2026-10-10T14:41:58Z https://api.figshare.com/v2/oai

oai:figshare.com:article/32720025 2026-10-01T16:31:56Z category_24706 item_type_3 month_year_10_2026

Supporting data for: Population structure and sampling shape genomic antimicrobial resistance patterns in 30,327 Clostridioides difficile genomes Arvin Gupta (24232728) Medical microbiology not elsewhere classified Clostridioides difficile antimicrobial resistance ABRicate BLASTn genomic surveillance RefSeq <blockquote>Version update, 1 October 2026: This version adds the revised phylogenetic analysis performed in response to peer review. 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.</blockquote> 2026-10-01T16:31:56Z Dataset Dataset 10.6084/m9.figshare.32720025.v3 https://figshare.com/articles/dataset/Supporting_data_for_A_reproducible_assembly-based_survey_of_acquired_antimicrobial_resistance_determinants_in_250_complete_Clostridioides_difficile_RefSeq_genomes/32720025 CC BY 4.0