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Reply to Baba and Kanamori.

Franz E, Rotariu O, Lopes BS, Bono JL, Laing C, Gannon V, van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJC.

Clin Infect Dis. 2019 Nov 11. pii: ciz1102. doi: 10.1093/cid/ciz1102. [Epub ahead of print] No abstract available.


Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

Tyson S, Peterson CL, Olson A, Tyler S, Knox N, Griffiths E, Dooley D, Hsiao W, Cabral J, Johnson RP, Laing C, Gannon V, Lynch T, Van Domselaar G, Brinkman F, Graham M.

Microbiol Resour Announc. 2019 Oct 10;8(41). pii: e00625-19. doi: 10.1128/MRA.00625-19.


Phylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7.

Franz E, Rotariu O, Lopes BS, MacRae M, Bono JL, Laing C, Gannon V, Söderlund R, van Hoek AHAM, Friesema I, French NP, George T, Biggs PJ, Jaros P, Rivas M, Chinen I, Campos J, Jernberg C, Gobius K, Mellor GE, Chandry PS, Perez-Reche F, Forbes KJ, Strachan NJC.

Clin Infect Dis. 2019 Jul 18;69(3):428-437. doi: 10.1093/cid/ciy919.


Multi-Year Persistence of Verotoxigenic Escherichia coli (VTEC) in a Closed Canadian Beef Herd: A Cohort Study.

Wang LYR, Jokinen CC, Laing CR, Johnson RP, Ziebell K, Gannon VPJ.

Front Microbiol. 2018 Aug 31;9:2040. doi: 10.3389/fmicb.2018.02040. eCollection 2018.


Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses.

Le KK, Whiteside MD, Hopkins JE, Gannon VPJ, Laing CR.

Database (Oxford). 2018 Jan 1;2018:1-10. doi: 10.1093/database/bay086.


Phylotyper: in silico predictor of gene subtypes.

Whiteside MD, Gannon VPJ, Laing CR.

Bioinformatics. 2017 Nov 15;33(22):3638-3641. doi: 10.1093/bioinformatics/btx459.


Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar.

Laing CR, Whiteside MD, Gannon VPJ.

Front Microbiol. 2017 Jul 31;8:1345. doi: 10.3389/fmicb.2017.01345. eCollection 2017.


A Genome-Wide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains.

Buchanan CJ, Webb AL, Mutschall SK, Kruczkiewicz P, Barker DOR, Hetman BM, Gannon VPJ, Abbott DW, Thomas JE, Inglis GD, Taboada EN.

Front Microbiol. 2017 Jun 30;8:1224. doi: 10.3389/fmicb.2017.01224. eCollection 2017.


Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold, Salt, Acid, or Desiccation Stress.

Hingston P, Chen J, Dhillon BK, Laing C, Bertelli C, Gannon V, Tasara T, Allen K, Brinkman FS, Truelstrup Hansen L, Wang S.

Front Microbiol. 2017 Mar 8;8:369. doi: 10.3389/fmicb.2017.00369. eCollection 2017.


The EpiQuant Framework for Computing Epidemiological Concordance of Microbial Subtyping Data.

Hetman BM, Mutschall SK, Thomas JE, Gannon VPJ, Clark CG, Pollari F, Taboada EN.

J Clin Microbiol. 2017 May;55(5):1334-1349. doi: 10.1128/JCM.01945-16. Epub 2017 Feb 15.


Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

Nadya S, Delaquis P, Chen J, Allen K, Johnson RP, Ziebell K, Laing C, Gannon V, Bach S, Topp E.

Front Cell Infect Microbiol. 2016 Apr 5;6:36. doi: 10.3389/fcimb.2016.00036. eCollection 2016.


SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli.

Whiteside MD, Laing CR, Manji A, Kruczkiewicz P, Taboada EN, Gannon VP.

BMC Microbiol. 2016 Apr 12;16:65. doi: 10.1186/s12866-016-0680-0.


Comparative Genomic Analysis of Escherichia coli O157:H7 Isolated from Super-Shedder and Low-Shedder Cattle.

Munns KD, Zaheer R, Xu Y, Stanford K, Laing CR, Gannon VP, Selinger LB, McAllister TA.

PLoS One. 2016 Mar 28;11(3):e0151673. doi: 10.1371/journal.pone.0151673. eCollection 2016.


Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources.

Klima CL, Cook SR, Zaheer R, Laing C, Gannon VP, Xu Y, Rasmussen J, Potter A, Hendrick S, Alexander TW, McAllister TA.

PLoS One. 2016 Feb 29;11(2):e0149520. doi: 10.1371/journal.pone.0149520. eCollection 2016.


The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VP, Nash JH, Taboada EN.

PLoS One. 2016 Jan 22;11(1):e0147101. doi: 10.1371/journal.pone.0147101. eCollection 2016.


Whole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.

Strachan NJ, Rotariu O, Lopes B, MacRae M, Fairley S, Laing C, Gannon V, Allison LJ, Hanson MF, Dallman T, Ashton P, Franz E, van Hoek AH, French NP, George T, Biggs PJ, Forbes KJ.

Sci Rep. 2015 Oct 7;5:14145. doi: 10.1038/srep14145.


The distribution of Salmonella enterica serovars and subtypes in surface water from five agricultural regions across Canada.

Jokinen CC, Koot J, Cole L, Desruisseau A, Edge TA, Khan IU, Koning W, Lapen DR, Pintar KD, Reid-Smith R, Thomas JL, Topp E, Wang LY, Wilkes G, Ziebell K, van Bochove E, Gannon VP.

Water Res. 2015 Jun 1;76:120-31. doi: 10.1016/j.watres.2015.02.038. Epub 2015 Mar 3.


A new pyrosequencing assay for rapid detection and genotyping of Shiga toxin, intimin and O157-specific rfbE genes of Escherichia coli.

Goji N, Mathews A, Huszczynski G, Laing CR, Gannon VP, Graham MR, Amoako KK.

J Microbiol Methods. 2015 Feb;109:167-79. doi: 10.1016/j.mimet.2014.12.003. Epub 2014 Dec 15.


Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems.

Franz E, Delaquis P, Morabito S, Beutin L, Gobius K, Rasko DA, Bono J, French N, Osek J, Lindstedt BA, Muniesa M, Manning S, LeJeune J, Callaway T, Beatson S, Eppinger M, Dallman T, Forbes KJ, Aarts H, Pearl DL, Gannon VP, Laing CR, Strachan NJ.

Int J Food Microbiol. 2014 Sep 18;187:57-72. doi: 10.1016/j.ijfoodmicro.2014.07.002. Epub 2014 Jul 11. Review. Erratum in: Int J Food Microbiol. 2015 Jan 16;193:159.


A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada.

Khan IU, Gannon V, Jokinen CC, Kent R, Koning W, Lapen DR, Medeiros D, Miller J, Neumann NF, Phillips R, Schreier H, Topp E, van Bochove E, Wilkes G, Edge TA.

Water Res. 2014 Sep 15;61:243-52. doi: 10.1016/j.watres.2014.05.027. Epub 2014 May 28.


The gluconeogenesis pathway is involved in maintenance of enterohaemorrhagic Escherichia coli O157:H7 in bovine intestinal content.

Bertin Y, Deval C, de la Foye A, Masson L, Gannon V, Harel J, Martin C, Desvaux M, Forano E.

PLoS One. 2014 Jun 2;9(6):e98367. doi: 10.1371/journal.pone.0098367. eCollection 2014.


Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired agricultural watersheds under controlled and conventional tile drainage management.

Wilkes G, Brassard J, Edge TA, Gannon V, Gottschall N, Jokinen CC, Jones TH, Khan IU, Marti R, Sunohara MD, Topp E, Lapen DR.

Appl Environ Microbiol. 2014 Jun;80(12):3708-20. doi: 10.1128/AEM.00254-14. Epub 2014 Apr 11.


Characteristics of clinical Shiga toxin-producing Escherichia coli isolated from British Columbia.

Allen KJ, Laing CR, Cancarevic A, Zhang Y, Mesak LR, Xu H, Paccagnella A, Gannon VP, Hoang L.

Biomed Res Int. 2013;2013:878956. doi: 10.1155/2013/878956. Epub 2013 Oct 2.


Using SWAT, Bacteroidales microbial source tracking markers, and fecal indicator bacteria to predict waterborne pathogen occurrence in an agricultural watershed.

Frey SK, Topp E, Edge T, Fall C, Gannon V, Jokinen C, Marti R, Neumann N, Ruecker N, Wilkes G, Lapen DR.

Water Res. 2013 Oct 15;47(16):6326-37. doi: 10.1016/j.watres.2013.08.010. Epub 2013 Aug 19.


Bacteria, viruses, and parasites in an intermittent stream protected from and exposed to pasturing cattle: prevalence, densities, and quantitative microbial risk assessment.

Wilkes G, Brassard J, Edge TA, Gannon V, Jokinen CC, Jones TH, Neumann N, Pintar KD, Ruecker N, Schmidt PJ, Sunohara M, Topp E, Lapen DR.

Water Res. 2013 Oct 15;47(16):6244-57. doi: 10.1016/j.watres.2013.07.041. Epub 2013 Aug 6.


Coherence among different microbial source tracking markers in a small agricultural stream with or without livestock exclusion practices.

Wilkes G, Brassard J, Edge TA, Gannon V, Jokinen CC, Jones TH, Marti R, Neumann NF, Ruecker NJ, Sunohara M, Topp E, Lapen DR.

Appl Environ Microbiol. 2013 Oct;79(20):6207-19. doi: 10.1128/AEM.01626-13. Epub 2013 Aug 2.


A Canadian application of one health: integration of Salmonella data from various Canadian surveillance programs (2005-2010).

Parmley EJ, Pintar K, Majowicz S, Avery B, Cook A, Jokinen C, Gannon V, Lapen DR, Topp E, Edge TA, Gilmour M, Pollari F, Reid-Smith R, Irwin R.

Foodborne Pathog Dis. 2013 Sep;10(9):747-56. doi: 10.1089/fpd.2012.1438. Epub 2013 Jun 20. Review.


Quantitative multi-year elucidation of fecal sources of waterborne pathogen contamination in the South Nation River basin using bacteroidales microbial source tracking markers.

Marti R, Gannon VP, Jokinen C, Lanthier M, Lapen DR, Neumann NF, Ruecker NJ, Scott A, Wilkes G, Zhang Y, Topp E.

Water Res. 2013 May 1;47(7):2315-24. doi: 10.1016/j.watres.2013.02.009. Epub 2013 Feb 14.


Spatiotemporal analysis of Cryptosporidium species/genotypes and relationships with other zoonotic pathogens in surface water from mixed-use watersheds.

Wilkes G, Ruecker NJ, Neumann NF, Gannon VP, Jokinen C, Sunohara M, Topp E, Pintar KD, Edge TA, Lapen DR.

Appl Environ Microbiol. 2013 Jan;79(2):434-48. doi: 10.1128/AEM.01924-12. Epub 2012 Nov 2.


An enhanced technique combining pre-enrichment and passive filtration increases the isolation efficiency of Campylobacter jejuni and Campylobacter coli from water and animal fecal samples.

Jokinen CC, Koot JM, Carrillo CD, Gannon VP, Jardine CM, Mutschall SK, Topp E, Taboada EN.

J Microbiol Methods. 2012 Dec;91(3):506-13. doi: 10.1016/j.mimet.2012.09.005. Epub 2012 Sep 14.


A comparison of Shiga-toxin 2 bacteriophage from classical enterohemorrhagic Escherichia coli serotypes and the German E. coli O104:H4 outbreak strain.

Laing CR, Zhang Y, Gilmour MW, Allen V, Johnson R, Thomas JE, Gannon VP.

PLoS One. 2012;7(5):e37362. doi: 10.1371/journal.pone.0037362. Epub 2012 May 23.


Spatial and temporal drivers of zoonotic pathogen contamination of an agricultural watershed.

Jokinen CC, Edge TA, Koning W, Laing CR, Lapen DR, Miller J, Mutschall S, Scott A, Taboada EN, Thomas JE, Topp E, Wilkes G, Gannon VP.

J Environ Qual. 2012 Jan-Feb;41(1):242-52. doi: 10.2134/jeq2011.0203.


Investigation of an Escherichia coli environmental benchmark for waterborne pathogens in agricultural watersheds in Canada.

Edge TA, El-Shaarawi A, Gannon V, Jokinen C, Kent R, Khan IU, Koning W, Lapen D, Miller J, Neumann N, Phillips R, Robertson W, Schreier H, Scott A, Shtepani I, Topp E, Wilkes G, van Bochove E.

J Environ Qual. 2012 Jan-Feb;41(1):21-30. doi: 10.2134/jeq2010.0253.


Development and validation of a comparative genomic fingerprinting method for high-resolution genotyping of Campylobacter jejuni.

Taboada EN, Ross SL, Mutschall SK, Mackinnon JM, Roberts MJ, Buchanan CJ, Kruczkiewicz P, Jokinen CC, Thomas JE, Nash JH, Gannon VP, Marshall B, Pollari F, Clark CG.

J Clin Microbiol. 2012 Mar;50(3):788-97. doi: 10.1128/JCM.00669-11. Epub 2011 Dec 14.


Identification of a novel prophage regulator in Escherichia coli controlling the expression of type III secretion.

Flockhart AF, Tree JJ, Xu X, Karpiyevich M, McAteer SP, Rosenblum R, Shaw DJ, Low CJ, Best A, Gannon V, Laing C, Murphy KC, Leong JM, Schneiders T, La Ragione R, Gally DL.

Mol Microbiol. 2012 Jan;83(1):208-23. doi: 10.1111/j.1365-2958.2011.07927.x. Epub 2011 Dec 9.


Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0.

Laing C, Villegas A, Taboada EN, Kropinski A, Thomas JE, Gannon VP.

Infect Genet Evol. 2011 Dec;11(8):2151-61. doi: 10.1016/j.meegid.2011.09.021. Epub 2011 Oct 1.


Associations among pathogenic bacteria, parasites, and environmental and land use factors in multiple mixed-use watersheds.

Wilkes G, Edge TA, Gannon VP, Jokinen C, Lyautey E, Neumann NF, Ruecker N, Scott A, Sunohara M, Topp E, Lapen DR.

Water Res. 2011 Nov 15;45(18):5807-25. doi: 10.1016/j.watres.2011.06.021. Epub 2011 Jun 26.


Everything at once: comparative analysis of the genomes of bacterial pathogens.

Laing CR, Zhang Y, Thomas JE, Gannon VP.

Vet Microbiol. 2011 Nov 21;153(1-2):13-26. doi: 10.1016/j.vetmic.2011.06.014. Epub 2011 Jun 26.


Gene cluster conferring streptomycin, sulfonamide, and tetracycline resistance in Escherichia coli O157:H7 phage types 23, 45, and 67.

Ziebell K, Johnson RP, Kropinski AM, Reid-Smith R, Ahmed R, Gannon VP, Gilmour M, Boerlin P.

Appl Environ Microbiol. 2011 Mar;77(5):1900-3. doi: 10.1128/AEM.01934-10. Epub 2011 Jan 14.


Molecular subtypes of Campylobacter spp., Salmonella enterica, and Escherichia coli O157:H7 isolated from faecal and surface water samples in the Oldman River watershed, Alberta, Canada.

Jokinen C, Edge TA, Ho S, Koning W, Laing C, Mauro W, Medeiros D, Miller J, Robertson W, Taboada E, Thomas JE, Topp E, Ziebell K, Gannon VP.

Water Res. 2011 Jan;45(3):1247-57. doi: 10.1016/j.watres.2010.10.001.


Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.

Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP.

BMC Bioinformatics. 2010 Sep 15;11:461. doi: 10.1186/1471-2105-11-461.


The occurrence and sources of Campylobacter spp., Salmonella enterica and Escherichia coli O157:H7 in the Salmon River, British Columbia, Canada.

Jokinen CC, Schreier H, Mauro W, Taboada E, Isaac-Renton JL, Topp E, Edge T, Thomas JE, Gannon VP.

J Water Health. 2010 Jun;8(2):374-86. doi: 10.2166/wh.2009.076. Epub 2009 Nov 9.


Lineage and host source are both correlated with levels of Shiga toxin 2 production by Escherichia coli O157:H7 strains.

Zhang Y, Laing C, Zhang Z, Hallewell J, You C, Ziebell K, Johnson RP, Kropinski AM, Thomas JE, Karmali M, Gannon VP.

Appl Environ Microbiol. 2010 Jan;76(2):474-82. doi: 10.1128/AEM.01288-09. Epub 2009 Nov 30.


A methods comparison for the isolation and detection of thermophilic Campylobacter in agricultural watersheds.

Khan IU, Gannon V, Loughborough A, Jokinen C, Kent R, Koning W, Lapen DR, Medeiros D, Miller J, Neumann N, Phillips R, Robertson W, Schreier H, Topp E, van Bochove E, Edge TA.

J Microbiol Methods. 2009 Dec;79(3):307-13. doi: 10.1016/j.mimet.2009.09.024. Epub 2009 Oct 6.


Two distinct groups of porcine enteropathogenic Escherichia coli strains of serogroup O45 are revealed by comparative genomic hybridization and virulence gene microarray.

Bruant G, Zhang Y, Garneau P, Wong J, Laing C, Fairbrother JM, Gannon VP, Harel J.

BMC Genomics. 2009 Aug 26;10:402. doi: 10.1186/1471-2164-10-402.


In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

Laing CR, Buchanan C, Taboada EN, Zhang Y, Karmali MA, Thomas JE, Gannon VP.

BMC Genomics. 2009 Jun 29;10:287. doi: 10.1186/1471-2164-10-287.


Acid-stress-induced changes in enterohaemorrhagic Escherichia coli O157 : H7 virulence.

House B, Kus JV, Prayitno N, Mair R, Que L, Chingcuanco F, Gannon V, Cvitkovitch DG, Barnett Foster D.

Microbiology. 2009 Sep;155(Pt 9):2907-2918. doi: 10.1099/mic.0.025171-0. Epub 2009 Jun 4.


Verocytotoxin-producing Escherichia coli (VTEC).

Karmali MA, Gannon V, Sargeant JM.

Vet Microbiol. 2010 Jan 27;140(3-4):360-70. doi: 10.1016/j.vetmic.2009.04.011. Epub 2009 Apr 10. Review.


Escherichia coli O157:H7 lineages in healthy beef and dairy cattle and clinical human cases in Alberta, Canada.

Sharma R, Stanford K, Louie M, Munns K, John SJ, Zhang Y, Gannon V, Chui L, Read R, Topp E, McAllister T.

J Food Prot. 2009 Mar;72(3):601-7.


Seasonal relationships among indicator bacteria, pathogenic bacteria, Cryptosporidium oocysts, Giardia cysts, and hydrological indices for surface waters within an agricultural landscape.

Wilkes G, Edge T, Gannon V, Jokinen C, Lyautey E, Medeiros D, Neumann N, Ruecker N, Topp E, Lapen DR.

Water Res. 2009 May;43(8):2209-23. doi: 10.1016/j.watres.2009.01.033. Epub 2009 Feb 11.


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