Application of advanced genomic tools in food safety rapid diagnostics: challenges and opportunities

Banerjee, Goutam; Agarwal, Saumya; Marshall, Austin; Jones, Daleniece Higgins; Sulaiman, Irshad M.; Sur, Shantanu; Banerjee, Pratik

doi:10.1016/j.cofs.2022.100886

Cited by 9 publications

(16 citation statements)

References 44 publications

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“…Therefore, without publicly available information on the GMM strains of interest, this isolation step is particularly challenging due to the enormous list of microbial growth conditions to be tested, including possible auxotrophic mutations [15,48,[50][51][52][53][54]. In the absence of prior knowledge, a high-throughput sequencing strategy, like metagenomics, represents an interesting and promising option, as recently demonstrated [49,[55][56][57][58][59][60]. Nonetheless, metagenomics for the detection of GMMs in fermentation products is not yet mature enough to be implemented at the level of enforcement laboratories.…”

Section: Discussionmentioning

confidence: 99%

Development of a Taxon-Specific Real-Time Polymerase Chain Reaction Method to Detect Trichoderma reesei Contaminations in Fermentation Products

Fraiture,

Gobbo,

Papazova

et al. 2023

Fermentation

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Recently, a genetically modified microorganism (GMM) detection strategy using real-time PCR technology was developed to control fermentation products commercialized in the food and feed chain, allowing several unexpected GMM contaminations to be highlighted. Currently, only bacterial strains are targeted by this strategy. Given that fungal strains, like Trichoderma reesei, are also frequently used by the food industry to produce fermentation products, a novel real-time PCR method specific to this fungal species was developed and validated in this study to reinforce the GMM detection strategy. Designed to cover a sequence of 130 bp from the translation elongation factor alpha 1 (Tef1) gene of T. reesei, this real-time PCR method, namely TR, allows for the screening of commercial fermentation products contaminated with T. reesei, genetically modified or not, which is one of the major fungal species used as an industrial platform for the manufacturing of fermentation products. The developed real-time PCR TR method was assessed as specific and sensitive (LOD95% = eight copies). In addition, the developed real-time PCR TR method performance was confirmed to be in line with the “Minimum Performance Requirements for Analytical Methods of GMO Testing” of the European Network of GMO Laboratories. The validated real-time PCR TR method was also demonstrated to be applicable to commercial microbial fermentation products. Based on all these results, the novel real-time PCR TR method was assessed as valuable for strengthening the current GMM detection strategy regarding major fungal species used by the food industry to produce microbial fermentation products.

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Section: Discussionmentioning

confidence: 99%

Development of a Taxon-Specific Real-Time Polymerase Chain Reaction Method to Detect Trichoderma reesei Contaminations in Fermentation Products

Fraiture,

Gobbo,

Papazova

et al. 2023

Fermentation

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“…Surveillance programs that include genome sequencing of Clostridial isolates with robust epidemiologic analyses provide critical information to aid in the rule-in or rule-out potential outbreak clusters. However, these species present unique challenges given the additional equipment and expertise needed to cultivate obligate anaerobes, including their selective culture from microbially dense samples such as stool or soil, or from food products that may have low pathogen concentrations 86 . While enrichment methods, including heat or alcoholtreatment of samples to enrich for spores can be employed, further specific lab equipment, personnel training, and infrastructure including BSL-2 and in some instances BSL-3 space for C. botulinum are required to support effective microbiologic cultivation 87 .…”

Section: Implementing Genomically Surveillance Programs For Toxigenic...mentioning

confidence: 99%

“…More recently, metagenomic approaches to detect pathogenic Clostridia in foodstuffs and in samples harboring complex microbial communities have been used 86 . Untargeted metagenomic sequencing, as well as with methods using ex vivo enrichment methods for biologic amplification of target species, has worked successfully with pathogens such as Salmonella enterica 88 and Listeria monocytogenes 89,90 , and is amenable for use with toxigenic Clostridia given readily available methods to enrich for spores in materials inoculated into pre-reduced anaerobic growth media which can be handled in the absence of anaerobic cultivating equipment required for agar plates.…”

Section: Introductionmentioning

confidence: 99%

Approaching pathogenicClostridiafrom a One Health perspective

Cersosimo,

Worley,

Bry

2024

Preprint

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Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens includingC.botulinum,C.difficile, andC.perfringensenable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI’s Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.

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“…For example, the time from sample collection to positive culture for Salmonella is up to 7 days, involving 48-72 hours of enrichment culture, and 48-72 hours of growth on selective agar followed by biochemical testing to confirm presumptive Salmonella colonies [3]. In recent years, there has been increasing interest in exploring culture-independent diagnostic tests (CIDTs) such as quantitative PCR (qPCR), metabarcode sequencing, and metagenome sequencing for detecting pathogens in food [5,6,7] and environmental samples [8,9], and for infectious disease diagnostics in clinical settings [10,11,12,13]. These methods could offer lower costs, increased speed, and the potential to detect multiple pathogens in a single analysis.…”

Section: Introductionmentioning

confidence: 99%

Limit of detection ofSalmonellaser. Enteritidis using culture-based versus culture-independent diagnostic approaches

Bradford,

Yao,

Anastasiadis

et al. 2024

Preprint

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In order to prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time- and labour- intensive, leading to increasing interest in exploring culture-independent diagnostic tests (CIDTs) for pathogen detection. However, sensitivity and reliability of these CIDTs relative to current approaches has not been well established. To address this issue, we conducted a comparison of the limit of detection (LOD50) forSalmonellabetween a culture-based method and three CIDT methods: qPCR (targetinginvAandstn), metabarcode (16S) sequencing, and shotgun metagenomic sequencing. Samples of chicken feed and chicken caecal contents were spiked withSalmonellaserovar Enteritidis and subjected to culture- and DNA-based detection methods. To explore the impact of non-selective enrichment on LOD50, all samples underwent both immediate DNA extraction and an overnight enrichment prior to gDNA extraction. In addition to this spike-in experiment, feed and caecal samples acquired from the field were tested with culturing, qPCR, and metabarcoding. In general, LOD50was comparable between qPCR and shotgun sequencing methods. Overnight microbiological enrichment resulted in an improvement in LOD50with up to a three log decrease, comparable to culture-based detection. However,Salmonellareads were detected in some unspiked feed samples, suggesting false-positive detection ofSalmonella. Additionally, the LOD50in feeds was three logs lower than in caecal contents, underscoring the impact of background microbiota onSalmonelladetection using all methods.

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Application of advanced genomic tools in food safety rapid diagnostics: challenges and opportunities

Cited by 9 publications

References 44 publications

Development of a Taxon-Specific Real-Time Polymerase Chain Reaction Method to Detect Trichoderma reesei Contaminations in Fermentation Products

Development of a Taxon-Specific Real-Time Polymerase Chain Reaction Method to Detect Trichoderma reesei Contaminations in Fermentation Products

Approaching pathogenicClostridiafrom a One Health perspective

Limit of detection ofSalmonellaser. Enteritidis using culture-based versus culture-independent diagnostic approaches

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