Phenotypic and Genotypic Characterization of Antimicrobial-Resistant (AMR) Strains from the ATCC Collection: A Key Resource for Diagnostics and Therapeutic Development
Poster
ASM Microbe 2025
Los Angeles, California, United States
June 22, 2025Abstract
Antimicrobial resistance (AMR) is a global health emergency highlighted during a recent United Nations meeting. To counter this growing threat, researchers need access to authenticated, well-characterized strains to use as standards during the development of diagnostic assays, therapeutics, or other applications. Here, we describe the phenotypic and genotypic characterization of ninety-four AMR strains from the ATCC collection that were selected based on their relevance and presence on the 2024 WHO Bacterial Priority Pathogen list (WHO BPPL). We evaluated the phenotypic profile of each strain using VITEK 2 (bioMérieux, SA) and then compiled the minimal inhibitory concentration profile (MIC) using the Clinical Laboratory Standard Institute (CLSI), 27th Edition. For genomic analyses, we used our ISO 9001-compliant standardized sequencing, assembly, and annotation pipelines for each strain. We extracted high-quality DNA and sequenced the material on both the Illumina (Illumina, Inc.) and Oxford Nanopore Technologies (ONT; Oxford Nanopore Technologies plc.) instruments. The data were analyzed for quality and then both data sets were combined to produce a complete de novo hybrid assembly. All de novo assemblies were then annotated for AMR-related genes using PGAP (NCBI Prokaryotic Genome Annotation Pipeline), ResFinder (Technical University of Denmark), and the Comprehensive Antibiotic Resistance Database (CARD; McMaster University). Methylation profiles were generated with ONT data using the Dorado basecaller (ONT). The annotated genomes and corresponding methylation profile for each strain are now available to qualified researchers through the ATCC Genome Portal, and the susceptibility profiles are provided on our website (atcc.org). Overall, this diverse collection of highly characterized AMR strains provides a valuable resource for diagnostics and therapeutic development.
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Briana Benton, BS
Technical Manager, ATCC
Briana Benton is a Program Manager for ATCC’s Sequencing and Bioinformatics department. Her current focus is on the ATCC Genome Portal and expanding the collection of published reference genomes. Briana previously worked on the development of mock microbial communities for microbiome research and synthetic molecular standards for molecular diagnostics assays. Prior to joining ATCC, she developed molecular diagnostic assays for the Henry M. Jackson Foundation.
