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11 results on '"Burnett, Elton"'

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

Author

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

Subjects
Salmonella, antibiotic resistance, bacterial genomics, database, foodborne pathogen, next-generation sequencing, phylogeny, Genetics, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Prevention, Vaccine Related, Foodborne Illness, Digestive Diseases, Human Genome, Infection, Good Health and Well Being, Environmental Science and Management, Soil Sciences, Microbiology
Abstract

The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.

Published
2017

5. Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

Author

Burnett, Elton, primary, Ishida, Maria, additional, de Janon, Sofia, additional, Naushad, Sohail, additional, Duceppe, Marc-Olivier, additional, Gao, Ruimin, additional, Jardim, Armando, additional, Chen, Jessica C., additional, Tagg, Kaitlin A., additional, Ogunremi, Dele, additional, and Vinueza-Burgos, Christian, additional

Published
2021
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6. The Plasmidome as a Reservoir of Antibiotic Resistance

Author

Emond-Rheault, Jean-Guillaume, Hamel, Jérémie, Jeukens, Julie, Freschi, Luca, Kukavica-Ibrulj, Irena, Boyle, Brian, Tamber, Sandeep, Malo, Danielle, Franz, Eelco, Burnett, Elton, Daigle, France, Arya, Gitanjali, Sanderson, Kenneth, Wiedmann, Martin, Slawson, Robin M, Weadge, Joel T, Stephan, Roger, Bekal, Sadjia, Gruenheid, Samantha, Goodridge, Lawrence D, and Levesque, Roger C

Subjects
hybrid assembly, plasmid, long-read sequencing, Salmonella enterica, antimicrobial resistance
Abstract

The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades. The increase in antimicrobial resistance has been expanding via plasmids as mobile genetic elements encoding antimicrobial resistance (AMR) genes that are transferred vertically and horizontally. This study focuses on Salmonella enterica, one of the leading foodborne pathogens in industrialized countries. S. enterica is known to carry several plasmids involved not only in virulence but also in AMR. In the current paper, we present an integrated strategy to detect plasmid scaffolds in whole genome sequencing (WGS) assemblies. We developed a two-step procedure to predict plasmids based on i) the presence of essential elements for plasmid replication and mobility, as well as ii) sequence similarity to a reference plasmid. Next, to confirm the accuracy of the prediction in 1750 S. enterica short-read sequencing data, we combined Oxford Nanopore MinION long-read sequencing with Illumina MiSeq short-read sequencing in hybrid assemblies for 84 isolates to evaluate the proportion of plasmid that has been detected. At least one scaffold with an origin of replication (ORI) was predicted in 61.3% of the Salmonella isolates tested. The results indicated that IncFII and IncI1 ORIs were distributed in many S. enterica serotypes and were the most prevalent AMR genes carrier, whereas IncHI2A/IncHI2 and IncA/C2 were more serotype restricted but bore several AMR genes. Comparison between hybrid and short-read assemblies revealed that 81.1% of plasmids were found in the short-read sequencing using our pipeline. Through this process, we established that plasmids are prevalent in S. enterica and we also substantially expand the AMR genes in the resistome of this species.

Published
2020

7. The Salmonella enterica Plasmidome as a Reservoir of Antibiotic Resistance

Author

Emond-Rheault, Jean-Guillaume, primary, Hamel, Jérémie, additional, Jeukens, Julie, additional, Freschi, Luca, additional, Kukavica-Ibrulj, Irena, additional, Boyle, Brian, additional, Tamber, Sandeep, additional, Malo, Danielle, additional, Franz, Eelco, additional, Burnett, Elton, additional, Daigle, France, additional, Arya, Gitanjali, additional, Sanderson, Kenneth, additional, Wiedmann, Martin, additional, Slawson, Robin M., additional, Weadge, Joel T., additional, Stephan, Roger, additional, Bekal, Sadjia, additional, Gruenheid, Samantha, additional, Goodridge, Lawrence D., additional, and Levesque, Roger C., additional

Published
2020
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9. Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Author

Mottawea, Walid, primary, Duceppe, Marc-Olivier, additional, Dupras, Andrée A., additional, Usongo, Valentine, additional, Jeukens, Julie, additional, Freschi, Luca, additional, Emond-Rheault, Jean-Guillaume, additional, Hamel, Jeremie, additional, Kukavica-Ibrulj, Irena, additional, Boyle, Brian, additional, Gill, Alexander, additional, Burnett, Elton, additional, Franz, Eelco, additional, Arya, Gitanjali, additional, Weadge, Joel T., additional, Gruenheid, Samantha, additional, Wiedmann, Martin, additional, Huang, Hongsheng, additional, Daigle, France, additional, Moineau, Sylvain, additional, Bekal, Sadjia, additional, Levesque, Roger C., additional, Goodridge, Lawrence D., additional, and Ogunremi, Dele, additional

Published
2018
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10. Investigating the dynamics of Salmonellacontamination in integrated poultry companies using a whole genome sequencing approach

Author

Medina-Santana, José L., Ortega-Paredes, David, de Janon, Sofia, Burnett, Elton, Ishida, Maria, Sauders, Brian, Stevens, Mieke, and Vinueza-Burgos, Christian

Abstract

The study of non-typhoid Salmonellain broiler integrations has been limited by the resolution of typing techniques. Although serotyping of Salmonellaisolates is used as a traditional approach, it is not of enough resolution to clearly understand the dynamics of this pathogen within poultry companies. The aim of this research was to investigate the epidemiology and population dynamics of Salmonellaserotypes in 2 poultry integrations using a whole genome sequencing approach. Two hundred and forty-three Salmonellaisolates recovered from the broiler production chain of 2 integrated poultry companies were whole genome sequenced and analyzed with dedicated databases and bioinformatic software. The analyses of sequences revealed that S. Infantis was the most frequent serotype (82.3%). Most isolates showed a potential for resistance against medically important antibiotics and disinfectants. Furthermore, 97.5% of isolates harbored the pESI-like mega plasmid, that plays an important role in the global dissemination of AMR. SNP tree analysis showed that there were clones that are niche-specific while other ones were distributed throughout the broiler production chains. In this study, we demonstrated the potential of whole genome sequencing analysis for a comprehensive understanding of Salmonelladistribution in integrated poultry companies. Data obtained with these techniques allow determination of the presence of genetic factors that play an important role in the environmental fitness and pathogenicity of Salmonella.

Published
2022
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11. Whole-Genome Sequencing Reveals the Presence of the bla CTX-M-65  Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands.

Author

Burnett, Elton, Ishida, Maria, de Janon, Sofia, Naushad, Sohail, Duceppe, Marc-Olivier, Gao, Ruimin, Jardim, Armando, Chen, Jessica C., Tagg, Kaitlin A., Ogunremi, Dele, Vinueza-Burgos, Christian, and Rojas, Laura J.

Subjects
BETA lactamases, BROILER chickens, MOBILE genetic elements, ENTEROBACTER cloacae, SALMONELLA, SALMONELLA enterica serovar Typhi, MULTIDRUG resistance, POULTRY products
Abstract

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring blaCTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to blaCTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR blaCTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens. [ABSTRACT FROM AUTHOR]

Published
2021
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