<b>Supporting data for: Population structure and sampling shape genomic antimicrobial resistance patterns in 30,327</b><b> </b><b><i>Clostridioides difficile</i></b><b> </b><b>genomes</b>

The previous 247-genome representative phylogeny has been replaced for manuscript interpretation by a 428-genome diversity-informed UBCG core-gene phylogeny. Genome-wide Mash screening of all 30,327 final assemblies was used to construct a 399-genome marker-blind diversity backbone, supplemented with 35 PnimB^G-only diversity representatives.

Six genomes were excluded after alignment-level QC, leaving 428 genomes. The update includes the final UBCG alignment, IQ-TREE outputs, diversity-sampling manifests, QC-exclusion audit, same-ST core-gene analyses, revised Figure 4, and updated supplementary tables. The final tree was inferred under TIM2+F+R5 with 1,000 SH-aLRT and 1,000 ultrafast-bootstrap replicates.</p></blockquote><p></p>