Literature DB >> 28835478

Towards a Universal Molecular Microbiological Test.

Richard J N Allcock1,2, Amy V Jennison3, David Warrilow4.   

Abstract

The standard paradigm for microbiological testing is dependent on the presentation of a patient to a clinician. Tests are then requested based on differential diagnoses using the patient's symptoms as a guide. The era of high-throughput genomic methods has the potential to replace this model for the first time with what could be referred to as "hypothesis-free testing." This approach utilizes one of a variety of methodologies to obtain a sequence from potentially any nucleic acid in a clinical sample, without prior knowledge of its content. We discuss the advantages of such an approach and the challenges in making this a reality. © Crown copyright 2017.

Entities:  

Keywords:  bacteriology; bioinformatics; diagnostics; genome analysis; high-throughput sequencing; hypothesis-free testing; next-generation sequencing; personalized medicine; virology

Mesh:

Year:  2017        PMID: 28835478      PMCID: PMC5654900          DOI: 10.1128/JCM.01155-17

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


  37 in total

1.  Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.

Authors:  Erin H Graf; Keith E Simmon; Keith D Tardif; Weston Hymas; Steven Flygare; Karen Eilbeck; Mark Yandell; Robert Schlaberg
Journal:  J Clin Microbiol       Date:  2016-01-27       Impact factor: 5.948

2.  Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples.

Authors:  Justine Cheval; Virginie Sauvage; Lionel Frangeul; Laurent Dacheux; Ghislaine Guigon; Nicolas Dumey; Kevin Pariente; Claudine Rousseaux; Fabien Dorange; Nicolas Berthet; Sylvain Brisse; Ivan Moszer; Hervé Bourhy; Claude Jean Manuguerra; Marc Lecuit; Ana Burguiere; Valérie Caro; Marc Eloit
Journal:  J Clin Microbiol       Date:  2011-06-29       Impact factor: 5.948

3.  Towards a European consensus for reporting incidental findings during clinical NGS testing.

Authors:  Jayne Y Hehir-Kwa; Mireille Claustres; Ros J Hastings; Conny van Ravenswaaij-Arts; Gabrielle Christenhusz; Maurizio Genuardi; Béla Melegh; Anne Cambon-Thomsen; Philippos Patsalis; Joris Vermeesch; Martina C Cornel; Beverly Searle; Aarno Palotie; Ettore Capoluongo; Borut Peterlin; Xavier Estivill; Peter N Robinson
Journal:  Eur J Hum Genet       Date:  2015-06-03       Impact factor: 4.246

Review 4.  Managing the ethical challenges of next-generation sequencing in genomic medicine.

Authors:  Angus J Clarke
Journal:  Br Med Bull       Date:  2014-08-13       Impact factor: 4.291

5.  Antiviral resistance among highly pathogenic influenza A (H5N1) viruses isolated worldwide in 2002-2012 shows need for continued monitoring.

Authors:  Elena A Govorkova; Tatiana Baranovich; Patrick Seiler; Jianling Armstrong; Andrew Burnham; Yi Guan; Malik Peiris; Richard J Webby; Robert G Webster
Journal:  Antiviral Res       Date:  2013-02-28       Impact factor: 5.970

Review 6.  Host Genetic Susceptibility to Enteric Viruses: A Systematic Review and Metaanalysis.

Authors:  Anita Kambhampati; Daniel C Payne; Veronica Costantini; Benjamin A Lopman
Journal:  Clin Infect Dis       Date:  2015-10-26       Impact factor: 9.079

7.  Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis.

Authors:  Alexander L Greninger; Samia N Naccache; Scot Federman; Guixia Yu; Placide Mbala; Vanessa Bres; Doug Stryke; Jerome Bouquet; Sneha Somasekar; Jeffrey M Linnen; Roger Dodd; Prime Mulembakani; Bradley S Schneider; Jean-Jacques Muyembe-Tamfum; Susan L Stramer; Charles Y Chiu
Journal:  Genome Med       Date:  2015-09-29       Impact factor: 11.117

8.  To disclose, or not to disclose? Context matters.

Authors:  Vasiliki Rahimzadeh; Denise Avard; Karine Sénécal; Bartha Maria Knoppers; Daniel Sinnett
Journal:  Eur J Hum Genet       Date:  2014-06-11       Impact factor: 4.246

Review 9.  The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis.

Authors:  Inga Patarčić; Andrea Gelemanović; Mirna Kirin; Ivana Kolčić; Evropi Theodoratou; Kenneth J Baillie; Menno D de Jong; Igor Rudan; Harry Campbell; Ozren Polašek
Journal:  Sci Rep       Date:  2015-11-03       Impact factor: 4.379

Review 10.  Standardization and quality management in next-generation sequencing.

Authors:  Christoph Endrullat; Jörn Glökler; Philipp Franke; Marcus Frohme
Journal:  Appl Transl Genom       Date:  2016-07-01
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  8 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

2.  Shotgun Metagenomic Detection of Pathogens: a Micro-Comic Strip.

Authors:  Alexander J McAdam
Journal:  J Clin Microbiol       Date:  2018-07-26       Impact factor: 5.948

Review 3.  Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies.

Authors:  Zisis Kozlakidis; Alex van Belkum; Olivier Vandenberg; Géraldine Durand; Marie Hallin; Andreas Diefenbach; Vanya Gant; Patrick Murray
Journal:  Clin Microbiol Rev       Date:  2020-02-26       Impact factor: 26.132

4.  Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study.

Authors:  Yangyang Guo; Yanlin Yang; Ming Xu; Guangzhi Shi; Jianxin Zhou; Jindong Zhang; Hongliang Li
Journal:  Front Cell Infect Microbiol       Date:  2022-04-29       Impact factor: 6.073

5.  Infection in xenotransplantation: opportunities and challenges.

Authors:  Jay A Fishman
Journal:  Curr Opin Organ Transplant       Date:  2019-10       Impact factor: 2.640

6.  Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.

Authors:  Roby P Bhattacharyya; Mark Walker; Rich Boykin; Sophie S Son; Jamin Liu; Austin C Hachey; Peijun Ma; Lidan Wu; Kyungyong Choi; Kaelyn C Cummins; Maura Benson; Jennifer Skerry; Hyunryul Ryu; Sharon Y Wong; Marcia B Goldberg; Jongyoon Han; Virginia M Pierce; Lisa A Cosimi; Noam Shoresh; Jonathan Livny; Joseph Beechem; Deborah T Hung
Journal:  Sci Rep       Date:  2019-03-14       Impact factor: 4.379

7.  Illumina sequencing of clinical samples for virus detection in a public health laboratory.

Authors:  Bixing Huang; Amy Jennison; David Whiley; Jamie McMahon; Glen Hewitson; Rikki Graham; Amanda De Jong; David Warrilow
Journal:  Sci Rep       Date:  2019-04-01       Impact factor: 4.379

8.  Diagnostic value and clinical application of next-generation sequencing for infections in immunosuppressed patients with corticosteroid therapy.

Authors:  Sen Wang; Jingwen Ai; Peng Cui; Yimin Zhu; Honglong Wu; Wenhong Zhang
Journal:  Ann Transl Med       Date:  2020-03
  8 in total

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