Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges

Abstract

Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.

Keywords: foodborne disease surveillance; metagenomics; whole-genome sequencing.

FIG. 1.

Comparison of isolate based on culture-independent public health surveillance workflows. CL, clinical laboratory; PHL, public health laboratory.

FIG. 2.

Disambiguation of amplicon targets in highly multiplexed amplicon sequencing. Using single-copy pathogen and species target for Shiga toxin–producing Escherichia coli and E. coli to obtain genome copy number, algorithms can be used to classify gene locus variants as belonging to pathogen (A1) or commensal (A2).

FIG. 3.

CRSIPR-Cas9 DASH and FLASH approaches to targeted sequencing. DASH targets background abundant sequences (in orange) for cleavage by Cas9. The targeted library no longer has adaptors on both ends of the sequence and is not subsequently amplified and sequenced. FLASH-Cas9 approach cleaves targeted low-abundant DNA that is subsequently available for adaptor ligation, amplification, and sequencing. DASH, Depletion of Abundant Sequences by Hybridization; FLASH, Finding Low Abundance Sequences by Hybridization.