FEATURE
“ Through DNA metabarcoding , you can use high-throughput sequencing and circumvent the sorting and isolation of the thousands of individuals in bulk mixed samples of organisms ,” Sevinsky said . He also notes that metabarcoding is higher throughput and less costly than shotgun metagenomics , which he calls a valuable tool but not practical for public health laboratories due to its expense , the time it takes to sequence and the staff .
Grim said FDA is fortunate that there have been few barriers or challenges in implementing these systems .
“ One of the challenges to maintaining these systems are the frequent hardware and software upgrades from vendors and integrating those upgrades with our internal scientific system security configurations . Most vendors are working towards keeping the government scientific systems securities in mind when implementing the upgrades .”
In contrast , the FDA has automated platforms and instrumentation that they utilize for all sequencing workflows .
“ Our Regulatory Genomics team utilizes a
Genomics LIMS system to coordinate all our foodborne isolate genomics workflows ,” said Grim . “ We are working to integrate metagenomic sequencing data collection and analysis workflows into the same system . Additionally , we have recently developed a metadata standard for essential contextual data collection .”
In terms of materials utilized ( e . g ., sputum , wastewater , etc .) Grim said they include DNA extracted from environmental samples ( water , soil , air , compost , animal scat ), several food matrices ( leafy greens , flour , low moisture food , high moisture foods ), and culturebased bacterial enrichments that are pathogen-specific but paired with the commodity ( quasi metagenomics ). For diagnostics and industry applications , FDA is using metagenomic-based approaches and results for research-only purposes for evaluation and improvement of culturebased bacterial analytical methods .
As for data privacy on samples , especially when more than one condition is found , FDA / CFSAN is using metagenomic-based
FDA CFSAN Research Biologist Amanda Windsor performs target capture with oligonucleotide probes for enrichment of Salmonella enterica signatures from shotgun metagenomic sequencing libraries . Photo : FDA
approaches for evaluation only and not for regulatory decision making . In addition , it does not process or analyze human clinical samples , so data privacy in that regard does not apply , according to Grim .
“ For research studies , such as our longitudinal research studies in Yuma and California , we keep participant identifiers private , including when the research work is published .”
Consider the Data
Since sequencing technologies have rapidly increased their throughput and reduced the cost of sequencing per base pair , a great amount of data is being generated and a careful evaluation regarding their use , analysis and storage is needed .
“ Currently , there is no unique consensus regarding the best assembly strategy , since it has been noticed that the assembler performances depend on both biological and technical factors , and different assemblers work better on different datasets ,” Grim said . “ And since the data obtained with metagenomic sequencing is complex , created pipelines should offer a comprehensive view of genomes of all the microbes present in the sample .”
This approach also requires high sequence coverage , so that taxa in small proportion are represented in the data . The large amount of data that are generated require additional data storage and specialized analysis pipelines to efficiently discern the sequences .
Metagenomics is clearly the way of the future and , due to the pandemic , has shown its worth in promoting public health . The challenge is implementing it within the public health laboratory system . As Omoregie and others noted , today ’ s metagenomics is not being used in public health laboratories due to multiple factors . How to make the transition to use metagenomics in public health laboratories is the next step researchers will be studying in the next few years . n
|
|
|
Summer 2021 LAB MATTERS 9 |