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.
Highlights
Within the last few years, a revolution has taken place in clinical testing
The widespread use of this assay revealed that a substantial portion of Shiga toxin–producing E. coli (STEC) infections were caused by non-O157 serotypes not recognized in culture
The ideal metagenomic solution is a timely and cost-effective bedside test that serves both clinical and public health needs. This could be a small sequencer attached to an internet-connected smartphone app that analyzes shotgun metagenomic sequences as they are generated and sends reports to both the patient’s physician and to the local public health laboratory
Summary
Within the last few years, a revolution has taken place in clinical testing. Clinical diagnostic laboratories are increasingly moving away from traditional culture-based methods to culture-independent diagnostic tests (CIDTs) which are molecular tests that identify pathogens directly in the specimen without producing an isolate (Atkinson et al, 2013; Iwamoto et al, 2015).Among the first CIDTs were enzyme immunoassays (EIAs) detecting single or multiple pathogens. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. 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.
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