Lab Matters Summer 2025 | Page 32

FOOD SAFETY

By Sydney Comet, MPH, associate specialist, Environmental Health; Erin Morin, MHS, specialist, Environmental Health; Tyler Wolford, MS, senior program manager, Public Health Preparedness and Response; and Kirsten Larson, MPH, senior program manager, Food Safety

Metagenomics, the study of all genetic material within an environment, is a revolutionary science that can be used to tackle complex public health challenges. In comparison to traditional microbiology methods, such as pathogenspecific amplicon-based sequencing or culture-based methods, metagenomics enables an unbiased, comprehensive approach to pathogen identification and characterization. Pathogen-agnostic approaches can be used for identifying unculturable microorganisms or detecting emerging, rare or unexpected pathogens, while targeted approaches are used for pathogen-specific surveillance. The potential of metagenomics makes it a powerful tool to address threats to public health. This article will provide examples and considerations of how metagenomics may be used in public health laboratories.

Enteric Disease Outbreaks of Unknown Etiology

The US Centers for Disease Control and Prevention’ s( CDC’ s) Enteric Diseases Laboratory Branch, APHL and nine state public health departments are collaborating on an Undetermined Outbreaks( UnO) Pilot Project intended to characterize enteric disease outbreaks of unknown etiology( OUEs) using a two-tiered pathway. Well-characterized OUEs, those with robust epidemiological information, are initially analyzed for known pathogens using highly multiplexed amplicon sequencing( HMAS). Outbreaks that are negative or ambiguous for known pathogens on the HMAS panel, are then analyzed via a shotgun metagenomic workflow. Both reference-based and referencefree approaches are used to identify common genomic material across outbreak specimens to place them phylogenetically, relative to known organisms on the tree of life.

Solving OUEs is an important activity for public health. OUEs provide a powerful means for identifying new or under-recognized pathogens affecting the population. In addition to increasing our understanding of the etiology of foodborne disease, OUE investigations can also function as a quality control measure for culture independent diagnostic tests( CIDTs) which largely dominate testing for enteric pathogens in clinical settings.

Threat-agnostic Sentinel Surveillance

A collaborative effort is currently underway between CDC, APHL, the Johns Hopkins University Applied Physics Laboratory and a combination of state, veterinary and federal laboratories to develop and optimize laboratory workflows and a bioinformatics pipeline for pathogen-agnostic detection using direct-from-specimen metagenomic sequencing of various specimen types. These workflows will provide public health laboratories with the ability to screen specimens for a wide variety of pathogens using platforms already available in most public health laboratories.

This project also includes development of a standardized, open-sourced metagenomics pipeline for public health laboratory use for identification of pathogens using metagenomic sequencing techniques. Development of a bioinformatics pipeline will allow laboratories to better leverage directfrom-specimen next-generation sequencing( NGS) methods while reducing the need for dedicated bioinformatics staff. Additionally, implementation flexibilities will allow for wider adoption and capabilities without requiring local high-power computing resources.

These methods can be leveraged by public health laboratories for a variety of use cases( e. g., facilitating outbreak investigations, serving as a stopgap diagnostic for novel pathogens, characterizing genomes of novel or modified organisms). Additionally, these methods can help augment existing or yet-to-be developed surveillance and early warning systems to improve frontline detection capabilities for emerging pathogens for which no current tests exist.

Wastewater Surveillance

Metagenomics of wastewater may provide critical information regarding microorganisms present in a pooled community sample, potentially identifying an emerging infectious disease threat. However, compared to clinical metagenomics, it has limited practical uses for public health laboratories because the current technology and approaches for wastewater metagenomics are slow, expensive and generally cannot produce deep, accurate information about the full microbial community composition. This is due to the heterogenous nature of wastewater that inhibits the number of recognizable genome fragments that can be accurately tied to specific microorganisms.

Wastewater surveillance programs may be able to use PCR coupled with metagenomics to gain greater insight into a community’ s disease burden. Given its potential and the rapidly developing technology, there could be expanded use for metagenomics to help further identify pathogens in wastewater in the future, but more research is needed to uncover its practical applicability.

While metagenomics may not be appropriate for all public health activities, it is a powerful tool that offers many advantages, though brings many additional considerations. APHL’ s Next Generation Sequencing( NGS) subcommittee is currently developing a resource for laboratories as they look to onboard metagenomic assays. g