Literature DB >> 22210216

Rapid genomic-scale analysis of Escherichia coli O104:H4 by using high-resolution alternative methods to next-generation sequencing.

Scott A Jackson1, Michael L Kotewicz, Isha R Patel, David W Lacher, Jayanthi Gangiredla, Christopher A Elkins.   

Abstract

Two technologies, involving DNA microarray and optical mapping, were used to quickly assess gene content and genomic architecture of recent emergent Escherichia coli O104:H4 and related strains. In real-time outbreak investigations, these technologies can provide congruent perspectives on strain, serotype, and pathotype relationships. Our data demonstrated clear discrimination between clinically, temporally, and geographically distinct O104:H4 isolates and rapid characterization of strain differences.

Entities:  

Mesh：

Substances：

Year:  2011        PMID： 22210216      PMCID： PMC3294476          DOI： 10.1128/AEM.07464-11

Source DB:  PubMed          Journal:  Appl Environ Microbiol        ISSN： 0099-2240            Impact factor:   4.792


  18 in total

1.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors:  B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

2.  Whole-genome shotgun optical mapping of Rhodospirillum rubrum.

Authors:  Susan Reslewic; Shiguo Zhou; Mike Place; Yaoping Zhang; Adam Briska; Steve Goldstein; Chris Churas; Rod Runnheim; Dan Forrest; Alex Lim; Alla Lapidus; Cliff S Han; Gary P Roberts; David C Schwartz
Journal:  Appl Environ Microbiol       Date:  2005-09       Impact factor: 4.792

3.  Prevalence and characterization of non-O157 shiga toxin-producing Escherichia coli isolates from commercial ground beef in the United States.

Authors:  Joseph M Bosilevac; Mohammad Koohmaraie
Journal:  Appl Environ Microbiol       Date:  2011-01-21       Impact factor: 4.792

4.  Parallel evolution of virulence in pathogenic Escherichia coli.

Authors:  S D Reid; C J Herbelin; A C Bumbaugh; R K Selander; T S Whittam
Journal:  Nature       Date:  2000-07-06       Impact factor: 49.962

5.  The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.

Authors:  David A Rasko; M J Rosovitz; Garry S A Myers; Emmanuel F Mongodin; W Florian Fricke; Pawel Gajer; Jonathan Crabtree; Mohammed Sebaihia; Nicholas R Thomson; Roy Chaudhuri; Ian R Henderson; Vanessa Sperandio; Jacques Ravel
Journal:  J Bacteriol       Date:  2008-08-01       Impact factor: 3.490

6.  Chronic diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome associated with HEp-2 adherent Escherichia coli in adults infected with human immunodeficiency virus in Bangui, Central African Republic.

Authors:  Christian Mossoro; Philippe Glaziou; Simon Yassibanda; Nguyen Thi Phuong Lan; Claudine Bekondi; Pierre Minssart; Christine Bernier; Chantal Le Bouguénec; Yves Germani
Journal:  J Clin Microbiol       Date:  2002-08       Impact factor: 5.948

7.  Identification of an aggregative adhesion fimbria (AAF) type III-encoding operon in enteroaggregative Escherichia coli as a sensitive probe for detecting the AAF-encoding operon family.

Authors:  Christine Bernier; Pierre Gounon; Chantal Le Bouguénec
Journal:  Infect Immun       Date:  2002-08       Impact factor: 3.441

8.  Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies.

Authors:  Scott A Jackson; Isha R Patel; Tammy Barnaba; Joseph E LeClerc; Thomas A Cebula
Journal:  BMC Genomics       Date:  2011-07-06       Impact factor: 3.969

9.  Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

Authors:  Alexander Mellmann; Dag Harmsen; Craig A Cummings; Emily B Zentz; Shana R Leopold; Alain Rico; Karola Prior; Rafael Szczepanowski; Yongmei Ji; Wenlan Zhang; Stephen F McLaughlin; John K Henkhaus; Benjamin Leopold; Martina Bielaszewska; Rita Prager; Pius M Brzoska; Richard L Moore; Simone Guenther; Jonathan M Rothberg; Helge Karch
Journal:  PLoS One       Date:  2011-07-20       Impact factor: 3.240

10.  Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Authors:  Marie Touchon; Claire Hoede; Olivier Tenaillon; Valérie Barbe; Simon Baeriswyl; Philippe Bidet; Edouard Bingen; Stéphane Bonacorsi; Christiane Bouchier; Odile Bouvet; Alexandra Calteau; Hélène Chiapello; Olivier Clermont; Stéphane Cruveiller; Antoine Danchin; Médéric Diard; Carole Dossat; Meriem El Karoui; Eric Frapy; Louis Garry; Jean Marc Ghigo; Anne Marie Gilles; James Johnson; Chantal Le Bouguénec; Mathilde Lescat; Sophie Mangenot; Vanessa Martinez-Jéhanne; Ivan Matic; Xavier Nassif; Sophie Oztas; Marie Agnès Petit; Christophe Pichon; Zoé Rouy; Claude Saint Ruf; Dominique Schneider; Jérôme Tourret; Benoit Vacherie; David Vallenet; Claudine Médigue; Eduardo P C Rocha; Erick Denamur
Journal:  PLoS Genet       Date:  2009-01-23       Impact factor: 5.917
View more
  10 in total

1.  Optical Whole-Genome Restriction Mapping as a Tool for Rapidly Distinguishing and Identifying Bacterial Contaminants in Clinical Samples.

Authors:  Richard R Chapleau; James C Baldwin
Journal:  J Clin Diagn Res       Date:  2015-08-01

2.  Whole genome mapping as a fast-track tool to assess genomic stability of sequenced Staphylococcus aureus strains.

Authors:  Julia S Sabirova; Basil Britto Xavier; Margareta Ieven; Herman Goossens; Surbhi Malhotra-Kumar
Journal:  BMC Res Notes       Date:  2014-10-08

3.  Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli.

Authors:  Baoguang Li; Huanli Liu; Weimin Wang
Journal:  BMC Microbiol       Date:  2017-11-09       Impact factor: 3.605

4.  Noise reduction in single time frame optical DNA maps.

Authors:  Paola C Torche; Vilhelm Müller; Fredrik Westerlund; Tobias Ambjörnsson
Journal:  PLoS One       Date:  2017-06-22       Impact factor: 3.240

5.  DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces.

Authors:  Pragathi B Shridhar; Isha R Patel; Jayanthi Gangiredla; Lance W Noll; Xiaorong Shi; Jianfa Bai; Christopher A Elkins; Nancy Strockbine; T G Nagaraja
Journal:  PLoS One       Date:  2018-04-30       Impact factor: 3.240

6.  Ultrasensitive and rapid count of Escherichia coli using magnetic nanoparticle probe under dark-field microscope.

Authors:  Haixu Xu; Fang Tang; Jianjun Dai; Chengming Wang; Xin Zhou
Journal:  BMC Microbiol       Date:  2018-09-03       Impact factor: 3.605

7.  Genomic characterization of Listeria monocytogenes strains involved in a multistate listeriosis outbreak associated with cantaloupe in US.

Authors:  Pongpan Laksanalamai; Lavin A Joseph; Benjamin J Silk; Laurel S Burall; Cheryl L Tarr; Peter Gerner-Smidt; Atin R Datta
Journal:  PLoS One       Date:  2012-07-31       Impact factor: 3.240

8.  Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.

Authors:  Fatma Onmus-Leone; Jun Hang; Robert J Clifford; Yu Yang; Matthew C Riley; Robert A Kuschner; Paige E Waterman; Emil P Lesho
Journal:  PLoS One       Date:  2013-04-17       Impact factor: 3.240

9.  Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2.

Authors:  Sanaa A Ahmed; Joy Awosika; Carson Baldwin; Kimberly A Bishop-Lilly; Biswajit Biswas; Stacey Broomall; Patrick S G Chain; Olga Chertkov; Otar Chokoshvili; Susan Coyne; Karen Davenport; J Chris Detter; William Dorman; Tracy H Erkkila; Jason P Folster; Kenneth G Frey; Matroner George; Cheryl Gleasner; Matthew Henry; Karen K Hill; Kyle Hubbard; Joseph Insalaco; Shannon Johnson; Aaron Kitzmiller; Michael Krepps; Chien-Chi Lo; Truong Luu; Lauren A McNew; Timothy Minogue; Christine A Munk; Brian Osborne; Mohit Patel; Krista G Reitenga; C Nicole Rosenzweig; April Shea; Xiaohong Shen; Nancy Strockbine; Cheryl Tarr; Hazuki Teshima; Eric van Gieson; Kathleen Verratti; Mark Wolcott; Gary Xie; Shanmuga Sozhamannan; Henry S Gibbons
Journal:  PLoS One       Date:  2012-11-01       Impact factor: 3.240

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

Authors:  Isha R Patel; Jayanthi Gangiredla; David W Lacher; Mark K Mammel; Scott A Jackson; Keith A Lampel; Christopher A Elkins
Journal:  Appl Environ Microbiol       Date:  2016-05-16       Impact factor: 4.792
  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.