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Items: 1 to 20 of 28

1.
Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds
Thorsten Bufe, André Hennig, Jochen Klumpp, Agnes Weiss, Kay Nieselt, Herbert Schmidt
BMC Microbiol. 2019; 19: 212. Published online 2019 Sep 5. doi: 10.1186/s12866-019-1578-4
PMCID:
PMC6729007
AbstractArticlePDF–1.5M
2.
Sex pilus specific bacteriophage to drive bacterial population towards antibiotic sensitivity
Joan Colom, Diego Batista, Abiyad Baig, Ying Tang, Siyang Liu, Fangzhong Yuan, Aouatif Belkhiri, Lucas Marcelino, Fernanda Barbosa, Marcela Rubio, Robert Atterbury, Angelo Berchieri, Paul Barrow
Sci Rep. 2019; 9: 12616. Published online 2019 Aug 30. doi: 10.1038/s41598-019-48483-9
PMCID:
PMC6717204
AbstractArticlePDF–1.4M
3.
Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex
Marcus M. Dillon, Shalabh Thakur, Renan N. D. Almeida, Pauline W. Wang, Bevan S. Weir, David S. Guttman
Genome Biol. 2019; 20: 3. Published online 2019 Jan 3. doi: 10.1186/s13059-018-1606-y
PMCID:
PMC6317194
AbstractArticlePDF–4.0M
4.
Escherichia coli O157:H7 transcriptome datasets for comparison of RNA-seq and microarray platforms
Ewa Grabowiecka, David Martin, Louise Crozier, Nicola Holden
Data Brief. 2019 Feb; 22: 126–131. Published online 2018 Nov 30. doi: 10.1016/j.dib.2018.11.136
PMCID:
PMC6297237
AbstractArticlePDF–406K
5.
Comparative genomics reveals differences in mobile virulence genes of Escherichia coli O103 pathotypes of bovine fecal origin
Lance W. Noll, Jay N. Worley, Xun Yang, Pragathi B. Shridhar, Justin B. Ludwig, Xiaorong Shi, Jianfa Bai, Doina Caragea, Jianghong Meng, T. G. Nagaraja
PLoS One. 2018; 13(2): e0191362. Published online 2018 Feb 1. doi: 10.1371/journal.pone.0191362
PMCID:
PMC5794082
AbstractArticlePDF–11M
6.
Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations
Eric Marinier, Rahat Zaheer, Chrystal Berry, Kelly A. Weedmark, Michael Domaratzki, Philip Mabon, Natalie C. Knox, Aleisha R. Reimer, Morag R. Graham, Linda Chui, Laura Patterson-Fortin, Jian Zhang, Franco Pagotto, Jeff Farber, Jim Mahony, Karine Seyer, Sadjia Bekal, Cécile Tremblay, Judy Isaac-Renton, Natalie Prystajecky, Jessica Chen, Peter Slade, Gary Van Domselaar
Nucleic Acids Res. 2017 Oct 13; 45(18): e159. Published online 2017 Aug 17. doi: 10.1093/nar/gkx702
PMCID:
PMC5737611
AbstractArticlePDF–1.3M
7.
Draft Genome Sequence of Enterohemorrhagic Escherichia coli O157:H7 Strain MC2 Isolated from Cattle in France
Pauline Auffret, Audrey Segura, Yolande Bertin, Christophe Klopp, Olivier Bouchez, Monique Kérourédan, Delphine Bibbal, Hubert Brugère, Evelyne Forano
Genome Announc. 2017 Oct; 5(40): e01097-17. Published online 2017 Oct 5. doi: 10.1128/genomeA.01097-17
PMCID:
PMC5629061
AbstractArticlePDF–140K
8.
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie C. Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly Weedmark, Rahat Zaheer, Lee S. Katz, Celine Nadon, Aleisha Reimer, Eduardo Taboada, Robert G. Beiko, William Hsiao, Fiona Brinkman, Morag Graham, Gary Van Domselaar
Microb Genom. 2017 Jun 30; 3(6): e000116. Published online 2017 Jun 8. doi: 10.1099/mgen.0.000116
PMCID:
PMC5628696
AbstractArticlePDF–240K
9.
Prevalence and Genomic Characterization of Escherichia coli O157:H7 in Cow-Calf Herds throughout California
Jay N. Worley, Kristopher A. Flores, Xun Yang, Jennifer A. Chase, Guojie Cao, Shuai Tang, Jianghong Meng, Edward R. Atwill
Appl Environ Microbiol. 2017 Aug 15; 83(16): e00734-17. Prepublished online 2017 May 26. Published online 2017 Aug 1. doi: 10.1128/AEM.00734-17
PMCID:
PMC5541215
AbstractArticlePDF–1.3M
10.
Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
Thea King, Chawalit Kocharunchitt, Kari Gobius, John P. Bowman, Tom Ross
Mol Cell Proteomics. 2016 Nov; 15(11): 3331–3347. Published online 2016 Sep 11. doi: 10.1074/mcp.M116.063065
PMCID:
PMC5098033
AbstractArticlePDF–1.2M
11.
First step in using molecular data for microbial food safety risk assessment; hazard identification of Escherichia coli O157:H7 by coupling genomic data with in vitro adherence to human epithelial cells
Annemarie Pielaat, Martin P. Boer, Lucas M. Wijnands, Angela H.A.M. van Hoek, El Bouw, Gary C. Barker, Peter F.M. Teunis, Henk J.M. Aarts, Eelco Franz
Int J Food Microbiol. 2015 Nov 20; 213: 130–138. doi: 10.1016/j.ijfoodmicro.2015.04.009
PMCID:
PMC4613885
AbstractArticle
12.
Is Shiga Toxin-Negative Escherichia coli O157:H7 Enteropathogenic or Enterohemorrhagic Escherichia coli? Comprehensive Molecular Analysis Using Whole-Genome Sequencing
Mithila Ferdous, Kai Zhou, Alexander Mellmann, Stefano Morabito, Peter D. Croughs, Richard F. de Boer, Anna M. D. Kooistra-Smid, John W. A. Rossen, Alexander W. Friedrich
J Clin Microbiol. 2015 Nov; 53(11): 3530–3538. Prepublished online 2015 Aug 26. Published online 2015 Oct 16. doi: 10.1128/JCM.01899-15
PMCID:
PMC4609726
AbstractArticlePDF–2.8M
13.
Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-serotypes of Shiga toxin-producing Escherichia coli O104
Xianghe Yan, Pina M Fratamico, James L Bono, Gian Marco Baranzoni, Chin-Yi Chen
BMC Microbiol. 2015; 15: 83. Published online 2015 Apr 3. doi: 10.1186/s12866-015-0413-9
PMCID:
PMC4393859
AbstractArticlePDF–2.2M
14.
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers
Sebastian Jünemann, Karola Prior, Andreas Albersmeier, Stefan Albaum, Jörn Kalinowski, Alexander Goesmann, Jens Stoye, Dag Harmsen
PLoS One. 2014; 9(9): e107014. Published online 2014 Sep 8. doi: 10.1371/journal.pone.0107014
Correction in:
PLoS One. 2015; 10(3): e0118741.
Correction in:
PLoS One. 2024; 19(2): e0299269.
PMCID:
PMC4157817
AbstractArticlePDF–469K
15.
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
Marten Boetzer, Walter Pirovano
BMC Bioinformatics. 2014; 15: 211. Published online 2014 Jun 20. doi: 10.1186/1471-2105-15-211
PMCID:
PMC4076250
AbstractArticlePDF–400K
16.
Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Temperature Downshift
Thea King, Chawalit Kocharunchitt, Kari Gobius, John P. Bowman, Tom Ross
PLoS One. 2014; 9(6): e99627. Published online 2014 Jun 13. doi: 10.1371/journal.pone.0099627
PMCID:
PMC4057180
AbstractArticlePDF–859K
17.
Reducing assembly complexity of microbial genomes with single-molecule sequencing
Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono, Dayna M Harhay, Scott D Mcvey, Diana Radune, Nicholas H Bergman, Adam M Phillippy
Genome Biol. 2013; 14(9): R101. Published online 2013 Sep 13. doi: 10.1186/gb-2013-14-9-r101
PMCID:
PMC4053942
AbstractArticlePDF–1.2M
18.
Global Genome Response of Escherichia coli O157∶H7 Sakai during Dynamic Changes in Growth Kinetics Induced by an Abrupt Downshift in Water Activity
Chawalit Kocharunchitt, Thea King, Kari Gobius, John P. Bowman, Tom Ross
PLoS One. 2014; 9(3): e90422. Published online 2014 Mar 3. doi: 10.1371/journal.pone.0090422
PMCID:
PMC3940904
AbstractArticlePDF–1.0M
19.
Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7
Kerry K Cooper, Robert E Mandrell, Jacqueline W Louie, Jonas Korlach, Tyson A Clark, Craig T Parker, Steven Huynh, Patrick S Chain, Sanaa Ahmed, Michelle Qiu Carter
BMC Genomics. 2014; 15: 17. Published online 2014 Jan 10. doi: 10.1186/1471-2164-15-17
PMCID:
PMC3893438
AbstractArticlePDF–2.4M
20.
Complete DNA Sequence Analysis of Enterohemorrhagic Escherichia coli Plasmid pO157_2 in β-Glucuronidase-Positive E. coli O157:H7 Reveals a Novel Evolutionary Path
L. V. Rump, J. Meng, E. A. Strain, G. Cao, M. W. Allard, N. Gonzalez-Escalona
J Bacteriol. 2012 Jul; 194(13): 3457–3463. doi: 10.1128/JB.00197-12
PMCID:
PMC3434749
AbstractArticlePDF–1.4M

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