New publication on AMRFinder, a tool that identifies resistance genes in pathogen genomes!


Read the recent publication (PMID: 31427293) on the AMRFinder, a tool that identifies antimicrobial resistance (AMR) genes in bacterial genome sequences using a high-quality curated AMR gene reference database.  We use the AMRFinder to identify AMR genes in the hundreds of bacterial genomes that NCBI receives every day, and the results of AMRFinder are used in NCBI’s Isolates Browser to provide accurate assessments of AMR gene content. You can install AMRFinder locally and run it yourself. Follow the instructions on our GitHub site.

Since the publication we have upgraded AMRFinder to AMRFinderPlus. The enhanced tool now

  • supports searches based on protein annotations, nucleotide sequences, or both for best results
  • identifies point mutations in CampylobacterE. coli, Shigella, and Salmonella
  • optionally identifies many genes involved in biocide, heat, metal, and stress resistance, as well as many antigenicity and virulence genes
  • provides information about gene function, including resistance to individual antibiotics and other phenotypes

You can learn more about NCBI’s role in helping to combat antimicrobial resistance at the National Database of Antibiotic Resistant Organisms.

Improved search makes it easier to find antimicrobial resistance protein information


It’s now easier to find known antimicrobial resistance (AMR) protein information at NCBI. You can search by gene symbol, protein name, or accession across NCBI databases and retrieve the best representative DNA sequence that is a reference for antimicrobial resistance genes from the National Database of Antibiotic Resistant Organisms (NDARO).

AMR_allele

Continue reading

Track pathogenic organisms promptly with the National Database of Antibiotic Resistant Organisms


In response to the rising threat of antimicrobial resistance (AMR), NCBI built the National Database of Antibiotic Resistant Organisms (NDARO). With NDARO, you can:

FIG 1

Figure 1. Filter your Isolates Browser results based on date, location, and for antibiotic resistance (whether the isolate has any AMR genes, or any Antimicrobial Susceptibility Testing (AST) phenotype submitted).

Continue reading