Tag: Antimicrobial resistance

Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects

Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects

With support from the National Institute of Allergy and Infectious Diseases (NIAID)’s Office of Genomics and Advanced Technologies and the NCBI Pathogen Detection Project Team, NCBI hosted a successful virtual event, Resistance is Futile: A codeathon to combat antimicrobial resistance. This codeathon took place September 23-27, 2024, and brought together experts in the field of antimicrobial resistance and those with bioinformatic, data science skills from around the world.

Because infections caused by antimicrobial-resistant bacteria do not always respond to routinely prescribed antibiotics, they can be difficult for healthcare providers to treat. Unfortunately, this is becoming an increasingly frequent worldwide problem. This codeathon examined the association of antimicrobial resistance (AMR) with genetic sequence adaptations, mutations in bacterial receptors and efflux pumps, and emergence of mobile genetic elements in common and difficult-to-treat bacterial pathogens. Continue reading “Successful NCBI-NIAID Codeathon Collaborating on Antimicrobial Resistance Data Analysis Projects” →

NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon

NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon

Resistance is Futile: A codeathon to combat antimicrobial resistance 

Do you perform antimicrobial resistance (AMR) research, or would you like to join a team to work on microbial and AMR data analysis? NCBI is joining forces with the National Institute of Allergy and Infectious Diseases (NIAID) to co-host a virtual codeathon, Resistance is Futile: A codeathon to combat antimicrobial resistance, which will take place September 23-27, 2024.   Continue reading “NCBI & NIAID Join Forces to Co-Host Virtual AMR Codeathon” →

View Global Distribution of Microbial AMR Genes with the New MicroBIGG-E Map

View Global Distribution of Microbial AMR Genes with the New MicroBIGG-E Map

Graphical display provides new way to explore data!

NCBI’s Pathogen Detection project provides the Microbial Browser for Identification of Genetic and Genomic Elements (MicroBIGG-E) which lets you browse anti-microbial resistance (AMR), stress response, virulence genes, and genomic elements found in genomes from the NCBI Isolates Browser. 

We are excited to introduce the MicroBIGG-E Map, an easy-to-use visualization tool to help you quickly and easily explore and compare the global distribution of MicroBIGG-E data with location information. Check out the MicroBIGG-E Map Details page for more information about the displayed data.  Continue reading “View Global Distribution of Microbial AMR Genes with the New MicroBIGG-E Map” →

Full-scale access to microbial Pathogen Detection data in the Cloud!

Full-scale access to microbial Pathogen Detection data in the Cloud!

NCBI’s Pathogen Detection resource now provides selected data on the Google Cloud Platform (GCP) allowing you better access to over 1 million bacterial isolates.

Data on GCP include:

  1. The tables from the MicroBIGG-E database of anti-microbial resistance (AMR), stress response, virulence genes, and genomic elements and the Pathogen Isolates Browser that are both accessible through Google BigQuery.
  2. The MicroBIGG-E sequences in FASTA format that are available from Google Cloud Storage.

Features & Benefits

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).

Continue reading “Full-scale access to microbial Pathogen Detection data in the Cloud!” →

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 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

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 “Improved search makes it easier to find antimicrobial resistance protein information” →

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