Integrating Genomic Data into Public Health Surveillance for Multidrug-Resistant Organisms, Washington, USA

Abstract 

Mitigating antimicrobial resistance (AMR) is a public health priority to preserve antimicrobial treatment options. The Washington State Department of Health in Washington, USA, piloted a process to leverage longitudinal genomic surveillance on the basis of whole-genome sequencing (WGS) and a genomics-first cluster definition to enhance AMR surveillance.

BigBacter

BigBacter is a pipeline aimed at simplifying bacterial genomic surveillance. At the Washington State Department of Health, we use BigBacter to support molecular epidemiological analysis and reporting for multidrug resistant organisms, Corynebacterium diptheriae, legionella, and others. 

Fundamentals of Bacterial Genomics

In this three part short course, Stephanie Lunn introduces the molecular microbiology and genomics of bacterial pathogens, including:

  • What encompasses a bacterial genome, and how is it organized?
  • What are the important assumptions and principles of bacterial genomes when performing bioinformatic analysis and using them for genomic epidemiology?
  • An introduction to the core, accessory, and pan genome.
  • A discussion of horizontal gene transfer, including impacts to the genome and implications for genomic epidemiological inference.
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