Pathogen Detection data on GCP allows you larger-scale access than is currently available through the web or from FTP. Notably, there is no FTP access to MicroBIGG-E; the web interface is limited to 100K rows and sequence downloads are restricted. There are no such restrictions on GCP. MicroBIGG-E at BigQuery also allows you to download all AMRFinderPlus results. Currently there are more than 20 million rows of antimicrobial resistance, virulence, and stress response genes, and point mutations, identified in more than 1 million pathogen isolates.
Here are two examples where researchers have used MicroBIGG-E and AMFinderPlus data to advance research on antimicrobial resistance:
Identifying conserved functional regions in erythromycin resistance methyltransferases (PMID: 34795028).
Assessing the health risks of antibiotic resistance genes (PMCID: PMC8346589).
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 Campylobacter, E.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
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).