Lab Matters Summer 2021 | Page 16


A Whole New World : Metagenomics and Food Safety by Kirsten Larson , manager , Food Safety

Public health laboratories are moving toward metagenomics , which the NIH National Human Genome Research Institute defines as the study of a collection of genetic material such as genomes from a mixed community of organisms . In food safety , the metagenomics approach will give public health laboratories new insights and tools to study the complex microbial environment that begets foodborne illness . Four members of APHL ’ s Food Safety Committee discussed how the science and application of metagenomics relates to food safety and public health laboratories . In lieu of an in-person podcast , this discussion reflects a summary originally planned in-person before the COVID-19 pandemic .
Complex Benefits and Challenges
Metagenomics offers several benefits over traditional microbiological testing and molecular and current transitional sequencing methods . Culturing of organisms requires enrichment and time for growth while molecular methods such as PCR rely on an a priori approach to detect a specific target of interest . Metagenomics removes that isolation effect or bias inherent to current food safety methods and provides an opportunity to look for and identify unculturable pathogens .
Kelly Oakeson , PhD , chief scientist for bioinformatics and next generation sequencing ( NGS ) at the Utah Public Health Laboratory , used metagenomics to successfully recover O157 Shiga toxinproducing Escherichia coli from positive culture independent diagnostic test ( CIDT ) specimens that previously tested negative by culture . In the expanding era of CIDTs , public health laboratories are increasingly tasked with recovering isolates from positive clinical specimens . Metagenomics will make that costly and time-intensive work obsolete .
Metagenomics testing will also give public health laboratories the ability to learn more about microbial community profiles ,
At the federal level , the US Centers for Disease Control and Prevention ( CDC ) is developing an advanced metagenomics pipeline for outbreaks of undetermined etiology ( OUEs ) that will be available to state public health laboratories in the next year or two .
especially from the environmental standpoint . Joel Sevinsky , PhD , founder and CEO of Theiagen Genomics , points out that as laboratorians learn about such community profiles , scientists will better predict where contamination will occur and then focus efforts on prevention instead of outbreak response activities .
Although the benefits will be exceedingly rich , there are a few challenges with implementing metagenomics for enteric pathogens . For example , fecal matter is composed of undigested fats , protein , food residue and a huge diversity of microbes , which make data analysis extremely demanding .
“ There is so much stuff in stool ,” says David Boxrud , MS , Enterics Unit supervisor at the Minnesota Department of Health . “ You couldn ’ t design a more challenging specimen .”
Rich Data Improves Food Safety
In addition , the amount of data generated by metagenomics is another current limitation .
“ Public health laboratories are generating a ton of data ,” said Kenneth Yeh , MS , senior director for Program Development at MRIGlobal . “ But we ’ re not mining everything or using big data principles to generate and look at all that data ...” Lastly , the magnitude of human DNA sequenced will present more data privacy issues than sequencing for specific pathogens .
“ Metagenomics comes in many flavors — depletion , enrichment , amplification or just shotgun approaches that sequence everything ,” says Sevinsky .
The questions asked and the answers sought will dictate the type of metagenomics approach used and the
14 LAB MATTERS Summer 2021
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