Tag: Pathogen Detection

Search NCBI’s Pathogen Detection websites with simple keywords

We’ve redesigned the filters on NCBI’s Pathogen Detection websites to make searching easier!

For example, say you wanted to search for outbreak isolates related to flour. Before the filters were redesigned, you’d have to know that some of the available metadata terms include “flour”, “All-purpose Wheat flour”, and “wheat flour”, along with seventeen other terms. Now, you can see all of your available options after typing in your search term and select only those that are relevant to your search.

Figure 1. Isolates Browser. The “Filters” button to see and search all filters.

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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.

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

May 15, 2019 Webinar: Using taxonomic information and other improvements in standalone BLAST+ (2.9.0) and the v5 databases

Next Wednesday, May 15, 2019 at 11AM, NCBI staff will show you how to use the latest version of standalone BLAST+ (2.9.0) and the new accession-based DBv5 databases with built-in taxonomy information. You will learn how to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy without having to download an identifier list. You will also learn about additional improvements in the BLAST databases and programs that make them compatible with the new PDB identifiers and gi-less proteins from the Pathogen Detection Project.

Date and time: Wed, May 15, 2018 11:00 AM – 11:30 AM EDT

Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Recent enhancements to BLAST+ (2.9.0): built-in taxonomy and access to proteins from the Pathogen Detection Project

We have made some recent improvements to the BLAST+ applications that take full advantage of the version 5 BLAST databases (BLASTDBv5), which include built in taxonomic information for sequences and no longer rely on the integer sequence identifiers (gi numbers).

With the latest version of BLAST, you can now:

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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).

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NCBI releases enhanced Pathogen Detection (Beta) Isolates Browser

NCBI has introduced a new and improved Pathogen DetectionBeta Isolates Browser. The browser is a key component of NCBI’s Pathogen Detection Project, a collaboration with FDA, CDC, USDA, and others to use whole genome sequencing data to monitor and investigate outbreaks of foodborne disease. Federal, state and other labs sequence pathogens (such as Salmonella and Listeria) isolated from patients, food, and environmental samples and submit the data in real time to NCBI. We then use our analysis pipeline to assemble the sequences and cluster them with all other isolates in the database to identify closely related sequences, thereby making it easier to identify cases that could be involved in an outbreak.

What’s new?

The browser is a completely updated interface that offers many improvements, like:

  • An enhanced search and browse interface
  • A new tree viewer that allows easy navigation of large SNP clusters

The NCBI Pathogen DetectionBeta home page allows direct access to sequence data, submission resources, and documentation.

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March 21 webinar – Introducing the NCBI Pathogen Detection Isolates Browser

March 21 webinar – Introducing the NCBI Pathogen Detection Isolates Browser

In this next NCBI webinar, you will learn how to use the Pathogen Detection Isolate Browser to search for pathogen isolates, identify closely related isolates of interest, and find pathogens encoding particular antimicrobial resistance genes.

Date and time: Wed, Mar 21, 2018 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

The Pathogen Detection Isolate Browser is a web-based portal that integrates the genomic sequences, metadata, antibiotic susceptibility and resistance gene information, and SNP cluster information.

Each year in the U.S. approximately 48 million Americans (approximately 1 in 6) are affected by foodborne illnesses, 128,000 are hospitalized and 3,000 die, as estimated by the CDC. The NCBI Pathogen Detection Project was created in collaboration with FDA, CDC, USDA and others to use whole genome sequencing data for foodborne disease surveillance. Pathogens isolated from patients, food and environmental samples, from state, federal, and other labs, are sequenced and the data submitted in real time to NCBI. The Pathogen Detection analysis pipeline assembles the sequences and compares them to other isolates in its database to identify closely related sequences, thereby facilitating identification of cases involved in an outbreak and potential sources of contamination.