Whole genome sequencing: an efficient approach to ensuring food safety

Lakicević, Brankica; Nastasijević, Ivan; Dimitrijević, Mirjana

doi:10.1088/1755-1315/85/1/012052

Cited by 3 publications

(1 citation statement)

References 10 publications

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“…Despite the differences among WGS technologies, sequencing-based approaches consistently provide greater resolution and discriminatory power for distinguishing closely related bacterial species compared to previous methods, thus improving foodborne pathogen surveillance systems and trace back investigations [ 4 , 5 , 18 , 19 , 20 , 21 , 22 ]. WGS datasets can be simultaneously used in multiple investigative analyses (e.g., subtyping, antibiotic resistance profiling, virulence genetic markers, screening of mobile genetic markers, etc.)…”

Section: Introductionmentioning

confidence: 99%

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

Therrien

Konganti²,

Gill

et al. 2021

Microorganisms

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In 2013, the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) began transitioning to whole genome sequencing (WGS) for foodborne disease outbreak- and recall-associated isolate identification of select bacterial species. While WGS offers greater precision, certain hurdles must be overcome before widespread application within the food industry is plausible. Challenges include diversity of sequencing platform outputs and lack of standardized bioinformatics workflows for data analyses. We sequenced DNA from USDA-FSIS approved, non-pathogenic E. coli surrogates and a derivative group of rifampicin-resistant mutants (rifR) via both Oxford Nanopore MinION and Illumina MiSeq platforms to generate and annotate complete genomes. Genome sequences from each clone were assembled separately so long-read, short-read, and combined sequence assemblies could be directly compared. The combined sequence data approach provides more accurate completed genomes. The genomes from these isolates were verified to lack functional key E. coli elements commonly associated with pathogenesis. Genetic alterations known to confer rifR were also identified. As the food industry adopts WGS within its food safety programs, these data provide completed genomes for commonly used surrogate strains, with a direct comparison of sequence platforms and assembly strategies relevant to research/testing workflows applicable for both processors and regulators.

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Section: Introductionmentioning

confidence: 99%

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

Therrien

Konganti²,

Gill

et al. 2021

Microorganisms

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A Listeria monocytogenes aptasensor on laser inscribed graphene for food safety monitoring in hydroponic water

Cavallaro,

Moreira,

Vanegas

et al. 2024

Discov Food

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Consumption of fresh produce, such as leafy greens, is often encouraged as part of a healthy diet. Hence, indoor facilities for hydroponic production of leafy greens are increasingly being established. However, fresh produce entails a higher risk of microbial foodborne illnesses than processed foods. Listeria monocytogenes is a major source of fresh produce contamination and is among the leading causes of severe foodborne illnesses in the United States, with a 16% mortality rate. Tools for rapid monitoring are needed for pathogens such as L. monocytogenes to prevent outbreaks. In this manuscript, we have demonstrated the feasibility of a multi-aptamer approach for development of label-free aptasensors targeting L. monocytogenes in irrigation water for lettuce hydroponic production. We use screening studies with surface plasmon resonance to rationally develop mixtures of relevant aptamers for targeting L. monocytogenes. Based on this screening, multiple aptamers targeting extracellular structures on intact L. monocytogenes were tethered to platinum-modified laser inscribed graphene electrodes. This is the first report of a L. monocytogenes biosensor based on laser inscribed graphene. We show that mixing multiple aptamers with varying affinity improves the diagnostic performance over one aptamer alone in complex sample matrices (lettuce hydroponic water). Multi-aptamer biosensors showed high accuracy for L. monocytogenes and were at least three times more selective than Escherichia coli (Crooks, K12, O157:H7) with an accuracy of 85%. The limit of detection (10 CFU/10 mL) is based on data which were significantly different after calibration toward L. monocytogenes or E. coli (Crooks) and validated against gold standard molecular analysis (polymerase chain reaction). Rapid screening of pathogens is a global need to meet food safety and water quality regulations. This study shows the importance of sensors targeting more than one bacterial surface structure in complex samples relevant to the food-water nexus.

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Recent trends in molecular techniques for food pathogen detection

Rao

Arora

2020

Chemical Analysis of Food

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Whole genome sequencing: an efficient approach to ensuring food safety

Cited by 3 publications

References 10 publications

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

A Listeria monocytogenes aptasensor on laser inscribed graphene for food safety monitoring in hydroponic water

Recent trends in molecular techniques for food pathogen detection

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