A reproducible assembly-based survey of acquired antimicrobial resistance determinants in 250 complete Clostridioides difficile RefSeq genomes
Abstract
Background: : Clostridioides difficile is a major cause of antibiotic-associated diarrhea and healthcare-associated gastrointestinal infection. Genomic surveillance can identify resistance determinants, but small manually selected genome sets can overestimate prevalence and miss lower-frequency marker combinations. Methods. This study analyzed 250 complete C. difficile RefSeq genome assemblies downloaded from NCBI on 15 June 2026. ABRicate v1.4.0 was used to screen assemblies against the NCBI AMR database at 80% identity and 80% coverage, with the ResFinder database used for validation. Because ABRicate detects gene matches but does not perform formal SNP calling, targeted BLASTn searches were performed for the gyrA Thr82Ile-associated fluoroquinolone resistance marker and the nimB promoter-associated metronidazole resistance marker using BLAST+ v2.17.0. Results. ABRicate identified 33 unique resistance genes across 755 total hits. After excluding three intrinsic beta-lactamase genes, 30 acquired resistance genes remained for analysis. The most common acquired determinants were erm(B), detected in 72 of 250 genomes (28.8%), and tet(M), detected in 50 genomes (20.0%). Targeted BLASTn detected the gyrA-associated marker in 43 genomes (17.2%) and the nimB promoter-associated marker in 30 genomes (12.0%). The markers remained strongly associated by Fisher's exact test (p = 3.05 × 10^-26), but the relationship was not absolute: 14 genomes carried gyrA without nimB, distributed…
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