A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce

Ogunremi, Dele; Dupras, Andrée Ann; Naushad, Sohail; Gao, Ruimin; Duceppe, Marc‐Olivier; Omidi, Katayoun; Márquez, Imelda Galván; Huang, Hongsheng; Goodridge, Lawrence; Lévesque, Roger C.; Hasan, Nur A.; Dadlani, Manoj; Magierowski, Sebastian; Masson, Luke

doi:10.3389/fmicb.2020.00602

Cited by 10 publications

(6 citation statements)

References 41 publications

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“…In Canada, Salmonella remains one of the most burdensome foodborne pathogens, with more than 17.3 cases of salmonellosis per 100,000 inhabitants reported each year, with the number of affected people probably being up to 30 times higher due to underdiagnosis or underreporting (18,42). More than 2,600 Salmonella serotypes have been identified, but a limited number of these serotypes are commonly linked to foodborne diseases in humans (38). Clinical manifestations of salmonellosis are usually characterized by fever, abdominal pain, nausea, and vomiting.…”

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confidence: 99%

“…Several studies have reported that live birds originating from Salmonella-positive flocks are responsible for the introduction of the pathogen into poultry processing plants; the introduction can occur through plumage contamination or via damage to the gut during the slaughter activities, resulting in a leakage of Salmonella-contaminated intestinal content (34,49). Although a limited number of Salmonella serotypes have been isolated from poultry, different prevalences and within-serotype diversities have been observed between geographic regions and farms (2,27,38).…”

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Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

Boubendir

Arsenault

Quessy

et al. 2021

Journal of Food Protection

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Salmonella is a foodborne pathogen commonly associated with poultry products. The aims of this work were to 1) estimate the impact of critical steps of the slaughter process on Salmonella detection from broiler chicken carcasses in two commercial poultry slaughter plants in Quebec, Canada, 2) investigate the presence of the pathogen in the slaughter plant environment, 3) describe, using a high resolution melting (HRM) approach, the HRM Salmonella profiles and serotypes present on carcasses and in the slaughter plant environment and 4) evaluate if the HRM flock status after chilling could be predicted by the flock status at previous steps of the slaughter process, or by the status of previous flocks, or by the status of the processing environment, for a same HRM profile. Eight visits were conducted in each slaughter plant over a 6-month period. A total of 379 carcass rinsates from 79 flocks were collected at 5 critical steps of the slaughter process. Environmental samples were also collected from seven critical sites in each slaughter plant. The bleeding step was the most contaminated with >92% of positive carcasses. A decrease of the contamination along the slaughtering process was noted, with carcasses sampled after dry-air chilling showing ≤2.5% Salmonella prevalence. The most frequently isolated serotypes were S. Heidelberg, S. Kentucky and S. Schwarzengrund. The detection of the S. Heidelberg 1-1-1 HRM profile on carcasses after chilling was significantly associated with its detection at previous steps of the slaughter process and in previously slaughtered flocks during a same sampling day. Results highlight the importance of the chilling step in the control of Salmonella on broiler chicken carcasses and the need to further describe and compare the competitive advantage of Salmonella serotypes to survive processing. The current study also illustrates the usefulness of HRM typing in investigating Salmonella contamination along the slaughter process.

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Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

Boubendir

Arsenault

Quessy

et al. 2021

Journal of Food Protection

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“…A few have streamlined the process flow and improved reproducibility (e.g., Roche, Qiagen, Thermo Fisher Scientific, Clear Labs). Many are actively investigating new or existing commercial HTS applications to replace traditional methods reliant on binary (yes/no) and/or culture-based tests (e.g., IEH, Clear Labs, CosmosID 21 ). Additionally, many proprietary or public sequence databases have been created, customized and curated for specific purposes addressing authenticity, food spoilage and adulteration, genetic modifications (e.g., GMO), microbial composition, detection of a particular microorganism, speciation and serotyping (e.g., Creme Global, Clear Labs, CosmosID, IEH 22 ).…”

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confidence: 99%

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

et al. 2022

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The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.

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“…This may be an increasingly important function since some agencies are leaning towards Culture Independent Diagnostic Tests (CIDTs). Failure to maintain relevant strain banks could limit access to living organisms in the future for conducting applied research, developing vaccines, and assessing control measures [ 38 ]. It is also important that the international language developed through the KWL scheme to discuss S. enterica incidence, prevalence, and epidemiology be referenced even as it is refined.…”

Section: Coordinating Schemes For Communicating S Enterica ...mentioning

confidence: 99%

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

Guard

2022

Pathogens

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This review revisits previous concepts on biological phenomenon contributing to the success of the Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.

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A New Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Rapid Detection of Salmonella in Lettuce

Cited by 10 publications

References 41 publications

Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

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