Literature DB >> 23363821

Whole-genome mapping: a new paradigm in strain-typing technology.

J Michael Miller1.   

Abstract

Strain-typing technology in support of outbreak identification and resolution has evolved from phenotypic analysis, such as serology and biotypes, to much-more-robust molecular genetic approaches, such as pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Whole-genome mapping (WGM) has been recently applied to subtyping analysis, and it bridges the gap between PFGE (∼20 bands sorted by size) and whole-genome sequencing. WGM utilizes restriction site analysis but arranges 200 to 500 bands in the order they appear on the chromosome. WGM is able to quickly and cost-effectively generate high-resolution, ordered whole-genome maps of bacteria.

Mesh：

Year:  2013        PMID： 23363821      PMCID： PMC3666824          DOI： 10.1128/JCM.00093-13

Source DB:  PubMed          Journal:  J Clin Microbiol        ISSN： 0095-1137            Impact factor:   5.948


  31 in total

1.  Multi-virulence-locus sequence typing clarifies epidemiology of recent listeriosis outbreaks in the United States.

Authors:  Yi Chen; Wei Zhang; Stephen J Knabel
Journal:  J Clin Microbiol       Date:  2005-10       Impact factor: 5.948

Review 2.  Advanced sequencing technologies and their wider impact in microbiology.

Authors:  Neil Hall
Journal:  J Exp Biol       Date:  2007-05       Impact factor: 3.312

3.  Genomes for all.

Authors:  George M Church
Journal:  Sci Am       Date:  2006-01       Impact factor: 2.142

4.  Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms.

Authors:  M C Maiden; J A Bygraves; E Feil; G Morelli; J E Russell; R Urwin; Q Zhang; J Zhou; K Zurth; D A Caugant; I M Feavers; M Achtman; B G Spratt
Journal:  Proc Natl Acad Sci U S A       Date:  1998-03-17       Impact factor: 11.205

Review 5.  Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing.

Authors:  F C Tenover; R D Arbeit; R V Goering; P A Mickelsen; B E Murray; D H Persing; B Swaminathan
Journal:  J Clin Microbiol       Date:  1995-09       Impact factor: 5.948

6.  Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

Authors:  D C Schwartz; X Li; L I Hernandez; S P Ramnarain; E J Huff; Y K Wang
Journal:  Science       Date:  1993-10-01       Impact factor: 47.728

7.  Multilocus sequence typing lacks the discriminatory ability of pulsed-field gel electrophoresis for typing Salmonella enterica serovar Typhimurium.

Authors:  Mohamed K Fakhr; Lisa K Nolan; Catherine M Logue
Journal:  J Clin Microbiol       Date:  2005-05       Impact factor: 5.948

8.  A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease.

Authors:  Mark C Enright; Brian G Spratt
Journal:  Microbiology (Reading)       Date:  1998-11       Impact factor: 2.777

9.  Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12.

Authors:  Qing Chen; Stephen J Savarino; Malabi M Venkatesan
Journal:  Microbiology       Date:  2006-04       Impact factor: 2.777

10.  Optical maps distinguish individual strains of Escherichia coli O157 : H7.

Authors:  Michael L Kotewicz; Scott A Jackson; J Eugene LeClerc; Thomas A Cebula
Journal:  Microbiology (Reading)       Date:  2007-06       Impact factor: 2.777
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  11 in total

1.  A Novel Peptidomic Approach to Strain Typing of Clinical Acinetobacter baumannii Isolates Using Mass Spectrometry.

Authors:  Honghui Wang; Steven K Drake; Chen Yong; Marjan Gucek; Margaret Tropea; Avi Z Rosenberg; John P Dekker; Anthony F Suffredini
Journal:  Clin Chem       Date:  2016-04-26       Impact factor: 8.327

Review 2.  Analysis of single nucleic acid molecules in micro- and nano-fluidics.

Authors:  Sarah M Friedrich; Helena C Zec; Tza-Huei Wang
Journal:  Lab Chip       Date:  2016-03-07       Impact factor: 6.799

3.  Whole genome sequencing confirms source of pathogens associated with bacterial foodborne illness in pets fed raw pet food.

Authors:  Jennifer L Jones; Leyi Wang; Olgica Ceric; Sarah M Nemser; David S Rotstein; Dominika A Jurkovic; Yamir Rosa; Beverly Byrum; Jing Cui; Yan Zhang; Cathy A Brown; Anne L Burnum; Susan Sanchez; Renate Reimschuessel
Journal:  J Vet Diagn Invest       Date:  2019-01-19       Impact factor: 1.279

4.  Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China.

Authors:  Chao Teng; Zhengfu Zhou; István Molnár; Xinna Li; Ran Tang; Ming Chen; Lin Wang; Shiyou Su; Wei Zhang; Min Lin
Journal:  PLoS One       Date:  2015-04-01       Impact factor: 3.240

5.  OMBlast: alignment tool for optical mapping using a seed-and-extend approach.

Authors:  Alden King-Yung Leung; Tsz-Piu Kwok; Raymond Wan; Ming Xiao; Pui-Yan Kwok; Kevin Y Yip; Ting-Fung Chan
Journal:  Bioinformatics       Date:  2017-02-01       Impact factor: 6.937

6.  Insertion sequence polymorphism and genomic rearrangements uncover hidden Wolbachia diversity in Drosophila suzukii and D. subpulchrella.

Authors:  Rupinder Kaur; Stefanos Siozios; Wolfgang J Miller; Omar Rota-Stabelli
Journal:  Sci Rep       Date:  2017-11-01       Impact factor: 4.379

Review 7.  Whole-genome sequencing in bacteriology: state of the art.

Authors:  Michael J Dark
Journal:  Infect Drug Resist       Date:  2013-10-08       Impact factor: 4.003

8.  Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

Authors:  Noam Eckshtain-Levi; Dafna Shkedy; Michael Gershovits; Gustavo M Da Silva; Dafna Tamir-Ariel; Ron Walcott; Tal Pupko; Saul Burdman
Journal:  Front Microbiol       Date:  2016-04-06       Impact factor: 5.640

Review 9.  Advances in Molecular Serotyping and Subtyping of Escherichia coli.

Authors:  Pina M Fratamico; Chitrita DebRoy; Yanhong Liu; David S Needleman; Gian Marco Baranzoni; Peter Feng
Journal:  Front Microbiol       Date:  2016-05-03       Impact factor: 5.640

10.  De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Authors:  Remi-Andre Olsen; Ignas Bunikis; Ievgeniia Tiukova; Kicki Holmberg; Britta Lötstedt; Olga Vinnere Pettersson; Volkmar Passoth; Max Käller; Francesco Vezzi
Journal:  Gigascience       Date:  2015-11-26       Impact factor: 6.524
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