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Research: Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
...K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, et al. 2001. Complete sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8: 11–22. doi:10.1093/dnares/8.1.11 ↵Hazen TH, Sahl JW, Fraser CM...
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Research: Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
- Stephen J. Salipante,
- David J. Roach,
- Jacob O. Kitzman,
- Matthew W. Snyder,
- Bethany Stackhouse,
- Susan M. Butler-Wu,
- Choli Lee,
- Brad T. Cookson,
- and Jay Shendure
Genome Res. January 2015 25: 119-128; Published in Advance November 4, 2014, doi:10.1101/gr.180190.114
...of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates. Environ Microbiol 8: 1975–1984. Falush D, Bowden R. 2006. Genome-wide association mapping in bacteria? Trends Microbiol 14: 353–355. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC...
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LETTER: Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
- Wei Zhang,
- Weihong Qi,
- Thomas J. Albert,
- Alifiya S. Motiwala,
- David Alland,
- Eija K. Hyytia-Trees,
- Efrain M. Ribot,
- Patricia I. Fields,
- Thomas S. Whittam,
- and Bala Swaminathan
Genome Res. June 2006 16: 757-767; Published in Advance April 10, 2006, doi:10.1101/gr.4759706
...Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms Single nucleotide polymorphisms in E. coli O157 Wei Zhang 1 , 5 , 1 , Weihong Qi 2 , Thomas J. Albert 3 , Alifiya S. Motiwala 4 , David...
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Methods: Whole-Genome Shotgun Optical Mapping of Rhodobacter sphaeroides strain 2.4.1 and Its Use for Whole-Genome Shotgun Sequence Assembly
- Shiguo Zhou,
- Erika Kvikstad,
- Andrew Kile,
- Jessica Severin,
- Dan Forrest,
- Rod Runnheim,
- Chris Churas,
- Jason W. Hickman,
- Chris Mackenzie,
- Madhusudan Choudhary,
- Timothy Donohue,
- Samuel Kaplan,
- and David C. Schwartz
Genome Res. September 2003 13: 2142-2151; doi:10.1101/gr.1128803
...., Anatharaman, T.S., et al. 1999 . A shotgun optical map of the entire Plasmodium falciparum . Nat. Genet. 23 : 309 –313. ↵ Lim, A., Dimalanta, E.T., Potamousis, K.D., Yen, G., Apodoca, J., Tao, C., Lin, J., Qi, R., Skiadas, J., Ramanathan, A., et al. 2001 . Shotgun optical maps of the whole Escherichia coli O...
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ARTICLE: A Complete Sequence of the T. tengcongensis Genome
- Qiyu Bao,
- Yuqing Tian,
- Wei Li,
- Zuyuan Xu,
- Zhenyu Xuan,
- Songnian Hu,
- Wei Dong,
- Jian Yang,
- Yanjiong Chen,
- Yanfen Xue,
- Yi Xu,
- Xiaoqin Lai,
- Li Huang,
- Xiuzhu Dong,
- Yanhe Ma,
- Lunjiang Ling,
- Huarong Tan,
- Runsheng Chen,
- Jian Wang,
- Jun Yu,
- and Huanming Yang
Genome Res. May 1, 2002 12: 689-700; doi:10.1101/gr.219302
...100101, China; 4Genome Center, University of Washington, Seattle, Washington 98195, USA Abstract Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we...
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Method: Factors impacting target-enriched long-read sequencing of resistomes and mobilomes
- Ilya B. Slizovskiy,
- Nathalie Bonin,
- Jonathan E. Bravo,
- Peter M. Ferm,
- Jacob Singer,
- Christina Boucher,
- and Noelle R. Noyes
Genome Res. November 2024 34: 2048-2060; Published in Advance November 5, 2024, doi:10.1101/gr.279226.124
...elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining...
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Method: Pathoscope: Species identification and strain attribution with unassembled sequencing data
- Owen E. Francis,
- Matthew Bendall,
- Solaiappan Manimaran,
- Changjin Hong,
- Nathan L. Clement,
- Eduardo Castro-Nallar,
- Quinn Snell,
- G. Bruce Schaalje,
- Mark J. Clement,
- Keith A. Crandall,
- and W. Evan Johnson
Genome Res. October 2013 23: 1721-1729; Published in Advance July 10, 2013, doi:10.1101/gr.150151.112
...al . 1724 Genome Research www..org received more reads than Escherichia, and five incorrect species received more reads than E. coli. After application of the Pathoscope reassignment, 89.5%of the reads were reassigned to the 55989 strain. The s with the next highest read proportions were the O157:H7...
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Methods: DNA Mapping Using Microfluidic Stretching and Single-Molecule Detection of Fluorescent Site-Specific Tags
- Eugene Y. Chan,
- Nuno M. Goncalves,
- Rebecca A. Haeusler,
- Amie J. Hatch,
- Jonathan W. Larson,
- Anthony M. Maletta,
- Gregory R. Yantz,
- Eugene D. Carstea,
- Martin Fuchs,
- Gordon G. Wong,
- Steven R. Gullans,
- and Rudolf Gilmanshin
Genome Res. June 2004 14: 1137-1146; doi:10.1101/gr.1635204
...sites in the extended molecules appear as visible gaps. The most striking use of this optical mapping technique was the mapping of the pathogenic Escherichia coli strain O157:H7 ( Lim et al. 2001 ), in which DNA was randomly broken into fragments between 150 and 2900 kb. To construct a map, data from...

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