A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

Emond-Rhéault, Jean-Guillaume; Jeukens, Julie; Freschi, Luca; Kukavica-Ibrulj, Iréna; Boyle, Brian; Dupont, Marie-Josée; Colavecchio, Anna; Barrère, Virginie; Cadieux, Brigitte; Arya, Gitanjali; Békal, Sadjia; Berry, Chrystal; Burnett, Elton; Cavestri, Camille; Chapin, Travis; Crouse, Alanna; Daigle, France; Danyluk, Michelle D.; Delaquis, Pascal; Dewar, Ken; Doualla-Bell, Florence; Fliss, Ismaı̈l; Fong, Karen; Fournier, Éric; Franz, Eelco; Garduño, Rafael A.; Gill, Alexander; Gruenheid, Samantha; Harris, Linda J.; Huang, Carol; Huang, Hongsheng; Johnson, Roger P.; Joly, Yann; Kerhoas, Maud; Kong, Nguyet; LaPointe, Gisèle; Larivière, Line; Loignon, Stéphanie; Malo, Danielle; Moineau, Sylvain; Mottawea, Walid; Mukhopadhyay, Kakali; Nadon, Céline; Nash, John H. E.; Feze, Ida Ngueng; Ogunremi, Dele; Perets, Ann; Pilar, Ana Victoria C.; Reimer, Aleisha; Robertson, James A.; Rohde, John R.; Sanderson, Kenneth E.; Song, Lingqiao; Stephan, Roger; Tamber, Sandeep; Thomassin, Paul J.; Tremblay, Denise M.; Usongo, Valentine; Vincent, Caroline; Wang, Siyun; Weadge, Joel T.; Wiedmann, Martin; Wijnands, Lucas M.; Wilson, Emily D.; Wittum, Thomas E.; Yoshida, Catherine; Youfsi, Khadija; Zhu, Lei; Weimer, Bart C.; Goodridge, Lawrence; Levesque, Roger C.

doi:10.3389/fmicb.2017.00996

Cited by 36 publications

(26 citation statements)

References 46 publications

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“…A whole-genome sequencing procedure described previously (McDermott et al, 2016;Emond-Rheault et al, 2017) was used to detect resistance genes in S. enterica in this study. A total of 88 resistance genes were thus listed, encoding resistance to aminoglycosides, beta-lactams, macrolides, fluoroquinolones, sulfonamides, diaminopyrimidines, fosfomycin, polymyxins, peptides in addition to efflux pump genes ( Fig.…”

Section: Resistance Genesmentioning

confidence: 99%

Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25

Said

Emond-Rhéault

Soltani

et al. 2020

Environmental Microbiology

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Summary In livestock production, antibiotics are used to promote animal growth, control infections and thereby increase profitability. This practice has led to the emergence of multiresistant bacteria such as Salmonella, of which some serovars are disseminated in the environment. The objective of this study is to evaluate microcin J25 as an inhibitor of Salmonella enterica serovars of various origins including human, livestock and food. Among the 116 isolates tested, 37 (31.8%) were found resistant to at least one antibiotic, and 28 were multiresistant with 19 expressing the penta‐resistant phenotype ACSSuT. Microcin J25 inhibited all isolates, with minimal inhibitory concentration values ranging from 0.06 μg/ml (28.4 nM) to 400 μg/ml (189 μM). Interestingly, no cross‐resistance was found between microcin J25 and antibiotics. Multiple sequence alignments of genes encoding for the different proteins involved in the recognition and transport of microcin J25 showed that only ferric‐hydroxamate uptake is an essential determinant for susceptibility of S. enterica to microcin J25. Examination of Salmonella strains exposed to microcin J25 by transmission electronic microscopy showed for the first‐time involvement of a pore formation mechanism. Microcin J25 was a strong inhibitor of several multiresistant isolates of Salmonella and may have a great potential as an alternative to antibiotics.

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Section: Resistance Genesmentioning

confidence: 99%

Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25

Said

Emond-Rhéault

Soltani

et al. 2020

Environmental Microbiology

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“…OMICS datasets have been found as a powerful tool to complement current studies that are starting to be used also in some risk assessment areas. In a current comprehensive study "Syst-OMICS," 4500 Salmonella genomes will be sequenced and analysis pipeline built in order to study Salmonella genome evolution, antibiotic resistance and virulence genes [88]. The data of the first 3377 genomes already sequenced are stored in the newly established Salmonella Foodborne Syst-OMICS database (SalFoS, https://salfos.ibis.…”

Section: The Role Of Whole Genome Sequencing In the Surveillance Of Amentioning

confidence: 99%

Antimicrobial Resistance of Common Zoonotic Bacteria in the Food Chain: An Emerging Threat

Rozman¹,

Matijašić²,

Možina³

2019

Antimicrobial Resistance - A Global Threat

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Antimicrobial resistance in the food chain is currently a subject of a major interest. The excessive use or rather misuse of antimicrobials coupled with a poor hygiene in the food production chain has led to a rise of resistant zoonotic bacteria, commonly transmitted by food. They pose a serious threat to human health. Campylobacteriosis is the leading bacterial food-borne illness and most commonly reported zoonosis in humans in the European Union for more than a decade. Salmonellosis is most frequently diagnosed in food-borne outbreaks. Fluoroquinolones are considered as critically important for treatment of severe cases of both zoonoses in humans. Due to an extremely prevalent resistant isolates, especially from broilers and meat, also the treatment of human Campylobacter infections with fluoroquinolones has become compromised. Salmonella isolates from poultry and poultry meat tend to be highly resistant to fluoroquinolones as well. Beside the resistance to this group of antibiotics, the threat of multiple drug resistant (MDR) Campylobacter and Salmonella strains is discussed in the light of most recent reports of animal, food and human clinical surveillance systems.

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“…Among the international initiatives to address the challenges presented by foodborne pathogens, the Syst-OMICS project (Emond-Rheault et al, 2017) builds upon the work done by past and ongoing large-scale genomic projects (see for example Freschi et al, 2015;100k Genome Project, 2017;CDC, 2017;Genomicepidemiology, 2017). The aims of the Syst-OMICS project are to take advantage of the increasing affordability of NGS and WGS technologies to assess Salmonella genomes.…”

Section: The Syst-omics Projectmentioning

confidence: 99%

For the Safety of Fresh Produce: Regulatory Considerations for Canada on the Use of Whole Genome Sequencing to Subtype Salmonella

Feze

Dalpé

Song

et al. 2018

Front. Sustain. Food Syst.

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Salmonella is one of the oldest bacteria known to man, yet it is also one of the most prevalent when it comes to foodborne-related diseases and outbreaks. Naturally present in the environment and difficult to treat on fresh produce, Salmonella represents an important food safety challenge. Emerging technologies such as whole genome sequencing (WGS) and next generation sequencing (NGS) now offer promising applications within the realm of food safety that can significantly change the way routine testing, inspections and disease surveillance are done. They offer potential avenues that may foster more sustainable agricultural and environmental practices to detect and reduce the presence of Salmonella. Strategies are being developed to better cluster, integrate and share genomic data to facilitate the development of diagnostic tests and control methods, as well as generate robust evidence to better inform future policy and regulatory decision-making. Using the approaches developed by the Salmonella Syst-OMICS consortium, a large-scale Canadian-based genomic project, this paper discusses the policy and regulatory considerations for the applications of WGS and NGS technologies in the development of testing and biocontrol tools for food safety. The paper presents an overview of the current regulatory framework for the approval of testing methodologies for Salmonella. It discusses considerations related to (1) the development of a new test for Salmonella, (2) the potential establishment of a Salmonella risk virulence classification scheme, and (3) the development of a biocontrol method to reduce the presence of Salmonella on fresh produce.

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A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

Cited by 36 publications

References 46 publications

Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25

Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25

Antimicrobial Resistance of Common Zoonotic Bacteria in the Food Chain: An Emerging Threat

For the Safety of Fresh Produce: Regulatory Considerations for Canada on the Use of Whole Genome Sequencing to Subtype Salmonella

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