Concordance of CARD/RGI, ResFinder, and BV-BRC Workflows for ESBL Allele Detection in 100 Escherichia coli Genomes

Extended-spectrum beta-lactamase (ESBL) genes confer resistance to extended-spectrum cephalosporins. Genomic analysistools may report differing results due to distinct databases and detection rules. This study compared CARD/RGI, ResFinder,and current BV-BRC Comprehensive Genome Analysis using the same set of Escherichia coli genomes and the reconstructedsequence-level ESBL reference. One hundred study rows were examined. Complete assembly-level genomic FASTA fileswere available for 99 rows. Study row 3 remained Unresolved because a complete assembly FASTA was unavailable and wasexcluded from binary agreement calculations. A genome was classified as Positive only when sequence evidence supported aspecific recognized ESBL allele and an intact open reading frame. CARD/RGI retained Perfect and Strict hits, ResFinder used90% identity and 60% minimum coverage using acquired-gene output, and BV-BRC used gene-level AMR/Specialty Geneevidence. There were 19 Positive genomes, 80 Negative genomes, and 1 Unresolved genome. CARD/RGI, ResFinder, andcurrent BV-BRC matched the reconstructed reference for all 99 eligible rows. Positive percent agreement (PPA) was 100.00%(95% exact CI, 82.35% to 100.00%), negative percent agreement (NPA) was 100.00% (95% exact CI, 95.49% to 100.00%),overall percent agreement (OPA) was 100.00% (95% exact CI, 96.34% to 100.00%), and Cohen kappa was 1.000. All 19Positive rows had matching qualifying allele sets across the reference and three workflows. The workflows agreed under thestudy’s defined sequence-based rules. These findings do not establish phenotypic accuracy, biological ground truth, or clinicalvalidity. Published in NHSJS Reports on October 7, 2026. This record contains the publisher-issued PDF of the article. Original publication: https://nhsjs.com/2026/concordance-of-card-rgi-resfinder-and-bv-brc-workflows-for-esbl-allele-detection-in-100-escherichia-coli-genomes/