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For: Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jenkins C, Malorny B, Ribeiro Duarte AS, Torpdahl M, da Silva Felício MT, Guerra B, Rossi M, Herman L; EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel). Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne microorganisms. EFSA J 2019;17:e05898. [PMID: 32626197 DOI: 10.2903/j.efsa.2019.5898] [Cited by in Crossref: 19] [Cited by in F6Publishing: 21] [Article Influence: 6.3] [Reference Citation Analysis]
Number Citing Articles
1 Koutsoumanis K, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Jordan K, Sampers I, Wagner M, Da Silva Felicio MT, Georgiadis M, Messens W, Mosbach-Schulz O, Allende A; EFSA Panel on Biological Hazards (BIOHAZ). The public health risk posed by Listeria monocytogenes in frozen fruit and vegetables including herbs, blanched during processing. EFSA J 2020;18:e06092. [PMID: 32874300 DOI: 10.2903/j.efsa.2020.6092] [Cited by in Crossref: 5] [Cited by in F6Publishing: 6] [Article Influence: 2.5] [Reference Citation Analysis]
2 Donaghy JA, Danyluk MD, Ross T, Krishna B, Farber J. Big Data Impacting Dynamic Food Safety Risk Management in the Food Chain. Front Microbiol 2021;12:668196. [PMID: 34093486 DOI: 10.3389/fmicb.2021.668196] [Reference Citation Analysis]
3 Usein CR, Oprea M, Ciontea AS, Dinu S, Cristea D, Zota LC, Kotila S. A Snapshot of the Genetic Diversity of Salmonella Enteritidis Population Involved in Human Infections in Romania Taken in the European Epidemiological Context. Pathogens 2021;10:1490. [PMID: 34832645 DOI: 10.3390/pathogens10111490] [Reference Citation Analysis]
4 Njage PMK, Leekitcharoenphon P, Hansen LT, Hendriksen RS, Faes C, Aerts M, Hald T. Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of Listeria monocytogenes. Microorganisms 2020;8:E1772. [PMID: 33187247 DOI: 10.3390/microorganisms8111772] [Cited by in Crossref: 1] [Article Influence: 0.5] [Reference Citation Analysis]
5 European Food Safety Authority (EFSA). EFSA statement on the requirements for whole genome sequence analysis of microorganisms intentionally used in the food chain. EFSA J 2021;19:e06506. [PMID: 34335919 DOI: 10.2903/j.efsa.2021.6506] [Cited by in F6Publishing: 3] [Reference Citation Analysis]
6 Barretto C, Rincón C, Portmann AC, Ngom-Bru C. Whole Genome Sequencing Applied to Pathogen Source Tracking in Food Industry: Key Considerations for Robust Bioinformatics Data Analysis and Reliable Results Interpretation. Genes (Basel) 2021;12:275. [PMID: 33671973 DOI: 10.3390/genes12020275] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
7 Buytaers FE, Saltykova A, Denayer S, Verhaegen B, Vanneste K, Roosens NHC, Piérard D, Marchal K, De Keersmaecker SCJ. Towards Real-Time and Affordable Strain-Level Metagenomics-Based Foodborne Outbreak Investigations Using Oxford Nanopore Sequencing Technologies. Front Microbiol 2021;12:738284. [PMID: 34803953 DOI: 10.3389/fmicb.2021.738284] [Reference Citation Analysis]
8 Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-aktug D, Capella-gutierrez S, Carrillo C, Cestaro A, Chan K, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec J, Mather AE, Mchardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021;10:80. [DOI: 10.12688/f1000research.39214.1] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
9 Buytaers FE, Saltykova A, Denayer S, Verhaegen B, Vanneste K, Roosens NHC, Piérard D, Marchal K, De Keersmaecker SCJ. A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine. Microorganisms 2020;8:E1191. [PMID: 32764329 DOI: 10.3390/microorganisms8081191] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
10 Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing. Front Microbiol 2021;12:637771. [PMID: 33776971 DOI: 10.3389/fmicb.2021.637771] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
11 Paranthaman K, Mook P, Curtis D, Evans EW, Crawley-Boevey E, Dabke G, Carroll K, McCormick J, Dallman TJ, Crook P. Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17. Epidemiol Infect 2021;149:e164. [PMID: 34196266 DOI: 10.1017/S0950268821001400] [Reference Citation Analysis]
12 Uelze L, Becker N, Borowiak M, Busch U, Dangel A, Deneke C, Fischer J, Flieger A, Hepner S, Huber I, Methner U, Linde J, Pietsch M, Simon S, Sing A, Tausch SH, Szabo I, Malorny B. Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany. Front Microbiol 2021;12:626941. [PMID: 33643254 DOI: 10.3389/fmicb.2021.626941] [Cited by in Crossref: 2] [Cited by in F6Publishing: 2] [Article Influence: 2.0] [Reference Citation Analysis]
13 Gattuso A, Cella E, Fillo S, Ortoffi MF, Angeletti S, Ciccozzi M, De Medici D, Lista F, Fiore A. Phylogenetic and Evolutionary Genomic Analysis of Listeria monocytogenes Clinical Strains in the Framework of Foodborne Listeriosis Risk Assessment. Front Microbiol 2022;13:816880. [DOI: 10.3389/fmicb.2022.816880] [Reference Citation Analysis]
14 Bogaerts B, Nouws S, Verhaegen B, Denayer S, Van Braekel J, Winand R, Fu Q, Crombé F, Piérard D, Marchal K, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods. Microb Genom 2021;7. [PMID: 33656437 DOI: 10.1099/mgen.0.000531] [Cited by in Crossref: 3] [Cited by in F6Publishing: 4] [Article Influence: 3.0] [Reference Citation Analysis]
15 Bernaquez I, Gaudreau C, Pilon PA, Bekal S. Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks. Microb Genom 2021;7. [PMID: 34730485 DOI: 10.1099/mgen.0.000672] [Reference Citation Analysis]
16 Chiaverini A, Guidi F, Torresi M, Acciari VA, Centorotola G, Cornacchia A, Centorame P, Marfoglia C, Blasi G, Di Domenico M, Migliorati G, Roussel S, Pomilio F, Sevellec Y. Phylogenetic Analysis and Genome-Wide Association Study Applied to an Italian Listeria monocytogenes Outbreak. Front Microbiol 2021;12:750065. [PMID: 34803971 DOI: 10.3389/fmicb.2021.750065] [Reference Citation Analysis]
17 Sacher-Pirklbauer A, Klein-Jöbstl D, Sofka D, Blanc-Potard AB, Hilbert F. Phylogenetic Groups and Antimicrobial Resistance Genes in Escherichia coli from Different Meat Species. Antibiotics (Basel) 2021;10:1543. [PMID: 34943755 DOI: 10.3390/antibiotics10121543] [Reference Citation Analysis]
18 Joshi A, Bhardwaj D, Kaushik A, Juneja VK, Taneja P, Thakur S, Kumra Taneja N. Advances in multi-omics based quantitative microbial risk assessment in the dairy sector: A semi-systematic review. Food Research International 2022;156:111323. [DOI: 10.1016/j.foodres.2022.111323] [Reference Citation Analysis]
19 European Food Safety Authority, European Centre for Disease Prevention and Control. The European Union One Health 2020 Zoonoses Report. EFS2 2021;19. [DOI: 10.2903/j.efsa.2021.6971] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
20 Sala C, Mordhorst H, Grützke J, Brinkmann A, Petersen TN, Poulsen C, Cotter PD, Crispie F, Ellis RJ, Castellani G, Amid C, Hakhverdyan M, Guyader SL, Manfreda G, Mossong J, Nitsche A, Ragimbeau C, Schaeffer J, Schlundt J, Tay MYF, Aarestrup FM, Hendriksen RS, Pamp SJ, De Cesare A. Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community. Microorganisms 2020;8:E1861. [PMID: 33255715 DOI: 10.3390/microorganisms8121861] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 0.5] [Reference Citation Analysis]
21 Höper D, Grützke J, Brinkmann A, Mossong J, Matamoros S, Ellis RJ, Deneke C, Tausch SH, Cuesta I, Monzón S, Juliá M, Petersen TN, Hendriksen RS, Pamp SJ, Leijon M, Hakhverdyan M, Walsh AM, Cotter PD, Chandrasekaran L, Tay MYF, Schlundt J, Sala C, De Cesare A, Nitsche A, Beer M, Wylezich C. Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset. Front Microbiol 2020;11:575377. [PMID: 33250869 DOI: 10.3389/fmicb.2020.575377] [Cited by in Crossref: 2] [Cited by in F6Publishing: 3] [Article Influence: 1.0] [Reference Citation Analysis]
22 Zwirzitz B, Wetzels SU, Dixon ED, Fleischmann S, Selberherr E, Thalguter S, Quijada NM, Dzieciol M, Wagner M, Stessl B. Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events. Front Microbiol 2021;12:632935. [PMID: 33613505 DOI: 10.3389/fmicb.2021.632935] [Cited by in Crossref: 1] [Cited by in F6Publishing: 2] [Article Influence: 1.0] [Reference Citation Analysis]
23 Saltykova A, Buytaers FE, Denayer S, Verhaegen B, Piérard D, Roosens NHC, Marchal K, De Keersmaecker SCJ. Strain-Level Metagenomic Data Analysis of Enriched In Vitro and In Silico Spiked Food Samples: Paving the Way towards a Culture-Free Foodborne Outbreak Investigation Using STEC as a Case Study. Int J Mol Sci 2020;21:E5688. [PMID: 32784459 DOI: 10.3390/ijms21165688] [Cited by in Crossref: 4] [Cited by in F6Publishing: 5] [Article Influence: 2.0] [Reference Citation Analysis]
24 Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-aktug D, Capella-gutierrez S, Carrillo C, Cestaro A, Chan K, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec J, Mather AE, Mchardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021;10:80. [DOI: 10.12688/f1000research.39214.2] [Reference Citation Analysis]
25 Buytaers FE, Saltykova A, Mattheus W, Verhaegen B, Roosens NHC, Vanneste K, Laisnez V, Hammami N, Pochet B, Cantaert V, Marchal K, Denayer S, De Keersmaecker SCJ. Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak. Microb Genom 2021;7. [PMID: 33826490 DOI: 10.1099/mgen.0.000547] [Reference Citation Analysis]
26 Grützke J, Gwida M, Deneke C, Brendebach H, Projahn M, Schattschneider A, Hofreuter D, El-Ashker M, Malorny B, Al Dahouk S. Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen. Microb Genom 2021;7. [PMID: 33945456 DOI: 10.1099/mgen.0.000552] [Cited by in F6Publishing: 1] [Reference Citation Analysis]
27 Cheng RA, Orsi RH, Wiedmann M. Phylogeographic Clustering Suggests that Distinct Clades of Salmonella enterica Serovar Mississippi Are Endemic in Australia, the United Kingdom, and the United States. mSphere 2021;6:e0048521. [PMID: 34550008 DOI: 10.1128/mSphere.00485-21] [Reference Citation Analysis]
28 Centorotola G, Guidi F, D'Aurizio G, Salini R, Di Domenico M, Ottaviani D, Petruzzelli A, Fisichella S, Duranti A, Tonucci F, Acciari VA, Torresi M, Pomilio F, Blasi G. Intensive Environmental Surveillance Plan for Listeria monocytogenes in Food Producing Plants and Retail Stores of Central Italy: Prevalence and Genetic Diversity. Foods 2021;10:1944. [PMID: 34441721 DOI: 10.3390/foods10081944] [Reference Citation Analysis]
29 Baert L, Gimonet J, Barretto C, Fournier C, Jagadeesan B. Genetic changes are introduced by repeated exposure of Salmonella spiked in low water activity and high fat matrix to heat. Sci Rep 2021;11:8144. [PMID: 33854082 DOI: 10.1038/s41598-021-87330-8] [Reference Citation Analysis]
30 Pasquali F, Remondini D, Snary EL, Hald T, Guillier L. Editorial: Integrating Whole Genome Sequencing Into Source Attribution and Risk Assessment of Foodborne Bacterial Pathogens. Front Microbiol 2021;12:795098. [PMID: 34899675 DOI: 10.3389/fmicb.2021.795098] [Reference Citation Analysis]
31 Yamamoto T, Taylor JN, Koseki S, Koyama K. Classification of food spoilage bacterial species and their sodium chloride, sodium acetate and glycine tolerance using chemometrics analysis and Raman spectroscopy. J Microbiol Methods 2021;190:106326. [PMID: 34517040 DOI: 10.1016/j.mimet.2021.106326] [Reference Citation Analysis]
32 Russini V, Corradini C, De Marchis ML, Bogdanova T, Lovari S, De Santis P, Migliore G, Bilei S, Bossù T. Foodborne Toxigenic Agents Investigated in Central Italy: An Overview of a Three-Year Experience (2018-2020). Toxins (Basel) 2022;14:40. [PMID: 35051016 DOI: 10.3390/toxins14010040] [Reference Citation Analysis]
33 Koutsoumanis K, Allende A, Álvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Argüello H, Berendonk T, Cavaco LM, Gaze W, Schmitt H, Topp E, Guerra B, Liébana E, Stella P, Peixe L; EFSA Panel on Biological Hazards (BIOHAZ). Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain. EFSA J 2021;19:e06651. [PMID: 34178158 DOI: 10.2903/j.efsa.2021.6651] [Reference Citation Analysis]