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Validation of Whole-Genome Sequencing for Identification and Characterization of Shiga Toxin-Producing Escherichia coli To Produce Standardized Data To Enable Data Sharing.

Holmes A, Dallman TJ, Shabaan S, Hanson M, Allison L.

J Clin Microbiol. 2018 Feb 22;56(3). pii: e01388-17. doi: 10.1128/JCM.01388-17. Print 2018 Mar.


Shiga Toxin-Producing Escherichia coli O157 Shedding Dynamics in an Australian Beef Herd.

Ahlstrom C, Muellner P, Lammers G, Jones M, Octavia S, Lan R, Heller J.

Front Vet Sci. 2017 Nov 27;4:200. doi: 10.3389/fvets.2017.00200. eCollection 2017.


Variations of Escherichia coli O157:H7 Survival in Purple Soils.

Zhang T, Hu S, Yang W.

Int J Environ Res Public Health. 2017 Oct 18;14(10). pii: E1246. doi: 10.3390/ijerph14101246.


The Mobilome; A Major Contributor to Escherichia coli stx2-Positive O26:H11 Strains Intra-Serotype Diversity.

Delannoy S, Mariani-Kurkdjian P, Webb HE, Bonacorsi S, Fach P.

Front Microbiol. 2017 Sep 6;8:1625. doi: 10.3389/fmicb.2017.01625. eCollection 2017.


Comparative genomics of two super-shedder isolates of Escherichia coli O157:H7.

Katani R, Cote R, Kudva IT, DebRoy C, Arthur TM, Kapur V.

PLoS One. 2017 Aug 10;12(8):e0182940. doi: 10.1371/journal.pone.0182940. eCollection 2017.


Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California.

Worley JN, Flores KA, Yang X, Chase JA, Cao G, Tang S, Meng J, Atwill ER.

Appl Environ Microbiol. 2017 Aug 1;83(16). pii: e00734-17. doi: 10.1128/AEM.00734-17. Print 2017 Aug 15.


Computational Analysis of Host-Pathogen Protein Interactions between Humans and Different Strains of Enterohemorrhagic Escherichia coli.

Bose T, Venkatesh KV, Mande SS.

Front Cell Infect Microbiol. 2017 Apr 19;7:128. doi: 10.3389/fcimb.2017.00128. eCollection 2017.


Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.

Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ, McAteer SP, Day M, Perry NT, Bono JL, Jenkins C, Gally DL.

Microb Genom. 2016 Sep 8;2(9):e000084. doi: 10.1099/mgen.0.000084. eCollection 2016 Sep.


NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats.

Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD, Aziz M, Driebe EM, Drees KP, Hicks ND, Williamson CHD, Hepp CM, Smith DE, Roe C, Engelthaler DM, Wagner DM, Keim P.

Microb Genom. 2016 Aug 25;2(8):e000074. doi: 10.1099/mgen.0.000074. eCollection 2016 Aug.


Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing.

Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, Gally DL.

Microb Genom. 2016 Dec 12;2(12):e000096. doi: 10.1099/mgen.0.000096. eCollection 2016 Dec.


Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK.

Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, Allison L, Hanson M, Holmes A, Gunn GJ, Chase-Topping ME, Woolhouse ME, Grant KA, Gally DL, Wain J, Jenkins C.

Microb Genom. 2015 Sep 14;1(3):e000029. doi: 10.1099/mgen.0.000029. eCollection 2015 Sep.


Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates.

Lupolova N, Dallman TJ, Matthews L, Bono JL, Gally DL.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11312-11317. Epub 2016 Sep 19.


Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions.

Koonin EV.

F1000Res. 2016 Jul 25;5. pii: F1000 Faculty Rev-1805. doi: 10.12688/f1000research.8737.1. eCollection 2016. Review.


Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

Rusconi B, Sanjar F, Koenig SS, Mammel MK, Tarr PI, Eppinger M.

Front Microbiol. 2016 Jun 30;7:985. doi: 10.3389/fmicb.2016.00985. eCollection 2016.


Whole Genome DNA Sequence Analysis of Salmonella subspecies enterica serotype Tennessee obtained from related peanut butter foodborne outbreaks.

Wilson MR, Brown E, Keys C, Strain E, Luo Y, Muruvanda T, Grim C, Jean-Gilles Beaubrun J, Jarvis K, Ewing L, Gopinath G, Hanes D, Allard MW, Musser S.

PLoS One. 2016 Jun 3;11(6):e0146929. doi: 10.1371/journal.pone.0146929. eCollection 2016.


Advances in Molecular Serotyping and Subtyping of Escherichia coli.

Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P.

Front Microbiol. 2016 May 3;7:644. doi: 10.3389/fmicb.2016.00644. eCollection 2016. Review.


FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.

Patel IR, Gangiredla J, Lacher DW, Mammel MK, Jackson SA, Lampel KA, Elkins CA.

Appl Environ Microbiol. 2016 May 16;82(11):3384-94. doi: 10.1128/AEM.04077-15. Print 2016 Jun 1.


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.


The Shiga toxin 2 production level in enterohemorrhagic Escherichia coli O157:H7 is correlated with the subtypes of toxin-encoding phage.

Ogura Y, Mondal SI, Islam MR, Mako T, Arisawa K, Katsura K, Ooka T, Gotoh Y, Murase K, Ohnishi M, Hayashi T.

Sci Rep. 2015 Nov 16;5:16663. doi: 10.1038/srep16663.


Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages.

Yin S, Rusconi B, Sanjar F, Goswami K, Xiaoli L, Eppinger M, Dudley EG.

BMC Genomics. 2015 Sep 29;16:733. doi: 10.1186/s12864-015-1934-1.

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