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For: Lambert D, Carrillo CD, Koziol AG, Manninger P, Blais BW. GeneSippr: a rapid whole-genome approach for the identification and characterization of foodborne pathogens such as priority Shiga toxigenic Escherichia coli. PLoS One 2015;10:e0122928. [PMID: 25860693 PMCID: PMC4393293 DOI: 10.1371/journal.pone.0122928] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/24/2015] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Zhang H, Yamamoto E, Markell A, Carrillo C, Locas A. Prevalence of Shiga Toxin-Producing Escherichia coli (STEC) and Risk Characterization Based on Virulence Genes in Retail Raw Ground Meat of Beef, Veal, and Lamb in Canada. J Food Prot 2025;88:100483. [PMID: 40081812 DOI: 10.1016/j.jfp.2025.100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 02/24/2025] [Accepted: 03/08/2025] [Indexed: 03/16/2025]
2
Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024;62:e0157623. [PMID: 38441926 PMCID: PMC11077942 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024]  Open
3
Genomically Informed Custom Selective Enrichment of Shiga Toxigenic Escherichia coli (STEC) Outbreak Strains in Foods Using Antibiotics. J Food Prot 2023;86:100052. [PMID: 36916559 DOI: 10.1016/j.jfp.2023.100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023]
4
Hodges LM, Taboada EN, Koziol A, Mutschall S, Blais BW, Inglis GD, Leclair D, Carrillo CD. Systematic Evaluation of Whole-Genome Sequencing Based Prediction of Antimicrobial Resistance in Campylobacter jejuni and C. coli. Front Microbiol 2021;12:776967. [PMID: 34867917 PMCID: PMC8635091 DOI: 10.3389/fmicb.2021.776967] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022]  Open
5
Carrillo CD, Blais BW. Whole-Genome Sequence Datasets: A Powerful Resource for the Food Microbiology Laboratory Toolbox. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.754988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
6
Zhang H, Yamamoto E, Murphy J, Carrillo C, Locas A. Shiga Toxin-Producing Escherichia coli (STEC) and STEC-Associated Virulence Genes in Raw Ground Pork in Canada. J Food Prot 2021;84:1956-1964. [PMID: 34197587 DOI: 10.4315/jfp-21-147] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/01/2021] [Indexed: 11/11/2022]
7
Bogaerts B, Winand R, Van Braekel J, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Marchal K, Vanneste K. Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations. Microb Genom 2021;7:000699. [PMID: 34739368 PMCID: PMC8743554 DOI: 10.1099/mgen.0.000699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/30/2021] [Indexed: 12/29/2022]  Open
8
Zhang H, Yamamoto E, Murphy J, Carrillo C, Hardie K, Locas A. Microbiological Survey of Wheat Flour Sold at Retail in Canada, 2018 to 2019. J Food Prot 2021;84:647-654. [PMID: 33159455 DOI: 10.4315/jfp-20-297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 01/06/2023]
9
Resistance determinants and their genetic context in enterobacteria from a longitudinal study of pigs reared under various husbandry conditions. Appl Environ Microbiol 2021;87:AEM.02612-20. [PMID: 33514521 PMCID: PMC8091121 DOI: 10.1128/aem.02612-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
10
Cooper AL, Carrillo CD, DeschÊnes M, Blais BW. Genomic Markers for Quaternary Ammonium Compound Resistance as a Persistence Indicator for Listeria monocytogenes Contamination in Food Manufacturing Environments. J Food Prot 2021;84:389-398. [PMID: 33038236 DOI: 10.4315/jfp-20-328] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
11
Bacteriological analysis of wheat flour associated with an outbreak of Shiga toxin-producing Escherichia coli O121. Food Microbiol 2019;82:474-481. [DOI: 10.1016/j.fm.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/19/2019] [Accepted: 03/19/2019] [Indexed: 01/18/2023]
12
Low AJ, Koziol AG, Manninger PA, Blais B, Carrillo CD. ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data. PeerJ 2019;7:e6995. [PMID: 31183253 PMCID: PMC6546082 DOI: 10.7717/peerj.6995] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/20/2019] [Indexed: 12/16/2022]  Open
13
Blais BW, Tapp K, Dixon M, Carrillo CD. Genomically Informed Strain-Specific Recovery of Shiga Toxin-Producing Escherichia coli during Foodborne Illness Outbreak Investigations. J Food Prot 2019;82:39-44. [PMID: 30586325 DOI: 10.4315/0362-028x.jfp-18-340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
14
Kiel M, Sagory-Zalkind P, Miganeh C, Stork C, Leimbach A, Sekse C, Mellmann A, Rechenmann F, Dobrindt U. Identification of Novel Biomarkers for Priority Serotypes of Shiga Toxin-Producing Escherichia coli and the Development of Multiplex PCR for Their Detection. Front Microbiol 2018;9:1321. [PMID: 29997582 PMCID: PMC6028524 DOI: 10.3389/fmicb.2018.01321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/30/2018] [Indexed: 12/22/2022]  Open
15
Shridhar PB, Patel IR, Gangiredla J, Noll LW, Shi X, Bai J, Elkins CA, Strockbine NA, Nagaraja TG. Genetic Analysis of Virulence Potential of Escherichia coli O104 Serotypes Isolated From Cattle Feces Using Whole Genome Sequencing. Front Microbiol 2018;9:341. [PMID: 29545780 PMCID: PMC5838399 DOI: 10.3389/fmicb.2018.00341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022]  Open
16
Le KK, Whiteside MD, Hopkins JE, Gannon VPJ, Laing CR. Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018;2018:1-10. [PMID: 30212910 PMCID: PMC6146121 DOI: 10.1093/database/bay086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/23/2018] [Indexed: 01/16/2023]
17
Cardinali G, Corte L, Robert V. Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry. Curr Opin Food Sci 2017. [DOI: 10.1016/j.cofs.2017.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
18
Draft Genome Sequences of Escherichia coli O104 Strains of Bovine and Human Origin. GENOME ANNOUNCEMENTS 2017;5:5/33/e00630-17. [PMID: 28818887 PMCID: PMC5604760 DOI: 10.1128/genomea.00630-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
19
Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: The Next Culture-Independent Game Changer. Front Microbiol 2017;8:1069. [PMID: 28725217 PMCID: PMC5495826 DOI: 10.3389/fmicb.2017.01069] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/29/2017] [Indexed: 02/01/2023]  Open
20
McMahon TC, Blais BW, Wong A, Carrillo CD. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures. Front Microbiol 2017;8:332. [PMID: 28303131 PMCID: PMC5332415 DOI: 10.3389/fmicb.2017.00332] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022]  Open
21
Carrillo CD, Koziol AG, Mathews A, Goji N, Lambert D, Huszczynski G, Gauthier M, Amoako K, Blais BW. Comparative Evaluation of Genomic and Laboratory Approaches for Determination of Shiga Toxin Subtypes in Escherichia coli. J Food Prot 2016;79:2078-2085. [PMID: 28221953 DOI: 10.4315/0362-028x.jfp-16-228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
22
Knowles M, Stinson S, Lambert D, Carrillo C, Koziol A, Gauthier M, Blais B. Genomic Tools for Customized Recovery and Detection of Foodborne Shiga Toxigenic Escherichia coli. J Food Prot 2016;79:2066-2077. [PMID: 28221970 DOI: 10.4315/0362-028x.jfp-16-220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
23
Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016;29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
24
A Primer on Infectious Disease Bacterial Genomics. Clin Microbiol Rev 2016;29:881-913. [PMID: 28590251 DOI: 10.1128/cmr.00001-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
25
Rusconi B, Sanjar F, Koenig SSK, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol 2016;7:985. [PMID: 27446025 PMCID: PMC4928038 DOI: 10.3389/fmicb.2016.00985] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/08/2016] [Indexed: 01/29/2023]  Open
26
Healy MJ, Tong W, Ostroff S, Eichler HG, Patak A, Neuspiel M, Deluyker H, Slikker W. Regulatory bioinformatics for food and drug safety. Regul Toxicol Pharmacol 2016;80:342-7. [PMID: 27208439 DOI: 10.1016/j.yrtph.2016.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 10/21/2022]
27
Alic AS, Ruzafa D, Dopazo J, Blanquer I. Objective review ofde novostand-alone error correction methods for NGS data. WILEY INTERDISCIPLINARY REVIEWS: COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1239] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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