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Changes Detected in the Genome Sequences of Escherichia coli, Listeria monocytogenes, Vibrio parahaemolyticus, and Salmonella enterica After Serial Subculturing.

Petronella N, Kundra P, Auclair O, Hebert K, Rao M, Kingsley K, De Bruyne K, Banerjee S, Pagotto F, Gill A, Tamber S, Ronholm J.

Can J Microbiol. 2019 Jul 29. doi: 10.1139/cjm-2019-0235. [Epub ahead of print]


Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.

Reimer A, Weedmark K, Petkau A, Peterson CL, Walker M, Knox N, Kent H, Mabon P, Berry C, Tyler S, Tschetter L, Jerome M, Allen V, Hoang L, Bekal S, Clark C, Nadon C, Van Domselaar G, Pagotto F, Graham M, Farber J, Gilmour M.

Microb Genom. 2019 Jan;5(1). doi: 10.1099/mgen.0.000237. Epub 2019 Jan 16.


Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

Marinier E, Zaheer R, Berry C, Weedmark KA, Domaratzki M, Mabon P, Knox NC, Reimer AR, Graham MR, Chui L, Patterson-Fortin L, Zhang J, Pagotto F, Farber J, Mahony J, Seyer K, Bekal S, Tremblay C, Isaac-Renton J, Prystajecky N, Chen J, Slade P, Van Domselaar G.

Nucleic Acids Res. 2017 Oct 13;45(18):e159. doi: 10.1093/nar/gkx702.


Tracking sources of Clostridium botulinum type E contamination in seal meat.

Leclair D, Farber JM, Pagotto F, Suppa S, Doidge B, Austin JW.

Int J Circumpolar Health. 2017;76(1):1380994. doi: 10.1080/22423982.2017.1380994.


Metagenomics: The Next Culture-Independent Game Changer.

Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A.

Front Microbiol. 2017 Jul 4;8:1069. doi: 10.3389/fmicb.2017.01069. eCollection 2017. Review.


Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology.

Tall BD, Gangiredla J, Grim CJ, Patel IR, Jackson SA, Mammel MK, Kothary MH, Sathyamoorthy V, Carter L, Fanning S, Iversen C, Pagotto F, Stephan R, Lehner A, Farber J, Yan QQ, Gopinath GR.

Microarrays (Basel). 2017 Mar 4;6(1). pii: E6. doi: 10.3390/microarrays6010006. Review.


Expression of Surface Protein LapB by a Wide Spectrum of Listeria monocytogenes Serotypes as Demonstrated with Anti-LapB Monoclonal Antibodies.

Boivin T, Elmgren C, Brooks BW, Huang H, Pagotto F, Lin M.

Appl Environ Microbiol. 2016 Oct 27;82(22):6768-6778. Print 2016 Nov 15.


Genome Sequence of the Listeria monocytogenes Food Isolate HPB913, Collected in Canada in 1993.

Pightling AW, Rand H, Strain E, Pagotto F.

Genome Announc. 2016 Sep 15;4(5). pii: e00911-16. doi: 10.1128/genomeA.00911-16.


Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing.

Ronholm J, Nasheri N, Petronella N, Pagotto F.

Clin Microbiol Rev. 2016 Oct;29(4):837-57. doi: 10.1128/CMR.00056-16. Review.


Genome Sequence of Listeria monocytogenes Strain HPB2088 (Serotype 1/2a), an Environmental Isolate Collected in Canada in 1994.

Pightling AW, Rand H, Strain E, Pagotto F.

Genome Announc. 2016 Aug 4;4(4). pii: e00760-16. doi: 10.1128/genomeA.00760-16.


Identification of Surface Protein Biomarkers of Listeria monocytogenes via Bioinformatics and Antibody-Based Protein Detection Tools.

Zhang CX, Brooks BW, Huang H, Pagotto F, Lin M.

Appl Environ Microbiol. 2016 Aug 15;82(17):5465-76. doi: 10.1128/AEM.00774-16. Print 2016 Sep 1.


Multi-Province Listeriosis Outbreak Linked to Contaminated Deli Meat Consumed Primarily in Institutional Settings, Canada, 2008.

Currie A, Farber JM, Nadon C, Sharma D, Whitfield Y, Gaulin C, Galanis E, Bekal S, Flint J, Tschetter L, Pagotto F, Lee B, Jamieson F, Badiani T, MacDonald D, Ellis A, May-Hadford J, McCormick R, Savelli C, Middleton D, Allen V, Tremblay FW, MacDougall L, Hoang L, Shyng S, Everett D, Chui L, Louie M, Bangura H, Levett PN, Wilkinson K, Wylie J, Reid J, Major B, Engel D, Douey D, Huszczynski G, Di Lecci J, Strazds J, Rousseau J, Ma K, Isaac L, Sierpinska U.

Foodborne Pathog Dis. 2015 Aug;12(8):645-52. doi: 10.1089/fpd.2015.1939. Epub 2015 Jun 3.


Genome Sequence of Listeria monocytogenes Strain HPB5415, Collected during a 2008 Listeriosis Outbreak in Canada.

Pightling AW, Pagotto F.

Genome Announc. 2015 Jun 11;3(3). pii: e00637-15. doi: 10.1128/genomeA.00637-15.


A proposed harmonized LPS molecular-subtyping scheme for Cronobacter species.

Yan Q, Jarvis KG, Chase HR, Hébert K, Trach LH, Lee C, Sadowski J, Lee B, Hwang S, Sathyamoorthy V, Mullane N, Pava-Ripoll M, Iversen C, Pagotto F, Fanning S, Tall BD.

Food Microbiol. 2015 Sep;50:38-43. doi: 10.1016/ Epub 2015 Mar 17.


Fatal false-negative transfusion infection involving a buffy coat platelet pool contaminated with biofilm-positive Staphylococcus epidermidis: a case report.

Kou Y, Pagotto F, Hannach B, Ramirez-Arcos S.

Transfusion. 2015 Oct;55(10):2384-9. doi: 10.1111/trf.13154. Epub 2015 May 18.


Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

Tall BD, Gangiredla J, Gopinath GR, Yan Q, Chase HR, Lee B, Hwang S, Trach L, Park E, Yoo Y, Chung T, Jackson SA, Patel IR, Sathyamoorthy V, Pava-Ripoll M, Kotewicz ML, Carter L, Iversen C, Pagotto F, Stephan R, Lehner A, Fanning S, Grim CJ.

Front Pediatr. 2015 Apr 30;3:36. doi: 10.3389/fped.2015.00036. eCollection 2015.


Cheese-related listeriosis outbreak, Portugal, March 2009 to February 2012.

Magalhaes R, Almeida G, Ferreira V, Santos I, Silva J, Mendes MM, Pita J, Mariano G, Mancio I, Sousa MM, Farber J, Pagotto F, Teixeira P.

Euro Surveill. 2015 Apr 30;20(17). pii: 21104.


Draft Genome Sequences of Two Clostridium botulinum Group II (Nonproteolytic) Type B Strains (DB-2 and KAPB-3).

Petronella N, Kenwell R, Pagotto F, Pightling AW.

Genome Announc. 2014 Nov 6;2(6). pii: e01111-14. doi: 10.1128/genomeA.01111-14.


Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.

Pightling AW, Petronella N, Pagotto F.

PLoS One. 2014 Aug 21;9(8):e104579. doi: 10.1371/journal.pone.0104579. eCollection 2014.


Draft Genome Sequence of Cronobacter sakazakii Clonal Complex 45 Strain HPB5174, Isolated from a Powdered Infant Formula Facility in Ireland.

Pightling AW, Pagotto F.

Genome Announc. 2014 Aug 7;2(4). pii: e00778-14. doi: 10.1128/genomeA.00778-14.


Proteomic identification of Listeria monocytogenes surface-associated proteins.

Zhang CX, Creskey MC, Cyr TD, Brooks B, Huang H, Pagotto F, Lin M.

Proteomics. 2013 Oct;13(20):3040-5. doi: 10.1002/pmic.201200449.


Subtyping of a large collection of historical Listeria monocytogenes strains from Ontario, Canada, by an improved multilocus variable-number tandem-repeat analysis (MLVA).

Saleh-Lakha S, Allen VG, Li J, Pagotto F, Odumeru J, Taboada E, Lombos M, Tabing KC, Blais B, Ogunremi D, Downing G, Lee S, Gao A, Nadon C, Chen S.

Appl Environ Microbiol. 2013 Oct;79(20):6472-80. doi: 10.1128/AEM.00759-13. Epub 2013 Aug 16.


Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation.

Grim CJ, Kotewicz ML, Power KA, Gopinath G, Franco AA, Jarvis KG, Yan QQ, Jackson SA, Sathyamoorthy V, Hu L, Pagotto F, Iversen C, Lehner A, Stephan R, Fanning S, Tall BD.

BMC Genomics. 2013 May 31;14:366. doi: 10.1186/1471-2164-14-366.


International Life Science Institute North America Cronobacter (Formerly Enterobacter sakazakii) isolate set.

Ivy RA, Farber JM, Pagotto F, Wiedmann M.

J Food Prot. 2013 Jan;76(1):40-51. doi: 10.4315/0362-028X.JFP-11-546.


Distribution of Clostridium botulinum type E strains in Nunavik, Northern Quebec, Canada.

Leclair D, Farber JM, Doidge B, Blanchfield B, Suppa S, Pagotto F, Austin JW.

Appl Environ Microbiol. 2013 Jan;79(2):646-54. doi: 10.1128/AEM.05999-11. Epub 2012 Nov 16.


Thermal tolerance and survival of Cronobacter sakazakii in powdered infant formula supplemented with vanillin, ethyl vanillin, and vanillic acid.

Yemiş GP, Pagotto F, Bach S, Delaquis P.

J Food Sci. 2012 Sep;77(9):M523-7. doi: 10.1111/j.1750-3841.2012.02834.x. Epub 2012 Aug 17.


Development and validation of a PulseNet standardized protocol for subtyping isolates of Cronobacter species.

Brengi SP, O'Brien SB, Pichel M, Iversen C, Arduino M, Binsztein N, Jensen B, Pagotto F, Ribot EM, Stephan R, Cernela N, Cooper K, Fanning S.

Foodborne Pathog Dis. 2012 Sep;9(9):861-7. doi: 10.1089/fpd.2012.1161. Epub 2012 Aug 14.


Structure of the O-antigen polysaccharide present in the lipopolysaccharide of Cronobacter dublinensis (subspecies lactaridi or lausannensis) HPB 3169.

MacLean LL, Vinogradov E, Pagotto F, Perry MB.

Can J Microbiol. 2012 Apr;58(4):540-6. doi: 10.1139/w2012-022. Epub 2012 Apr 2.


Sequence typing confirms that a predominant Listeria monocytogenes clone caused human listeriosis cases and outbreaks in Canada from 1988 to 2010.

Knabel SJ, Reimer A, Verghese B, Lok M, Ziegler J, Farber J, Pagotto F, Graham M, Nadon CA; Canadian Public Health Laboratory Network (CPHLN), Gilmour MW.

J Clin Microbiol. 2012 May;50(5):1748-51. doi: 10.1128/JCM.06185-11. Epub 2012 Feb 15.


Effect of vanillin, ethyl vanillin, and vanillic acid on the growth and heat resistance of Cronobacter species.

Yemiş GP, Pagotto F, Bach S, Delaquis P.

J Food Prot. 2011 Dec;74(12):2062-9. doi: 10.4315/0362-028X.JFP-11-230.


Development and validation of a microarray for the confirmation and typing of norovirus RT-PCR products.

Mattison K, Corneau N, Berg I, Bosch A, Duizer E, Gutiérrez-Aguirre I, L'homme Y, Lucero Y, Luo Z, Martyres A, Myrmel M, O'Ryan M, Pagotto F, Sano D, Svraka S, Urzua U, Bidawid S.

J Virol Methods. 2011 May;173(2):233-50. doi: 10.1016/j.jviromet.2011.02.011. Epub 2011 Feb 21.


The structure of the O-antigen of Cronobacter sakazakii HPB 2855 isolate involved in a neonatal infection.

Maclean LL, Vinogradov E, Pagotto F, Farber JM, Perry MB.

Carbohydr Res. 2010 Sep 3;345(13):1932-7. doi: 10.1016/j.carres.2010.06.020. Epub 2010 Jul 6.


Genotypic and phenotypic characterisation of a collection of Cronobacter (Enterobacter sakazakii) isolates.

Miled-Bennour R, Ells TC, Pagotto FJ, Farber JM, Kérouanton A, Meheut T, Colin P, Joosten H, Leclercq A, Besse NG.

Int J Food Microbiol. 2010 Apr 30;139(1-2):116-25. doi: 10.1016/j.ijfoodmicro.2010.01.045. Epub 2010 Feb 10.


Characterization of the O-antigen in the lipopolysaccharide of Cronobacter (Enterobacter) malonaticus 3267.

MacLean LL, Vinogradov E, Pagotto F, Farber JM, Perry MB.

Biochem Cell Biol. 2009 Dec;87(6):927-32. doi: 10.1139/O09-059.


Surveillance for Listeria monocytogenes and listeriosis, 1995-2004.

Clark CG, Farber J, Pagotto F, Ciampa N, Doré K, Nadon C, Bernard K, Ng LK; CPHLN.

Epidemiol Infect. 2010 Apr;138(4):559-72. doi: 10.1017/S0950268809990914. Epub 2009 Oct 12.


Cronobacter spp. (Enterobacter sakazakii): advice, policy and research in Canada.

Pagotto FJ, Farber JM.

Int J Food Microbiol. 2009 Dec 31;136(2):238-45. doi: 10.1016/j.ijfoodmicro.2009.05.010. Epub 2009 May 15. Review.


The feline calicivirus as a sample process control for the detection of food and waterborne RNA viruses.

Mattison K, Brassard J, Gagné MJ, Ward P, Houde A, Lessard L, Simard C, Shukla A, Pagotto F, Jones TH, Trottier YL.

Int J Food Microbiol. 2009 Jun 1;132(1):73-7. doi: 10.1016/j.ijfoodmicro.2009.04.002. Epub 2009 Apr 9.


Structure of the antigenic repeating pentasaccharide unit of the LPS O-polysaccharide of Cronobacter sakazakii implicated in the Tennessee outbreak.

MacLean LL, Pagotto F, Farber JM, Perry MB.

Biochem Cell Biol. 2009 Apr;87(2):459-65. doi: 10.1139/O09-004.


Listeria monocytogenes in two different poultry facilities: Manual and automatic evisceration.

Chiarini E, Tyler K, Farber JM, Pagotto F, Destro MT.

Poult Sci. 2009 Apr;88(4):791-7. doi: 10.3382/ps.2008-00396.


The structure of the O-antigen in the endotoxin of the emerging food pathogen Cronobacter (Enterobacter) muytjensii strain 3270.

MacLean LL, Pagotto F, Farber JM, Perry MB.

Carbohydr Res. 2009 Mar 31;344(5):667-71. doi: 10.1016/j.carres.2009.01.020. Epub 2009 Jan 23.


Enterobacter sakazakii in dried infant formulas and milk kitchens of maternity wards in São Paulo, Brazil.

Palcich G, Gillio Cde M, Aragon-Alegro LC, Pagotto FJ, Farber JM, Landgraf M, Destro MT.

J Food Prot. 2009 Jan;72(1):37-42. Erratum in: J Food Prot. 2009 May;72(5):926.


Development of unique bacterial strains for use as positive controls in the food microbiology testing laboratory.

Blais BW, Martinez-Perez A, Gauthier M, Allain R, Pagotto F, Tyler K.

J Food Prot. 2008 Nov;71(11):2301-6.


Development of a DNA microarray for the simultaneous detection and genotyping of noroviruses.

Pagotto F, Corneau N, Mattison K, Bidawid S.

J Food Prot. 2008 Jul;71(7):1434-41.


Assessment of biofilm-forming ability of coagulase-negative staphylococci isolated from contaminated platelet preparations in Canada.

Greco C, Mastronardi C, Pagotto F, Mack D, Ramirez-Arcos S.

Transfusion. 2008 May;48(5):969-77. doi: 10.1111/j.1537-2995.2007.01631.x. Epub 2008 Mar 12.


Growth and survival of Enterobacter sakazakii in human breast milk with and without fortifiers as compared to powdered infant formula.

Lenati RF, O'Connor DL, Hébert KC, Farber JM, Pagotto FJ.

Int J Food Microbiol. 2008 Feb 29;122(1-2):171-9. doi: 10.1016/j.ijfoodmicro.2007.11.084. Epub 2007 Dec 14.


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