This is an introductory level training course for genomic epidemiologists at state, territorial, local, tribal (STLT) governmental health departments to learn how to use free, online tools for analyzing molecular epidemiology data. It is part of the Advanced Molecular Detection (AMD) webinar series and has been modified from its original format. In this session, learners will be introduced to the National Center for Biotechnology (NCBI) databases that are publicly available tools for pathogen genomics. This session will feature both the NCBI Pathogen Detection and NCBI Virus tools. The NCBI databases are publicly available tools providing a variety of biological data relevant to pathogen genomics. They can be used to find clusters, investigate antimicrobial resistance and virulence genes, and search viral genome sequences as well as associated metadata.

Course Learning Objectives

By the end of the session, participants will be able to:

1. Describe the types of biological data available in NCBI databases that are relevant to pathogen genomics and explain how they are organized. 
2. Use NCBI Pathogen Detection to find samples and clusters, and investigate antimicrobial resistance and virulence genes. 
3. Navigate and search the NCBI Virus resource to find viral genome sequences and associated metadata. 

This training series was supported by Cooperative Agreement number NU38PW000005 from the Centers for Disease Control and Prevention (CDC) and CSTE and does not necessarily represent the views of CDC and CSTE.

• 1.4 – Data Analytics and Assessment Skills – Conducts surveillance activities
• 1.5 – Data Analytics and Assessment Skills – Investigates factors that affect the health of a community
• 1.6 – Data Analytics and Assessment Skills – Manages data
• 1.7 – Data Analytics and Assessment Skills – Analyzes data
• 1.8 – Data Analytics and Assessment Skills – Interprets results from data analysis
• 2.1 – Public Health Sciences Skills – Describes the source of factors affecting community health
• 2.3 – Public Health Sciences Skills – Applies public health informatics in using epidemiologic data, information, and knowledge