FEATURE
One way that we have applied metagenomic methods in our laboratory is through characterization of microbial contamination in flood waters . These studies serve to identify microbial hazards that accompany natural events and provide information that public health agencies and professionals can use to reduce potential exposure to disease-causing microorganisms .”
Jeffrey W . Mercante , PhD
The Public Health Impact of Metagenomics
Christopher J . Grim , PhD , research microbiologist at FDA ’ s
Center for Food Safety and Applied Nutrition ( CFSAN ) Office of Regulatory Science said that one way FDA / CFSAN is using metagenomics is in the evaluation and improvement of culture-based bacterial analytical methods . Even though most methods are based on commodity-pathogen pairings and have good sensitivity , they can be laborious and tedious , and not every method is optimal .
“ Metagenomics has allowed us to evaluate the food associated microbiome , not just the target pathogen , at each step of the culture enrichment process to understand the limitations and advantages of many of the variables that can be manipulated to optimize pathogen recovery . More sensitive methods lead to better analytical results .”
According to Mia Mattioli , PhD , an environmental engineer in CDC ’ s Environmental Microbiology and Engineering ( EME ) Laboratory of the
Waterborne Disease Prevention Branch , the COVID-19 pandemic not only showed the value of metagenomics , but accelerated its use across government agencies .
“ Metagenomics was used to identify SARS-CoV-2 in the community where traditional testing has faced barriers such as correction facilities , college dorms and nursing homes . We know that not everyone can or is willing to be tested for the virus , but everyone goes to the bathroom ! So , we can test for SARS-CoV-2 in water samples and assess its impact in community settings .”
While the science is still rapidly developing and not yet available for implementation , CDC envisions one future use of metagenomics in outbreak response , alongside other next generation sequencing tools , to conduct pathogen source tracking from wastewater samples . For example , early in the pandemic SARS-CoV-2 genomes shed into wastewater on the West Coast may have been more closely genetically related to SARS-CoV-2 strains originating from China , while genomes in wastewater from the Northeast may have been more closely related to strains circulating in Europe . Together this metagenomic application could have the potential to inform transmission dynamics and develop more effective community-level mitigation strategies .
Jeffrey W . Mercante , PhD , a research microbiologist in the EME Laboratory , notes that metagenomic exploration of environmental water is a fascinating area of study for their laboratory .
“ One way that we have applied metagenomic methods is through characterization of microbial contamination in flood waters . These studies serve to identify microbial hazards that accompany natural events and provide information that public health agencies and professionals can use to reduce potential exposure to diseasecausing microorganisms .”
A Cross-Disciplinary Approach
Metagenomics is a widely applicable tool that can capture a lot of information . As such , its usage commonly spans multiple disciplines , according to Padmini Ramachandran MA , researcher at FDA / CFSAN .
“ Metagenomics can tell us at high resolution which microbes are present in a setting , how dangerous they are and other traits , and what functions they are performing , just to name a few . As such , its usage commonly spans multiple disciplines .”
FDA / CFSAN has engaged with several stakeholders in regions in the West as an example of public-private partnerships outlined in FDA ’ s
New Era of Smarter Food Safety and as a component of FDA ’ s
Leafy Greens STEC Action plan to understand environmental or landscape factors that are impactful in the persistence and spread of foodborne pathogens .
“ It has been important to engage with all stakeholders , including growers , academic collaborators , our internal partners and other state and federal partners , in order to take a holistic , One Health approach to this continuing problem .” said Ramachandran .
Mercante reflected that metagenomics
6 LAB MATTERS Summer 2021