Literature DB >> 27307454

The Future of Whole-Genome Sequencing for Public Health and the Clinic.

Marc W Allard1.   

Abstract

An American Society for Microbiology (ASM) conference titled the Conference on Rapid Next-Generation Sequencing and Bioinformatic Pipelines for Enhanced Molecular Epidemiological Investigation of Pathogens provided a venue for discussing how technologies surrounding whole-genome sequencing (WGS) are advancing microbiology. Several applications in microbial taxonomy, microbial forensics, and genomics for public health pathogen surveillance were presented at the meeting and are reviewed. All of these studies document that WGS is revolutionizing applications in microbiology and that the impact of these technologies will be profound. ASM is providing support mechanisms to promote discussions of WGS techniques to foster applications and interpretations.
Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Mesh:

Year:  2016        PMID: 27307454      PMCID: PMC4963481          DOI: 10.1128/JCM.01082-16

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


  7 in total

1.  Identification of a salmonellosis outbreak by means of molecular sequencing.

Authors:  E Kurt Lienau; Errol Strain; Charles Wang; Jie Zheng; Andrea R Ottesen; Christine E Keys; Thomas S Hammack; Steven M Musser; Eric W Brown; Marc W Allard; Guojie Cao; Jianghong Meng; Robert Stones
Journal:  N Engl J Med       Date:  2011-02-23       Impact factor: 91.245

Review 2.  Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

Authors:  Marc W Allard; Errol Strain; David Melka; Kelly Bunning; Steven M Musser; Eric W Brown; Ruth Timme
Journal:  J Clin Microbiol       Date:  2016-03-23       Impact factor: 5.948

Review 3.  A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

Authors:  George M Garrity
Journal:  J Clin Microbiol       Date:  2016-05-18       Impact factor: 5.948

Review 4.  Expansion of Microbial Forensics.

Authors:  Sarah E Schmedes; Antti Sajantila; Bruce Budowle
Journal:  J Clin Microbiol       Date:  2016-02-24       Impact factor: 5.948

5.  Genomically Informed Surveillance for Carbapenem-Resistant Enterobacteriaceae in a Health Care System.

Authors:  Nicole D Pecora; Ning Li; Marc Allard; Cong Li; Esperanza Albano; Mary Delaney; Andrea Dubois; Andrew B Onderdonk; Lynn Bry
Journal:  MBio       Date:  2015-07-28       Impact factor: 7.867

6.  Comparative genomic analysis and virulence differences in closely related salmonella enterica serotype heidelberg isolates from humans, retail meats, and animals.

Authors:  Maria Hoffmann; Shaohua Zhao; James Pettengill; Yan Luo; Steven R Monday; Jason Abbott; Sherry L Ayers; Hediye N Cinar; Tim Muruvanda; Cong Li; Marc W Allard; Jean Whichard; Jianghong Meng; Eric W Brown; Patrick F McDermott
Journal:  Genome Biol Evol       Date:  2014-05       Impact factor: 3.416

Review 7.  Population and Functional Genomics of Neisseria Revealed with Gene-by-Gene Approaches.

Authors:  Martin C J Maiden; Odile B Harrison
Journal:  J Clin Microbiol       Date:  2016-04-20       Impact factor: 5.948

  7 in total
  10 in total

1.  Complete microbial genomes for public health in Australia and the Southwest Pacific.

Authors:  Sarah L Baines; Anders Gonçalves da Silva; Glen P Carter; Amy Jennison; Irani Rathnayake; Rikki M Graham; Vitali Sintchenko; Qinning Wang; Rebecca J Rockett; Verlaine J Timms; Elena Martinez; Susan Ballard; Takehiro Tomita; Nicole Isles; Kristy A Horan; William Pitchers; Timothy P Stinear; Deborah A Williamson; Benjamin P Howden; Torsten Seemann
Journal:  Microb Genom       Date:  2020-11-12

Review 2.  The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain.

Authors:  Elena A Oniciuc; Eleni Likotrafiti; Adrián Alvarez-Molina; Miguel Prieto; Jesús A Santos; Avelino Alvarez-Ordóñez
Journal:  Genes (Basel)       Date:  2018-05-22       Impact factor: 4.096

Review 3.  Rodent-borne diseases and their public health importance in Iran.

Authors:  Mohammad Hasan Rabiee; Ahmad Mahmoudi; Roohollah Siahsarvie; Boris Kryštufek; Ehsan Mostafavi
Journal:  PLoS Negl Trop Dis       Date:  2018-04-19

Review 4.  Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa.

Authors:  Anthony M Smith
Journal:  Afr J Lab Med       Date:  2019-03-14

5.  Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept.

Authors:  Bert Bogaerts; Raf Winand; Qiang Fu; Julien Van Braekel; Pieter-Jan Ceyssens; Wesley Mattheus; Sophie Bertrand; Sigrid C J De Keersmaecker; Nancy H C Roosens; Kevin Vanneste
Journal:  Front Microbiol       Date:  2019-03-06       Impact factor: 5.640

6.  Recommendations for performance optimizations when using GATK3.8 and GATK4.

Authors:  Jacob R Heldenbrand; Saurabh Baheti; Matthew A Bockol; Travis M Drucker; Steven N Hart; Matthew E Hudson; Ravishankar K Iyer; Michael T Kalmbach; Katherine I Kendig; Eric W Klee; Nathan R Mattson; Eric D Wieben; Mathieu Wiepert; Derek E Wildman; Liudmila S Mainzer
Journal:  BMC Bioinformatics       Date:  2019-11-08       Impact factor: 3.169

Review 7.  Poultry processing and the application of microbiome mapping.

Authors:  K M Feye; D R Thompson; M J Rothrock; M H Kogut; S C Ricke
Journal:  Poult Sci       Date:  2020-01-24       Impact factor: 3.352

Review 8.  Advances in the Microbiome: Applications to Clostridium difficile Infection.

Authors:  Eamonn P Culligan; Roy D Sleator
Journal:  J Clin Med       Date:  2016-09-21       Impact factor: 4.241

9.  Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR).

Authors:  James Robertson; Catherine Yoshida; Peter Kruczkiewicz; Celine Nadon; Anil Nichani; Eduardo N Taboada; John Howard Eagles Nash
Journal:  Microb Genom       Date:  2018-01-17

10.  Revisiting Polymorphic Diversity of Aminoglycoside N-Acetyltransferase AAC(6')-Ib Based on Bacterial Genomes of Human, Animal, and Environmental Origins.

Authors:  Dae-Wi Kim; Cung N Thawng; Kihyun Lee; Chang-Jun Cha
Journal:  Front Microbiol       Date:  2018-08-10       Impact factor: 5.640

  10 in total

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