Antibiotic susceptibility testing using a disk diffusion assay
The Isolates Browser was built to answer two specific questions for incoming pathogen genomes: 1) is this isolate clonally related to anything else in the database? and 2) what is the AMR repertoire of this isolate? It integrates pathogen metadata, links to SNP clusters for genetically related isolates, and antimicrobial resistance genotypes and phenotypes, allowing users to browse and search over 300,000 pathogen isolates, effectively and efficiently providing access to the National Database of Antibiotic Resistant Organisms
- Retrieve all isolates from the FDA-CDC Antimicrobial Resistance Bank
- Search for pathogen isolates containing blaKPC genes
- Search for pathogen isolates containing mobile colistin resistant genes
- Search for pathogen isolates with blaKPC with resistance to meropenem and imipenem but sensitive to doripenem
MicroBIGG-E contains genetic and genomic elements identifyed in assemblies analyzed by AMRFinderPlus as part of the Pathogen Detection Pipeline. See the MicroBIGG-E documentation, the AMRFinderPlus wiki for more information on how AMRFinderPlus works, and the Pathogen Detection Reference Gene Catalog and Reference Gene Hierarchy for the elements that AMRFinderPlus is searching for.Example searches:
The AMR Reference Database. NCBI curates an ever-growing reference set of antimicrobial resistance genes and proteins, point mutations, and is now starting to incorporate stress response (biocide, metal, heat resistance) and virulence genes. The source of input for this curated database include: 1) allele assignments, 2) exchanges with other external curated resources, 3) reports of novel antimicrobial resistance proteins in the literature.
- Search for all carbapenem resistant genes
- Search for all point mutations in Escherichia that confer resistance to quinolones
The Pathogen Detection Reference Gene Hierarchy is a web-based view into the hierarchy of genes, families, and upstream nodes that our curators use to organize and relate the genes and HMMs in the Pathogen Detection Reference Gene Catalog and Pathogen Detection Reference HMM Catalog. This hierarchy drives the gene identification and naming algorithm of AMRFinderPlus. is a web-based view into the hierarchy of genes, families, and upstream nodes that our curators use to organize and relate the genes and HMMs in the Pathogen Detection Reference Gene Catalog and Pathogen Detection Reference HMM Catalog. This hierarchy drives the gene identification and naming algorithm of AMRFinderPlus.The Pathogen Detection Reference HMM Catalog is a web-based portal to our highly curated database of reference hidden Markov models (HMMs) used by AMRFinderPlus in concert with gene sequences in the Pathogen Detection Reference Gene Catalog] to identify antimicrobial resistance (AMR) genes as well as some stress resistance and virulence genes.
The AMRFinderPlus software and databases identify acquired antimicrobial resistance genes in bacterial protein and/or assembled nucleotide sequences as well as known resistance-associated point mutations for several taxa. With AMRFinderPlus we added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes. AMRFinderPlus uses a combination of BLAST alignments, HMMER hidden Markov model searches, the Reference Gene Catalog, the Reference Gene Hierarchy, the Reference HMM Catalog, curated cutoffs, and a tuned ruleset to accurately detect and name genes and point mutations in assembled nucleotide and/or protein sequences.- Download AMRFinderPlus to identify AMR genes
- AMRFinderPlus wiki
- For more information on how AMRFinderPlus operates
- Installation instructions
MiCId is a software tool that processes mass spectrometry tandem spectra (MS/MS) data for identification and classification of microorganisms. Identify microorganism, biomass estimation, and antimicrobial resistance proteins.
In response to the rising threat of AMR, the White House developed the National Action Plan for Combating Antibiotic-Resistant Bacteria in 2015. NCBI has built resources and tools to achieve several specific project goals.
NIAID is funding and conducting research to better understand how microbes develop and pass on resistance genes. NIAID is also supporting the development of new and faster diagnostic tests to make it easier for doctors to prescribe the most effective drug.
CDC leads the U.S. public health response to combat antimicrobial resistance, a threat that can continuously emerge and spread across the world. CDC’s Antimicrobial Resistance (AR) Solutions Initiative invests in national infrastructure to detect, respond, contain, and prevent resistant infections across healthcare settings, communities, the food supply, and the environment (water, soil).
Isolate Bank isolates that are sequenced are deposited at NCBI and can be found in Pathogen Detection
FDA combating antibiotic resistance activities include: 1) new drug approvals, 2) labeling for proper use, 3) public awareness, and 4) encouraging new drug development.
There are signficant contributions towards combatting antibiotic resistant bacteria across multiple federal agenices.