AMD: Building Capacity

Implementing AMD in state and local health departments

The AMD program is helping build and integrate laboratory, bioinformatics, and epidemiology technologies across CDC and in state and local public health systems. The AMD program supports other programs across the agency to develop and pilot next-generation diagnostics and protocols with and for CDC and state and local public health labs. These tools are then implemented in public health labs nationwide.

Following are several examples of how CDC programs have implemented AMD technologies and methods:

• In 2015, AMD-funded DNA sequencing tools were used to confirm cases belonging to a Listeria outbreak across four states, including Oklahoma.
• In 2016, AMD-funded DNA sequencing tools helped public health laboratory and disease detectives solve an E. coli outbreak linked to flour.
• In 2017, the Minnesota Department of Health partnered with CDC and the Mayo Clinic to better identify tick-borne Borrelia infections. They discovered a bacterium, Borrelia johnsonii, in a human for the first time.
• In 2018, CDC scientists developed the Universal Parasite Diagnostic assay, a diagnostic method that can detect DNA from parasites, such as Wuchereria bancrofti, in blood.
• In 2019, whole-genome sequencing linked the bacteria from an E. coli outbreak to a similar strain in the fall of 2018 and a strain in late 2017. These data led growers to adopt more stringent irrigation water standards.
• In 2020, CDC launched the National Wastewater Surveillance System (NWSS) using whole-genome sequencing to monitor SARS-CoV-2 in wastewater.
• In 2021, CDC launched the Traveler-based SARS-CoV-2 Genomic Surveillance Program to detect SARS-CoV-2 lineages through pooled sample collection from arriving passengers.

Developing the AMD workforce

A workforce adept in pathogen genomics is essential for the AMD program's success. In the early years of the AMD program, many in the public health laboratory workforce in the United States had completed their training before genomics was such a prominent field within microbiology.

Now, AMD provides funding through the Epidemiology and Laboratory Capacity (ELC) Cooperative Agreement to support Workforce Development Regions. This provides a network of customized AMD support that helps develop skills and provides training assistance to public health labs across the country.

Expanding the epidemiology base

Epidemiologists routinely analyze and interpret data from outbreak investigations. Before AMD, few epidemiologists had experience incorporating genomic data into those investigations.

Through the AMD program, CDC professionals developed a course to introduce epidemiologists to AMD. This course focused on how to work with DNA data obtained through genomic sequencing. In 2017, CDC partnered with Cornell University and the Food Safety Centers of Excellence to expand this course into an online version for state and local epidemiologists.

In collaboration with the Association of Public Health Laboratories and the Council of State and Territorial Epidemiologists, the Office of AMD created AMD Academy to provide pathogen genomics training for epidemiologists and microbiologists.

Building the bioinformatics base

Because bioinformatics is a specialized field, CDC partnered with the Association of Public Health Laboratories to create a fellowship program to encourage high-demand professionals to spend 1–2 years working on AMD projects.

Since the fellowship program’s inception, many masters- and PhD-level graduates have taken the opportunity to apply their skills to real-world public health problems. In addition, the AMD program developed training programs for internal staff to build their bioinformatics skills. Through this multipronged approach of developing internal staff and recruiting external professionals, CDC increased the number of bioinformaticians from fewer than a dozen before 2013 to almost 60 after just three years.