitutions known to correlate with decreased penicillin susceptibility in streptococci [50 (link)]. In brief, the sequence of each PBP was aligned using muscle v3.8.1551 [51 (link)] and visualized in SEAVIEW v5.0.5 [52 (link)]. The prokka annotations of the Thai zoonotic clade were queried to identify acquired resistance genes in the outbreak strain using Panaroov1.2.9 [53 (link)]. In addition, the STC78 complete genome was scanned for integrative and conjugative elements (ICEs) and prophages using ICEFinder [54 (link)] and PHASTER [55 (link)], respectively. Acquired AMR genes and their genomic context were manually inspected using Artemis v18.1.0 [56 (link)]. PubMed was searched for primary research articles describing mobile genetic elements (MGEs) carrying the same AMR genes to identify putative homologous MGEs. The annotated MGEs were aligned using clinker and clustermap.js v.0.021 [57 (link)]. The plasmid acquired by the outbreak strain was visualized using ApE v3.0.8 [58 (link)] and a blastn [59 (link)] search was performed against bacterial reference genomes. To assess the presence of potential genes of interest, ABRicate (https://github.com/tseemann/abricate ) was used with a custom database containing the sequences of 52 genes previously found to be putatively associated with zoonotic potential of S. suis
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