TY - JOUR
T1 - Precision food safety
T2 - A paradigm shift in detection and control of foodborne pathogens
AU - Kovac, Jasna
N1 - Funding Information:
Thanks to the members of the Kovac lab Taejung Chung, Laura Rolon, Xiaoqing Tan, and Runan Yan, whose research is tapping into the unexplored nature of the food supply microbiomes. I acknowledge the support by the USDA National Institute of Food and Agriculture and Hatch Appropriations under project no. PEN04646 and accession no. 1015787. Due to reference limitation, many important publications relevant to this topic could not be included.
Funding Information:
The implementation of whole-genome sequencing (WGS) in foodborne pathogen surveillance in the United States resulted in a rapid increase in public availability of foodborne pathogen whole-genome sequences (5). By the end of the first quarter of 2019, GenomeTrakr and PulseNet networks have sequenced over 317,000 foodborne pathogen genomes, according to the fact sheet published on the GenomeTrakr website (https://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgram WGS/ucm403550.htm). The positive impacts of the real-time WGS surveillance are evident from the outcomes of the Listeria monocytogenes surveillance program that resulted in more frequently detected but smaller outbreaks since the implementation of the WGS in routine pathogen surveillance (6). The critical component of successful implementation of such enhanced surveillance programs is national and international data sharing and methods standardization. The data analyses and storage are supported by the National Center for Biotechnology Information, and the latter is currently coordinated by the Genomics for Food Safety (Gen-FS) within the United States and by the Global Microbial Identifier at international scale (5). Global standardization still represents a significant challenge and is a work in progress, while the positive impacts of the increased global availability of WGS are already evident. One of many positive outcomes is a successful investigation of a Salmonella Bareilly outbreak where comparative genomics led to the identification of an international source of contaminated tuna that would have otherwise remained under the radar (7). Apart from high-profile foodborne pathogens, WGS monitoring is proving to be relevant also for the investigation of underresearched pathogens such as the Bacillus cereus group studied in my lab (8). Using whole-genome sequencing in conjunction with an epidemiological investigation and phenotypic characterization of outbreak-associated isolates, we identified Bacillus paranthracis, a recently discovered B. cereus group species, as a causative agent of the outbreak (8). Using traditional methods, this pathogen species would not have been identified, as phenotypic methods lack sufficient discriminatory power. Despite outstanding successes of WGS in food safety, microbial isolation workflows coupled with WGS still overlook an estimated 38.4 million cases of domestically
Publisher Copyright:
Copyright © 2019 Kovac.
PY - 2019/5
Y1 - 2019/5
N2 - The implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology. Produced genomic data are also supporting the use of metagenomics and metatranscriptomics for detection and functional characterization of microbiological hazards in foods and food processing environments. In addition to that, many studies have shown that metabolic and pathogenic potential, antimicrobial resistance, and other phenotypes relevant to food safety can be predicted from whole-genome sequences, omitting the need for multiple laboratory tests. Nevertheless, further work in the area of functional inference is necessary to enable accurate interpretation of functional information inferred from genomic and metagenomic data, as well as real-time detection and tracking of high-risk pathogen subtypes and microbiomes.
AB - The implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology. Produced genomic data are also supporting the use of metagenomics and metatranscriptomics for detection and functional characterization of microbiological hazards in foods and food processing environments. In addition to that, many studies have shown that metabolic and pathogenic potential, antimicrobial resistance, and other phenotypes relevant to food safety can be predicted from whole-genome sequences, omitting the need for multiple laboratory tests. Nevertheless, further work in the area of functional inference is necessary to enable accurate interpretation of functional information inferred from genomic and metagenomic data, as well as real-time detection and tracking of high-risk pathogen subtypes and microbiomes.
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U2 - 10.1128/mSystems.00164-19
DO - 10.1128/mSystems.00164-19
M3 - Review article
C2 - 31186312
AN - SCOPUS:85067386448
VL - 4
JO - mSystems
JF - mSystems
SN - 2379-5077
IS - 3
M1 - e00164-19
ER -