Literature DB >> 23345298

A genomic day in the life of a clinical microbiology laboratory.

S Wesley Long1, Dawn Williams, Chandni Valson, Concepcion C Cantu, Patricia Cernoch, James M Musser, Randall J Olsen.   

Abstract

Next-generation sequencing technology is available to many clinical laboratories; however, it is not yet widely used in routine microbiology practice. To demonstrate the feasibility of using whole-genome sequencing in a routine clinical microbiology workflow, we sequenced the genome of every organism isolated in our laboratory for 1 day.

Mesh：

Year:  2013        PMID： 23345298      PMCID： PMC3666789          DOI： 10.1128/JCM.03237-12

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


  11 in total

Review 1.  Bacterial genomics in infectious disease and the clinical pathology laboratory.

Authors:  Randall J Olsen; S Wesley Long; James M Musser
Journal:  Arch Pathol Lab Med       Date:  2012-03-22       Impact factor: 5.534

2.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

3.  Rapidly progressive, fatal, inhalation anthrax-like infection in a human: case report, pathogen genome sequencing, pathology, and coordinated response.

Authors:  Angela M Wright; Stephen B Beres; Erin N Consamus; S Wesley Long; Anthony R Flores; Roberto Barrios; G Stefan Richter; So-Young Oh; Gabriella Garufi; Hannah Maier; Ashley L Drews; Kathryn E Stockbauer; Patricia Cernoch; Olaf Schneewind; Randall J Olsen; James M Musser
Journal:  Arch Pathol Lab Med       Date:  2011-08-09       Impact factor: 5.534

4.  Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.

Authors:  Stephen B Beres; Ronan K Carroll; Patrick R Shea; Izabela Sitkiewicz; Juan Carlos Martinez-Gutierrez; Donald E Low; Allison McGeer; Barbara M Willey; Karen Green; Gregory J Tyrrell; Thomas D Goldman; Michael Feldgarden; Bruce W Birren; Yuriy Fofanov; John Boos; William D Wheaton; Christiane Honisch; James M Musser
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-08       Impact factor: 11.205

5.  Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients.

Authors:  Eric E Smith; Danielle G Buckley; Zaining Wu; Channakhone Saenphimmachak; Lucas R Hoffman; David A D'Argenio; Samuel I Miller; Bonnie W Ramsey; David P Speert; Samuel M Moskowitz; Jane L Burns; Rajinder Kaul; Maynard V Olson
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-10       Impact factor: 11.205

6.  Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.

Authors:  Jennifer L Gardy; James C Johnston; Shannan J Ho Sui; Victoria J Cook; Lena Shah; Elizabeth Brodkin; Shirley Rempel; Richard Moore; Yongjun Zhao; Robert Holt; Richard Varhol; Inanc Birol; Marcus Lem; Meenu K Sharma; Kevin Elwood; Steven J M Jones; Fiona S L Brinkman; Robert C Brunham; Patrick Tang
Journal:  N Engl J Med       Date:  2011-02-24       Impact factor: 91.245

7.  Genomic anatomy of Escherichia coli O157:H7 outbreaks.

Authors:  Mark Eppinger; Mark K Mammel; Joseph E Leclerc; Jacques Ravel; Thomas A Cebula
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-30       Impact factor: 11.205

8.  Integrating rapid pathogen identification and antimicrobial stewardship significantly decreases hospital costs.

Authors:  Katherine K Perez; Randall J Olsen; William L Musick; Patricia L Cernoch; James R Davis; Geoffrey A Land; Leif E Peterson; James M Musser
Journal:  Arch Pathol Lab Med       Date:  2012-12-06       Impact factor: 5.534

9.  Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Authors:  Claudio U Köser; Matthew T G Holden; Matthew J Ellington; Edward J P Cartwright; Nicholas M Brown; Amanda L Ogilvy-Stuart; Li Yang Hsu; Claire Chewapreecha; Nicholas J Croucher; Simon R Harris; Mandy Sanders; Mark C Enright; Gordon Dougan; Stephen D Bentley; Julian Parkhill; Louise J Fraser; Jason R Betley; Ole B Schulz-Trieglaff; Geoffrey P Smith; Sharon J Peacock
Journal:  N Engl J Med       Date:  2012-06-14       Impact factor: 91.245

10.  Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.

Authors:  C A D'Souza; J W Kronstad; G Taylor; R Warren; M Yuen; G Hu; W H Jung; A Sham; S E Kidd; K Tangen; N Lee; T Zeilmaker; J Sawkins; G McVicker; S Shah; S Gnerre; A Griggs; Q Zeng; K Bartlett; W Li; X Wang; J Heitman; J E Stajich; J A Fraser; W Meyer; D Carter; J Schein; M Krzywinski; K J Kwon-Chung; A Varma; J Wang; R Brunham; M Fyfe; B F F Ouellette; A Siddiqui; M Marra; S Jones; R Holt; B W Birren; J E Galagan; C A Cuomo
Journal:  MBio       Date:  2011-02-08       Impact factor: 7.867
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  27 in total

1.  Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory.

Authors:  Daniel D Rhoads
Journal:  J Clin Microbiol       Date:  2018-08-27       Impact factor: 5.948

Review 2.  Whole-genome sequencing in outbreak analysis.

Authors:  Carol A Gilchrist; Stephen D Turner; Margaret F Riley; William A Petri; Erik L Hewlett
Journal:  Clin Microbiol Rev       Date:  2015-07       Impact factor: 26.132

Review 3.  Current and emerging Legionella diagnostics for laboratory and outbreak investigations.

Authors:  Jeffrey W Mercante; Jonas M Winchell
Journal:  Clin Microbiol Rev       Date:  2015-01       Impact factor: 26.132

4.  Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study.

Authors:  Randall J Olsen; Nahuel Fittipaldi; Priyanka Kachroo; Misu A Sanson; S Wesley Long; Kathryn J Como-Sabetti; Chandni Valson; Concepcion Cantu; Ruth Lynfield; Chris Van Beneden; Stephen B Beres; James M Musser
Journal:  J Clin Microbiol       Date:  2014-09-24       Impact factor: 5.948

Review 5.  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

Review 6.  Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories.

Authors:  Amy S Gargis; Lisa Kalman; Ira M Lubin
Journal:  J Clin Microbiol       Date:  2016-08-10       Impact factor: 5.948

Review 7.  Progress and potential: training in genomic pathology.

Authors:  Richard L Haspel; Randall J Olsen; Anna Berry; Charles E Hill; John D Pfeifer; Iris Schrijver; Karen L Kaul
Journal:  Arch Pathol Lab Med       Date:  2014-04       Impact factor: 5.534

8.  Human Infections Caused by Clonally Related African Clade (Clade III) Strains of Candida auris in the Greater Houston Region.

Authors:  S Wesley Long; Matthew Ojeda Saavedra; Paul A Christensen; James M Musser; Randall J Olsen
Journal:  J Clin Microbiol       Date:  2020-06-24       Impact factor: 5.948

9.  Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis.

Authors:  Laura Pérez-Lago; Miguel Martínez-Lirola; Sergio García; Marta Herranz; Igor Mokrousov; Iñaki Comas; Llúcia Martínez-Priego; Emilio Bouza; Darío García-de-Viedma
Journal:  J Clin Microbiol       Date:  2016-09-28       Impact factor: 5.948

10.  Deriving group A Streptococcus typing information from short-read whole-genome sequencing data.

Authors:  Taryn B T Athey; Sarah Teatero; Aimin Li; Alex Marchand-Austin; Bernard W Beall; Nahuel Fittipaldi
Journal:  J Clin Microbiol       Date:  2014-03-19       Impact factor: 5.948
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