Pathogen Genomics: Sequencing and Surveillance

The COVID-19 pandemic has shone new light on the importance of genomic sequencing in understanding pathogens and controlling the spread of disease. Harnessing the transformative power of this technology, including in response to SARS-CoV-2, requires the active engagement from a broad spectrum of stakeholders, including ASM members working in research laboratories, academic medical centers, hospitals and clinical microbiology laboratories, industry partners and public health labs. Supporting and advancing pathogen genomics surveillance and sequencing, through initiatives like the CDC's Advanced Molecular Detection (AMD) program, is a top priority for ASM.

ASM was awarded funding from CDC to develop deliver accredited training to educate the clinical microbiology workforce on NGS technology. Trainings will begin in early 2023.

ASM Applauds Funding for New Pathogen Genomics Centers

The CDC has announced that $90 million in funding from the American Rescue Plan will support the Pathogen Genomics Centers of Excellence.

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Take Action

Join ASM in urging Congress to bolster funding to $175 million per year for the AMD program.

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Academy Report

This 2016 Academy report provides suggestions for combating current limitations of NGS-based diagnostic tests in clinical settings.

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What is Next-Gen Sequencing and AMD?

DNA sequencing establishes the order of the bases that make up the genetic code of an organism. Next-generation DNA sequencing (NGS) refers to the use of technologies for sequencing DNA that became available shortly after the completion of the Human Genome Project. The CDC's AMD program harnesses the power of next-generation genomic sequencing, high-performance computing and epidemiology to study pathogens.

Microcosm Article Tracking Pathogens via Next Generation Sequencing

Since the discovery and isolation of DNA, investigative processes aiming to decipher life's complex and variable genetic codes have become indispensable to public health infrastructure.

Article Bacterial Species In the Age of Next-Generation Sequencing

NGS is allowing microbiologists to see diversity with unprecedented resolution and re-defining bacterial taxonomy and species definitions.

For Clinical Professionals Metagenomic Next Generation Sequencing

How does it work, and is it coming to your clinical microbiology lab?

Downloadable Factsheet AMD Fast Facts

This downloadable factsheet highlights the importance of next-generation sequencing and the need for continued investment.

ASM' Advocates for Next-Gen Sequencing

Working With Congress

Rep. Ami Bera thanks ASM for its advocacy work.

Supporting Legislation:

Urging Funding:

Addressing COVID-19:

Working with CDC

COVID-19 Variants and Next Steps for Pathogen Genomic Sequencing and Surveillance, with CDC's Greg Armstrong and former ASM President Susie Sharp

Previous Updates

World Microbe Forum Update (June 2021)
Feb 2021 Update
June 2020 Update

With $1.7 billion in multi-year funding from the American Rescue Plan Act of 2021, the AMD program is supporting state, local and territorial public health laboratories with more staff and resources to collect specimens for COVID-19 testing, sequence them to identify and track SARS-CoV-2 variants and share data. In addition to the current investments in state and local jurisdictions included in the data below, CDC has been supporting national SARS-CoV-2 sequencing capacity through contracts with large commercial diagnostic laboratories, which have received over $240 million to sequence specimens from across the United States.

CDC Investments in AMD

Why Invest in Genomic Sequencing?

Significantly boosting U.S. genetic surveillance and viral sequencing is key to moving beyond the current COVID-19 pandemic and effectively responding to future challenges, not only associated with novel and evolving infectious diseases, but also seasonal threats, antimicrobial resistance and food borne pathogens.

SARS-CoV-2 Sequencing Data: The Devil Is in the Genomic Detail

The study of SARS-CoV-2 whole genome sequencing data has led to many important findings about this virus, and we will need more sequence data from samples from all over the world in order to come up with effective approaches to control and prevent COVID-19 infections.

Genomic Sequencing of Ancient DNA Illuminates Plague Origins

Next-generation sequencing of ancient DNA samples collected from plague victims has advanced the scientific understanding of the origin and transmission of one of the most notorious infectious diseases known to humankind.

SARS-CoV-2 Variants vs. Vaccines

This article reviews some noteworthy amino acid changes to the S protein of SARS-CoV-2 variants and dissects emerging research about the resultant antibody responses of vaccinated individuals.

Whole Genome Sequencing as a Tool for Hospital Surveillance

Whole genome sequencing has been beneficial for identifying outbreaks and performing public health surveillance. The precise and detailed data that this technology provides can be especially beneficial to infection prevention efforts in the hospital setting.

Estimates of SARS-CoV-2 Variant Prevalence in the U.S.

Data Visualization Source: CDC.

Hear From Experts

Podcasts

Dr. Charles Chiu discusses his research on metagenomic sequencing as a diagnostic tool that can identify all potential pathogens in a given patient sample.

Dr. Joe DeRisi talks about how genomics helped solve the mystery of dying leopard sharks in San Francisco bay, how a “virochip” array helped identify the SARS virus, how genomics can help identify unknown causes of encephalitis, how the sewer may hold the key to predicting infectious disease outbreaks and how computational capabilities represent the current bottleneck to global benefit from genomics technologies.

The entire TWiV team assembles to discuss resurgence of COVID-19 in Manaus, Brazil, discovery of SARS-CoV-2 related viruses in bats in Southeast Asia and increased Ct values after administration of mRNA vaccine.

Webinars

Next generation sequencing (NGS) to identify the etiology of infectious disease has the potential to assist physicians in provided faster, pathogen-targeted antimicrobial therapy. ASM hosted a symposium on clinical metagenomics for infectious disease at World Microbe Forum 2021.

Network with Experts

The ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines taking place October 2022 in Baltimore, Md. will feature leading experts on topics including sequencing in clinical and public health microbiology, bioinformatic tools, data integration and more.

Register to Attend

CDC Advanced Molecular Detection Program

Latest from AMD

Pathogen AMD Database

The SPHERES consortium aligns federal laboratories and public health agencies with international genomics efforts and engages the private sector in efforts to better understand the genomics and patterns of SARS-CoV-2 transmission across the United States.

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PulseNet

PulseNet compares the DNA fingerprints of bacteria from patients to find clusters of disease that represent unrecognized outbreaks.

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Resources Pathogen Genomics: Sequencing and Surveillance