1.1 Introduction to Pathogen detection

Background

NCBI Pathogen Detection integrates bacterial and fungal pathogen genomic sequences from numerous ongoing surveillance and research efforts whose sources include food, environmental sources such as water or production facilities, and patient samples. Foodborne, hospital-acquired, and other clinically infectious pathogens are included.

The system provides two major automated real-time analyses: 1) it quickly clusters related pathogen genome sequences to identify potential transmission chains, helping public health scientists investigate disease outbreaks, and 2) 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, which enables scientists to track the spread of resistance genes and to understand the relationships among antimicrobial resistance, stress response, and virulence.

In this workshop we will be giving you a brief introduction to Pathogen Detection data and how to access it both on the web and using Google Cloud's BigQuery service.

Learning Objectives

• Understand the layout of the Pathogen Detection website and how to find the documentation and ask for help
• Demonstrate how isolates data are represented in the Isolates Browser and have a basic familiarity with Isolates Browser searches
• Be able to download data from the isolates browser for custom analysis and reporting
• Know how to search to the MicroBIGG-E and AST Browsers
• Know how to access Pathogen Detection data in Google Cloud
• Know how to run simple queries against Pathogen Detection Data in BigQuery

Note: These exercises use live data, so the numbers here could change as isolates are added to the system or withdrawn by submitters.

Introduction PowerPoint slides