Feb 26, 2024

Public workspaceQuerying for Bacterial Pathogen Genomic Data at NCBI

DOI
https://dx.doi.org/10.17504/protocols.io.36wgq3kbklk5/v1
Querying for Bacterial Pathogen Genomic Data at NCBI
  • Maria Balkey1,
  • Ruth Timme1,
  • Tina Lusk Pfefer1,
  • Candace Bias1
  • 1US Food and Drug Administration
Maria Balkey
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DOI: https://dx.doi.org/10.17504/protocols.io.36wgq3kbklk5/v1
Protocol Citation: Maria Balkey, Ruth Timme, Tina Lusk Pfefer, Candace Bias 2024. Querying for Bacterial Pathogen Genomic Data at NCBI. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgq3kbklk5/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 16, 2024
Last Modified: February 26, 2024
Protocol Integer ID: 93618
Keywords: genomic pathogen surveillance, INSDC, NCBI, bacterial pathogen genomic data at ncbi purpose, bacterial pathogen genomic data, ncbi pathogen detection, wgs data of bacterial pathogen, bacterial pathogen, ncbi for analysis, pathogen, pathogen detection, contextual information at ncbi, ncbi purpose, ncbi, genometrakr
Abstract
PURPOSE: This document provides detailed instructions on how to find bacterial pathogen genomic data and associated contextual information at NCBI, specifically at the BioSample, SRA, and Pathogen Detection databases.
SCOPE: This protocol is intended for use by any laboratory submitting WGS data of bacterial pathogens to NCBI for analysis within NCBI Pathogen Detection. This includes US labs connected to GenomeTrakr, NARMS, Vet-LIRN, NAHLN, and other international networks and submitters.


Troubleshooting
Before start
This protocol has three sections:

  • Section 1: NCBI-SRA Run Selector
  • Section 2: NCBI-BioSample
  • Section 3: NCBI-SRA
  • Section 4: NCBI-Pathogen Detection



NCBI SRA (Sequence Read Archive) Run Sector
WGS submissions of pathogen genomes will become public and searchable almost immediately in SRA Run Selector.

NCBI's SRA Run Selector serves as a platform for querying contextual data, or metadta, from both BioSample and SRA. This is a good first place to check for a recent submission, obtaining a single table containing a suite of NCBI accessions and metadata for both samples and sequence data. For our application, users could enter a single or comma-separated list of IDs.

Example query with SRA run accessions: SRR24927895,SRR24927896,SRR24937652,SRR24937653

Additionally, a BioProject accession (or multiple BioProject accessions) can be entered to retrieve a complete table of submissions linked to that BioProject(s).

Isolate and experimental metadata displayed in tabular format.

Download table: Click on the -Metadata- button to download the tab-delimited file.
NCBI Sequencing Read Archive (SRA)
Submissions should be available in SRA within 1-3 days.

Strain identifiers and/or NCBI accessions can be used as queries. Multiple isolate identifiers can be included in the search box by using the " OR " separator.

Example with SRA run accessions: SRR24927896 OR SRR24927895 OR SRR24937653 OR SRR24937652.

Users can click on the SRA records themselves, or they can send the results to SRA run selector for a tabular output.

Click -Send results to Run selector-



NCBI BioSample
Submissions should be available in BioSample within 1-3 days.

Strain identifiers and/or NCBI accessions can be used to query NCBI BioSample. Multiple isolate identifiers can be included in the search box using the "OR" separator.

Example with BioSample accessions: SAMN33598462 OR SAMN36638873 OR SAMN06712285


Users can click to view each BioSample query result to review the metadata submitted for that sample (or isolate for our use case). Each BioSample record also includes links to the connected BioProject, and sequenced data generated from that BioSample, for example, raw reads in SRA, and/or genome assemblies in the Nucleotide database, or GenBank.



BioSample query results can be exported in different formats by clicking on -Send To-.


NCBI Pathogen Detection
NCBI Pathogen Detection performs cluster analysis and genotyping screening for antimicrobial resistance, stress response and virulence genes. Visit NCBI-Pathogen Detection HowTo for extensive documentation on how to access analysis results.

Analysis results expected in <1 day for all organisms except Salmonella, which requires about two days for cluster results.



Strain identifiers and/or NCBI accessions can be used to query NCBI Pathogen Detection. Delimiters are not needed for querying this database.

Example query with BioSample accessions: SAMN33598462 SAMN36638873 SAMN06712285. Direct cut/paste from an excel table also works here.


For each query, users will see results summarized within two tables:
Table 1. Cluster-level results
Table 2. Isolate-level results



Protocol references