Tag: NCBI Pathogen Detection

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”

NCBI Pathogen Detection Presents the Antibiotic Susceptibility Test (AST) Browser

NCBI Pathogen Detection Presents the Antibiotic Susceptibility Test (AST) Browser

Have you ever wanted to compare antibiotic resistance data and resistance gene calls in bacteria? Now you can! Easily access and browse antibiotic susceptibility testing (AST) data and link to other NCBI resources using the new AST Browser. NCBI has collected AST data for many isolates in the Pathogen Detection system.  

Features and Benefits 
  • Data is in a searchable, tabular format 
  • Download data for further analysis 
  • Use the Cross-browser selection tool to link out to the Isolates Browser or MicroBIGG-E to identify the isolates and the genetic elements associated with each AST result 

Continue reading “NCBI Pathogen Detection Presents the Antibiotic Susceptibility Test (AST) Browser”

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”

NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype

NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype

Using the Pathogen Detection pipeline, we recently found new Shiga toxin 2 (stx2) subtypes in isolates from the United States collected as part of the Centers for Disease Control and Prevention (CDC) routine disease surveillance. Our pipeline relies on AMRFinderPlus to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. We screened over 60,000 E. coli and Shigella genomes for Shiga toxin, a factor associated with food borne illness. These analysis results and full AMRFinderPlus results for now over 270,000 E. coli and Shigella genomes are available in the MicroBIGG-E browser. Continue reading “NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype”

Join NCBI at ASM Microbe 2023

Join NCBI at ASM Microbe 2023

Houston, TX, June 15-19, 2023

NCBI is looking forward to seeing you in person at the American Society for Microbiology Annual Meeting (ASM Microbe 2023). NCBI staff will participate in a variety of activities and events and will also be available at our booth (#2410) to address your questions. We’re especially excited to share our recent efforts on the NCBI Pathogen Detection Project which integrates bacterial and fungal pathogen genomic sequences from numerous ongoing foodborne illness and environmental surveillance and research efforts. 

Check out our schedule of activities and events below (and on our conference webpage). All times are in CST.  Continue reading “Join NCBI at ASM Microbe 2023”

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!”

NCBI Workshop at the ASM NGS 2022 Meeting

NCBI Workshop at the ASM NGS 2022 Meeting

NCBI Microbial Pathogen and SARS-CoV-2 Resources in the Cloud

Get hands-on experience with NCBI Pathogen Detection and SARS-CoV-2 Surveillance data in the cloud. No prior cloud experience necessary!

NCBI staff are presenting a workshop at the American Society for Microbiology Next-Generation Sequencing (ASM NGS) 2022 Meeting on Sunday, October 16, 2022 from 10 am – 3 pm ET (with a 1 hour break) to help conference attendees learn about two NCBI cloud-hosted resources, Pathogen Detection and SARS-CoV-2 Genome Sequence datasets. Continue reading “NCBI Workshop at the ASM NGS 2022 Meeting”

ASM Microbe 2022 was a success!

ASM Microbe 2022 was a success!

NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks!

Reflections from a few of our NCBI experts

“It was a great honor for me to receive the ASM Elizabeth O. King Lecturer Award. Thank you to my colleagues, without whom so much of my work would not have been possible, and to all of those who attended my presentation on Making Genomics Accessible to Aid Public Health and Research.”

~Michael Feldgarden, Ph.D.  Continue reading “ASM Microbe 2022 was a success!”

Come see NCBI at the ASM Microbe Conference 2022

Come see NCBI at the ASM Microbe Conference 2022

The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C.

NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth (#1128) to address your questions. Drop by to see what’s new and provide your feedback. We hope to see you there! Check out NCBI’s schedule of activities:  Continue reading “Come see NCBI at the ASM Microbe Conference 2022”

Assembly database passes 1 million genome assemblies!

The NCBI Assembly database now provides sequence and metadata for more than 1 million genome assemblies from over 85,000 different species.

Assembly crossed the 1 million genome assemblies milestone on Sunday, April 18, 2021 (Figure 1).

Figure 1. Assembly status and growth. More than 1 million assemblies are now searchable through the NCBI web site (top panel). The number of genome assemblies at NCBI has accelerated rapidly in the past decade.

Continue reading “Assembly database passes 1 million genome assemblies!”