FOOD SAFETY associated resources and costs . The most limiting costs are the price of reagents , especially in low-volume settings , and the level of expertise needed to analyze the data . Highly multiplexed amplicon sequencing ( HMAS ), for example , may be amenable to BioNumerics or a Terra Platform already used in public health laboratories . However , for shotgun metagenomics , specialized regional or national bioinformaticists might be more appropriate ; this approach could be used more widely in public health laboratories as it becomes faster , cheaper and easier over time .
Next Steps for Food Safety
At the state level , Minnesota is currently one of two pilot sites performing HMAS on CIDT-positive Salmonella specimens . In its pilot , the laboratory is amplifying and sequencing targeted regions of a known
In the expanding era of CIDTs , public health laboratories are increasingly tasked with recovering isolates from positive clinical specimens . Metagenomics will make that costly and time-intensive work obsolete .
pathogen ’ s genome to obtain highly useful information such as serotype , resistance patterns or areas of diversity . Thus , Boxrud observed , HMAS could take the place of traditional culture until true metagenomics is widely available .
At the federal level , the
US Centers for Disease Control and Prevention ( CDC ) is developing an advanced metagenomics pipeline for outbreaks of undetermined etiology ( OUEs ) that will be available to state public health laboratories in the next year or two . The pipeline will use a tiered testing approach , including a HMAS panel with primers for known and suspected enteric pathogens , shotgun metagenomics with reference-based binning and assembly , and shotgun metagenomics with reference-free binning and assembly .
Metagenomics is an extremely valuable tool that will give public health laboratories the opportunity to re-examine assumptions long associated with foodborne disease . APHL is committed to working closely with federal and state food safety agencies and members to advocate for resources needed to make the metagenomics transition . n
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Summer 2021 LAB MATTERS 15 |