What is antimicrobial resistance and why is it a global health crisis?
AMR occurs when microorganisms develop the ability to survive exposure to antimicrobial agents (antibiotics, antivirals, antifungals, and antiparasitics). Resistance can be intrinsic (naturally occurring) or acquired through mutations and horizontal gene transfer. Under selective pressure from antimicrobials, resistant strains quickly emerge and can transfer resistance genes to other species through processes like conjugation, transformation, and transduction. In recent decades, the emergence and spread of resistant strains have been dramatically accelerated by the widespread use and misuse of antimicrobials in medicine, agriculture, and animal husbandry.
The consequences of AMR are profound:
- Rising mortality: In 2019, AMR was directly responsible for 1.27 million deaths globally, with millions more deaths associated with resistant infections.1
- Economic burden: AMR costs the US economy an estimated $4.6 billion annually.2
- Vulnerable populations: Infants and the elderly, immuno-compromised patients, those with chronic illnesses, and marginalized communities are at greatest risk.
- Community impact: Hospital environments where antibiotic use is high are hotspots for the development and spread of resistant infections. Resistant microbes can spread from hospitals to the broader community or from livestock and agriculture into the environment and food supply.
AMR also threatens the effectiveness of medical procedures such as surgeries, cancer treatments, and organ transplants, where infection control is critical. Without effective antimicrobials, even minor infections can become life-threatening.
The challenge of new drug development
Developing new antibiotics and antimicrobials is a lengthy, expensive process, often taking 10-17 years from basic research to market approval. Pharmaceutical companies are reluctant to invest due to low returns and stewardship practices that restrict the use of new drugs to preserve their effectiveness.3 As a result, the pipeline for new treatments is limited, and the scientific community must focus on surveillance, rapid diagnostics, and innovative research to combat AMR.
The role of surveillance and research resources
Global health organizations, including the World Health Organization (WHO), have identified priority pathogens and research areas to guide funding and policy.4,5 To improve surveillance, develop rapid diagnostics, and understand how resistance works, it's essential to have access to well-characterized microbial strains.
ATCC supports this effort by providing a diverse collection of authenticated microbial strains that include 100 priority AMR strains spanning 11 clinically relevant genera. These strains represent the most prevalent and problematic pathogens responsible for multidrug-resistant infections.
Key features of ATCC’s priority AMR strains
- Source metadata – Geographic origin, year of isolation, and clinical collection site details provided.
- Susceptibility data – Minimal inhibitory concentration (MIC) values and susceptibility profiles for targeted drugs.
- Genetic data – Complete de novo hybrid genome assembly with annotated antibiotic resistance genes.
AMR genomic data available in the ATCC Genome Portal
The genomic data for ATCC’s priority AMR strains are accessible through the ATCC Genome Portal—a centralized, authenticated resource linking high-quality genome assemblies to physical strains in the ATCC biorepository, ensuring full data provenance and ISO 9001–compliant curation standards.
- View assembly and annotation summaries
- Explore AMR gene content via an interactive genome browser using CARD,6 ResFinder,7,8 and AMR Finder9
- Download genome assemblies and annotations (with product purchase and lot number)
- Search by catalog number, taxonomy, or gene of interest
- Access related genomes and quality control metrics
The portal is designed for both laboratory scientists and bioinformaticians, with supporting memberships and REST API access available for broader data integration.
Accelerating solutions to the AMR crisis
ATCC’s commitment to combating antimicrobial resistance extends beyond providing strains and data. The organization also encourages researchers to deposit novel or outbreak-related isolates, ensuring the global community has access to the latest resources. By combining expertly curated strains, extensive phenotypic and genotypic data, and a user-friendly genome portal, ATCC empowers researchers to accelerate solutions to the AMR crisis.
Did you know?
ATCC provides antimicrobial resistance gene annotations for the microbial genomes available through the ATCC Genome Portal. We also offer resistome profiles, when applicable.
Meet the authors
Shahin Ali, PhD
Senior Scientist, Collections, ATCC
Dr. Ali is a Senior Scientist at ATCC with over 13 years of experience in the field of fungal biology and plant-pathogen interactions. Before joining ATCC, Dr. Ali worked for the USDA-ARS at Beltsville Agricultural Research Center, Maryland. He obtained his PhD from University College Dublin, Ireland.
Briana Benton, BS
Program 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.
Explore our featured resources
Drug-resistant Bacteria
ATCC offers authenticated antimicrobial-resistant bacterial strains that provide essential tools for the development of novel therapeutics and detection methods.
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Discover the ATCC Genome Portal
The ATCC Genome Portal is a rapidly growing ISO 9001–compliant database of high-quality reference genomes from authenticated microbial strains in the ATCC collection. Through this cloud-based platform, you can easily access and download meticulously curated whole-genome sequences from your browser or our secure API. With high-quality, annotated data at your fingertips, you can confidently perform bioinformatics analyses and make insightful correlations.
MorePhenotypic and Genotypic Characterization of Antimicrobial-Resistant (AMR) Strains from the ATCC® Collection: A Key Resource for Diagnostics and Therapeutic Development
This is a poster presented at ASM Microbe 2025 that showcases the extensive characterization of 100 antimicrobial-resistant priority pathogens.
MoreReferences
- Antimicrobial Resistance Collaborators. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399(10325): 629-655, 2022. PubMed: 35065702
- Nelson RE, et al. National Estimates of Healthcare Costs Associated with Multidrug-Resistant Bacterial Infections Among Hospitalized Patients in the United States. Clin Infect Dis 72(Suppl 1): S17-S26, 2021. PubMed: 33512523
- O’Neill J. Tackling Drug-Resistant Infections Globally: Final Report and Recommendations. Review on Antimicrobial Resistance; 2016. https://amr-review.org/sites/default/files/160518_Final%20paper_with%20cover.pdf.
- World Health Organization (WHO). Antimicrobial resistance; 2023. https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance
- World Health Organization (WHO). WHO publishes list of bacteria for which new antibiotics are urgently needed; 2024 https://www.who.int/news/item/27-02-2017-who-publishes-list-of-bacteria-for-which-new-antibiotics-are-urgently-needed
- Alcock BP, et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 51(D1): D690-D699, 2023. PubMed: 36263822
- Bortolaia V, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 75(12), 3491-3500, 2020. PubMed: 32780112
- Camacho C, et al. BLAST+: architecture and applications. BMC Bioinformatics 10(1): 421, 2009. PubMed: 20003500
- Feldgarden M, et al. Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother 63(11): e00483-19, 2019. PubMed: 31427293
