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Whole genome sequencing (WGS), the process of determining the complete nucleotide or DNA/RNA sequence of a genome at one time, has grown in popularity and made headlines for its potential to transform infectious disease management, particularly related to SARS-CoV-2 – the virus responsible for the COVID-19 pandemic.

In a recent study, scientists used WGS to compare the genomes from critically ill COVID-19 patients genomes with a control population. They highlighted genetic host factors that may underlie the development of life-threatening COVID-19, demonstrating the potential value of WGS in better understand the genetic makeup of SARS-CoV-2.

In the same way whole genome sequencing can help in fighting antimicrobial resistance (AMR). AMR is always a concern, but it can be an even greater problem during a pandemic. The US Centers for Disease Control and Prevention recently reported a 15% increase in antimicrobialresistant infections and death in hospital in 2020, due to the COVID-19 pandemic.

Generally, the use of WGS can have a positive impact on antibiotic prescribing at both the local and population levels. Sequencing can be used to identify specific individuals as sources of infection, which can help guide quarantine measures. “As we take the perspective of a larger population level, this can apply to local and regional levels to track emerging lineages of potentially enhanced virulence of antimicrobial resistance,” explains Stephen Vella, Ph.D., Medical Science Liaison at bioMérieux.

Whole genome sequencing can provide rich surveillance data for tracking pathogens and AMR worldwide. Advancements in sequencing technology, such as next-generation sequencing, expanded databases, and robust online tools, present opportunities to further shape how we manage antimicrobial resistance and infectious diseases.

Antimicrobial Susceptibility Testing and Infectious Disease Surveillance

WGS may provide “the potential to predict antimicrobial susceptibility from a single assay.” Whole genome sequencing antimicrobial susceptibility testing (WGS-AST) can identify all known resistance genotypes throughout the entire genome simultaneously, whereas phenotypic antimicrobial susceptibility results are often limited by the number and type of resistant mechanisms that can be detected using traditional culture-based methods. This additional information from whole genome sequencing can provide insight for identifying and tracking infectious diseases. Creating a holistic antimicrobial stewardship strategy is critical for fighting the emergence and spread of AMR.

“In addition to the adoption of WGS-AST, we should also consider pairing this technique with additional methods such as contextualized reporting of laboratory results to further support evidence-based interpretation. A more upstream option would be to educate providers during the process of ordering laboratory tests”

Stephen Vella, Ph.D. | Medical Science Liaison at bioMérieux

In addition to individual hospitals, whole genome sequencing has also provided benefits to public health. In 2018, the National Antimicrobial Resistance Monitoring System (NARMS) utilized whole genome sequencing to distinguish between two Salmonella outbreaks. The incident demonstrated how combining detailed genetic information with epidemiologic data helps scientists more precisely link illnesses to specific food or animal sources. Major food safety and public health organizations are adopting whole genome sequencing—in 2019, PulseNet, which is governed by the CDC, announced its laboratory network would transition to using whole genome sequencing to combat foodborne diseases more effectively.

The Future of Genomic Data

While whole genome sequencing can be a powerful addition to traditional AST methods, it also has the potential to contribute to other areas related to antimicrobial resistance. According to an article in BMJ Global Health, “WGS provides unique insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales.” Authors in the Journal of Clinical Microbiology also note that, “The accumulation of pathogen genomes in clinical laboratories also creates a data source that can be used to research the evolution of resistant pathogens.

Technological advancements may begin to provide more granular data from more sources, such as animals, food, and the environment, so that researchers and clinicians can more thoroughly and accurately track antimicrobial resistance. As these surveillance systems proliferate, expand, and mature, they will contribute the data that are needed to facilitate a One Health approach to managing antimicrobial resistance. Because microbes live everywhere and can develop resistance anywhere, this genomic data has the potential to help us truly grasp the extent of the microbiological ecosystems we live with, and effectively prevent or treat infectious diseases.


Opinions expressed in this article are not necessarily those of bioMérieux.


  • Infectious Diseases