Lab Matters Summer 2021 | Page 9

FEATURE

A CDC microbiologist prepares a sample of wastewater for PCR molecular testing . Photo : CDC / Laura Bishop

works best when used in conjunction with other next-generation sequencing approaches or with traditional methods of microbial characterization .

“ Our laboratory has explored combining metagenomics with other approaches . I would like to expand and evaluate using combined approaches for some of our US-based and international activities where it has not yet been employed .”

“ Ultimately our goal at FDA is to be able to use metagenomics in some capacity in our regulatory decision making ,” Grim observed . “ We see metagenomics and related culture independent sequencingbased methods as the next progression from isolate whole genome sequencing .” FDA ’ s GenomeTrakr initiative has been extremely important in outbreak investigations , providing increased resolution in microbial forensics . But

We see metagenomics and related culture independent sequencing-based methods as the next progression from isolate whole genome sequencing .”

Jeffrey W . Mercante , PhD

this technique would still require the pathogen to be cultured from a food sample . Metagenomics could circumvent the dependence on culture enrichment , which could shorten turnaround time considerably . But the levels of foodborne pathogens at the harvest and retail stage are often quite low compared to the intrinsic microbiota .

“ This challenge needs to be solved ,” said Grim .

Challenges and Barriers

Enoma Omoregie , PhD , associate director of Environmental Sciences at the New York City Department of Health and Mental Hygiene , has used metagenomic techniques to look at New York City ’ s water microbiome and detect pathogens in people ’ s blood .

“ Our water , food and built environment can provide a pathway for pathogen transmissions . Traditional environmental microbiological tests are limited to specific pathogens or indicators . Metagenomics methods allow the rapid and simultaneous detection of many pathogens .” However , Omoregie notes that besides proof-of-concept studies , metagenomics is not being used in New York City at this time .