Literature DB >> 22337979

Detection of a possible bioterrorism agent, Francisella sp., in a clinical specimen by use of next-generation direct DNA sequencing.

Makoto Kuroda1, Tsuyoshi Sekizuka, Fumiaki Shinya, Fumihiko Takeuchi, Takayuki Kanno, Tetsutaro Sata, Shigeyuki Asano.   

Abstract

Deep sequencing detected a potential bioterrorism agent, Francisella tularensis, in a human abscess sample (Iwaki-08) of unknown etiology. Identified single-nucleotide variations suggest that the Iwaki-08 case was associated with Francisella tularensis subsp. holarctica (biovar japonica) but not the highly virulent type A (Francisella tularensis subsp. tularensis).

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Year:  2012        PMID： 22337979      PMCID： PMC3347159          DOI： 10.1128/JCM.06715-11

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


  9 in total

1.  RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.

Authors:  A Stamatakis; T Ludwig; H Meier
Journal:  Bioinformatics       Date:  2004-12-17       Impact factor: 6.937

2.  Possession, use, and transfer of select agents and toxins. Final rule.

Authors: 
Journal:  Fed Regist       Date:  2005-03-18

3.  PathSeq: software to identify or discover microbes by deep sequencing of human tissue.

Authors:  Aleksandar D Kostic; Akinyemi I Ojesina; Chandra Sekhar Pedamallu; Joonil Jung; Roel G W Verhaak; Gad Getz; Matthew Meyerson
Journal:  Nat Biotechnol       Date:  2011-05       Impact factor: 54.908

Review 4.  Tularemia.

Authors:  Janet E Foley; Nathan C Nieto
Journal:  Vet Microbiol       Date:  2009-08-08       Impact factor: 3.293

5.  Infraspecific taxonomy of tularemia agent Francisella tularensis McCoy et Chapin.

Authors:  N G Olsufjev; I S Meshcheryakova
Journal:  J Hyg Epidemiol Microbiol Immunol       Date:  1982

6.  Phylogeography of Francisella tularensis: global expansion of a highly fit clone.

Authors:  Amy J Vogler; Dawn Birdsell; Lance B Price; Jolene R Bowers; Stephen M Beckstrom-Sternberg; Raymond K Auerbach; James S Beckstrom-Sternberg; Anders Johansson; Ashley Clare; Jordan L Buchhagen; Jeannine M Petersen; Talima Pearson; Josée Vaissaire; Michael P Dempsey; Paul Foxall; David M Engelthaler; David M Wagner; Paul Keim
Journal:  J Bacteriol       Date:  2009-02-27       Impact factor: 3.490

7.  The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue.

Authors:  Richard A Moore; René L Warren; J Douglas Freeman; Julia A Gustavsen; Caroline Chénard; Jan M Friedman; Curtis A Suttle; Yongjun Zhao; Robert A Holt
Journal:  PLoS One       Date:  2011-05-13       Impact factor: 3.240

8.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

9.  Comparative genomic characterization of Francisella tularensis strains belonging to low and high virulence subspecies.

Authors:  Mia D Champion; Qiandong Zeng; Eli B Nix; Francis E Nano; Paul Keim; Chinnappa D Kodira; Mark Borowsky; Sarah Young; Michael Koehrsen; Reinhard Engels; Matthew Pearson; Clint Howarth; Lisa Larson; Jared White; Lucia Alvarado; Mats Forsman; Scott W Bearden; Anders Sjöstedt; Richard Titball; Stephen L Michell; Bruce Birren; James Galagan
Journal:  PLoS Pathog       Date:  2009-05-29       Impact factor: 6.823
  9 in total
  13 in total

Review 1.  New Developments in Clinical Bacteriology Laboratories.

Authors:  Robin Patel
Journal:  Mayo Clin Proc       Date:  2016-08-21       Impact factor: 7.616

Review 2.  Routine use of microbial whole genome sequencing in diagnostic and public health microbiology.

Authors:  Claudio U Köser; Matthew J Ellington; Edward J P Cartwright; Stephen H Gillespie; Nicholas M Brown; Mark Farrington; Matthew T G Holden; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Sharon J Peacock
Journal:  PLoS Pathog       Date:  2012-08-02       Impact factor: 6.823

3.  Francisella tularensis subspecies holarctica, Tasmania, Australia, 2011.

Authors:  Justin Jackson; Alistair McGregor; Louise Cooley; Jimmy Ng; Mitchell Brown; Chong Wei Ong; Catharine Darcy; Vitali Sintchenko
Journal:  Emerg Infect Dis       Date:  2012-09       Impact factor: 6.883

Review 4.  PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets.

Authors:  Changjin Hong; Solaiappan Manimaran; William Evan Johnson
Journal:  Cancer Inform       Date:  2015-05-12

5.  Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+").

Authors:  Markus H Antwerpen; Karola Prior; Alexander Mellmann; Sebastian Höppner; Wolf D Splettstoesser; Dag Harmsen
Journal:  PLoS One       Date:  2015-04-09       Impact factor: 3.240

6.  MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing.

Authors:  Arun Rawat; David M Engelthaler; Elizabeth M Driebe; Paul Keim; Jeffrey T Foster
Journal:  PLoS One       Date:  2014-11-03       Impact factor: 3.240

7.  Comprehensive pathogen detection associated with four recurrent episodes of Kawasaki disease in a patient during a single year using next-generation sequencing.

Authors:  Hiromichi Hamada; Tsuyoshi Sekizuka; Kunihiro Oba; Harutaka Katano; Akiko Kinumaki; Masaru Terai; Tetsuya Mizutani; Makoto Kuroda
Journal:  JMM Case Rep       Date:  2016-02-01

8.  Current Bioinformatics resources in combating infectious diseases.

Authors:  Amr T M Saeb
Journal:  Bioinformation       Date:  2018-01-31

9.  Temporal differences of onset between primary skin lesions and regional lymph node lesions for tularemia in Japan: a clinicopathologic and immunohistochemical study of 19 skin cases and 54 lymph node cases.

Authors:  Shigeyuki Asano; Kikuo Mori; Kazuki Yamazaki; Tetsutaro Sata; Takayuki Kanno; Yuko Sato; Masaru Kojima; Hiromi Fujita; Yasushi Akaike; Haruki Wakasa
Journal:  Virchows Arch       Date:  2012-05-17       Impact factor: 4.064

10.  Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis.

Authors:  Akiko Kinumaki; Tsuyoshi Sekizuka; Hiromichi Hamada; Kengo Kato; Akifumi Yamashita; Makoto Kuroda
Journal:  Front Microbiol       Date:  2015-08-11       Impact factor: 5.640
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