Tag: NCBI Pathogen Detection

New Milestone! NCBI Pathogen Detection Reaches 2 Million Isolates

NCBI’s Pathogen Detection resource collects, analyzes, and reports on bacterial and fungal isolate genome sequences for outbreak identification and tracking. Pathogen Detection is also central to the surveillance of anti-microbial resistance, virulence, and stress resistance for 97 pathogenic taxa covering 753 species, and now includes analysis results for over 2 million isolates!

How does Pathogen Detection work?

Pathogen Detection provides two major automated real-time analyses:

It quickly clusters related pathogen genome sequences to identify potential transmission chains helping public health scientists investigate disease outbreaks.
As part of the National Database of Antibiotic Resistant Organisms (NDARO), NCBI screens genomic sequences using AMRFinderPlus to identify the antimicrobial resistance, stress response, and virulence genes found in bacterial genomic sequences. This enables scientists to track the spread of resistance genes and to understand the relationships among antimicrobial resistance, stress response, and virulence.

Continue reading “New Milestone! NCBI Pathogen Detection Reaches 2 Million Isolates” →

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

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

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

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

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” →

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

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” →