Literature DB >> 20573863

Evaluation of the integrated database network system (IDNS) SmartGene software for analysis of 16S rRNA gene sequences for identification of Nocardia species.

Patricia S Conville1, Patrick R Murray, Adrian M Zelazny.   

Abstract

16S rRNA gene sequences of 102 Nocardia isolates were analyzed using the Integrated Database Network System (IDNS) SmartGene centroid database. A total of 76% of the isolates were correctly identified. Discordant identifications were due to inadequate centroid length (3 species), inaccurate or insufficient entries in the public databases (5 species), and heterogeneous sequences among members of a species (1 species).

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Year:  2010        PMID： 20573863      PMCID： PMC2916559          DOI： 10.1128/JCM.00681-10

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


  10 in total

1.  Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species.

Authors:  C Y Turenne; L Tschetter; J Wolfe; A Kabani
Journal:  J Clin Microbiol       Date:  2001-10       Impact factor: 5.948

2.  Recognition of a Nocardia transvalensis complex by resistance to aminoglycosides, including amikacin, and PCR-restriction fragment length polymorphism analysis.

Authors:  R W Wilson; V A Steingrube; B A Brown; Z Blacklock; K C Jost; A McNabb; W D Colby; J R Biehle; J L Gibson; R J Wallace
Journal:  J Clin Microbiol       Date:  1997-09       Impact factor: 5.948

3.  Analysis of secA1 gene sequences for identification of Nocardia species.

Authors:  Patricia S Conville; Adrian M Zelazny; Frank G Witebsky
Journal:  J Clin Microbiol       Date:  2006-08       Impact factor: 5.948

4.  Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory.

Authors:  Keith E Simmon; Ann C Croft; Cathy A Petti
Journal:  J Clin Microbiol       Date:  2006-10-18       Impact factor: 5.948

5.  Identification of nocardia species by restriction endonuclease analysis of an amplified portion of the 16S rRNA gene.

Authors:  P S Conville; S H Fischer; C P Cartwright; F G Witebsky
Journal:  J Clin Microbiol       Date:  2000-01       Impact factor: 5.948

6.  Nocardia kruczakiae sp. nov., a pathogen in immunocompromised patients and a member of the "N. nova complex".

Authors:  Patricia S Conville; June M Brown; Arnold G Steigerwalt; Judy W Lee; Victoria L Anderson; Joel T Fishbain; Steven M Holland; Frank G Witebsky
Journal:  J Clin Microbiol       Date:  2004-11       Impact factor: 5.948

7.  Cefotaxime-resistant Nocardia asteroides strains are isolates of the controversial species Nocardia farcinica.

Authors:  R J Wallace; M Tsukamura; B A Brown; J Brown; V A Steingrube; Y S Zhang; D R Nash
Journal:  J Clin Microbiol       Date:  1990-12       Impact factor: 5.948

8.  Evaluation of partial 16S ribosomal DNA sequencing for identification of nocardia species by using the MicroSeq 500 system with an expanded database.

Authors:  Joann L Cloud; Patricia S Conville; Ann Croft; Dag Harmsen; Frank G Witebsky; Karen C Carroll
Journal:  J Clin Microbiol       Date:  2004-02       Impact factor: 5.948

9.  Sequence-based identification of aerobic actinomycetes.

Authors:  Jean Baldus Patel; Richard J Wallace; Barbara A Brown-Elliott; Tony Taylor; Carol Imperatrice; Deborah G B Leonard; Rebecca W Wilson; Linda Mann; Kenneth C Jost; Irving Nachamkin
Journal:  J Clin Microbiol       Date:  2004-06       Impact factor: 5.948

10.  Nocardia veterana as a pathogen in North American patients.

Authors:  Patricia S Conville; June M Brown; Arnold G Steigerwalt; Judy W Lee; Dorothy E Byrer; Victoria L Anderson; Susan E Dorman; Steven M Holland; Barbara Cahill; Karen C Carroll; Frank G Witebsky
Journal:  J Clin Microbiol       Date:  2003-06       Impact factor: 5.948
  10 in total
  6 in total

Review 1.  Clinical microbiology informatics.

Authors:  Daniel D Rhoads; Vitali Sintchenko; Carol A Rauch; Liron Pantanowitz
Journal:  Clin Microbiol Rev       Date:  2014-10       Impact factor: 26.132

2.  Biographical Feature: Patrick R. Murray, Ph.D.

Authors:  Karen C Carroll
Journal:  J Clin Microbiol       Date:  2016-06-08       Impact factor: 5.948

Review 3.  Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.

Authors:  Deirdre L Church; Lorenzo Cerutti; Antoine Gürtler; Thomas Griener; Adrian Zelazny; Stefan Emler
Journal:  Clin Microbiol Rev       Date:  2020-09-09       Impact factor: 26.132

4.  Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.

Authors:  Manal Helal; Fanrong Kong; Sharon C A Chen; Michael Bain; Richard Christen; Vitali Sintchenko
Journal:  PLoS One       Date:  2011-06-08       Impact factor: 3.240

5.  Actinomycetes from the Red Sea Sponge Coscinoderma mathewsi: Isolation, Diversity, and Potential for Bioactive Compounds Discovery.

Authors:  Yara I Shamikh; Aliaa A El Shamy; Yasser Gaber; Usama Ramadan Abdelmohsen; Hashem A Madkour; Hannes Horn; Hossam M Hassan; Abeer H Elmaidomy; Dalal Hussien M Alkhalifah; Wael N Hozzein
Journal:  Microorganisms       Date:  2020-05-23

6.  Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments.

Authors:  Manal Helal; Fanrong Kong; Sharon Ca Chen; Fei Zhou; Dominic E Dwyer; John Potter; Vitali Sintchenko
Journal:  Microb Inform Exp       Date:  2012-01-26
  6 in total

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