Literature DB >> 31881145

Pathogen Genomics in Public Health.

Gregory L Armstrong1, Duncan R MacCannell1, Jill Taylor1, Heather A Carleton1, Elizabeth B Neuhaus1, Richard S Bradbury1, James E Posey1, Marta Gwinn1.   

Abstract

Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.
Copyright © 2019 Massachusetts Medical Society.

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Year:  2019        PMID： 31881145      PMCID： PMC7008580          DOI： 10.1056/NEJMsr1813907

Source DB:  PubMed          Journal:  N Engl J Med        ISSN： 0028-4793            Impact factor:   91.245


  92 in total

1.  Next-generation sequencing-based user-friendly platforms for drug-resistant tuberculosis diagnosis: A promise for the near future.

Authors:  David L Dolinger; Rebecca E Colman; David M Engelthaler; Timothy C Rodwell
Journal:  Int J Mycobacteriol       Date:  2016-10-28

2.  Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.

Authors:  Timothy J Dallman; Lisa Byrne; Philip M Ashton; Lauren A Cowley; Neil T Perry; Goutam Adak; Liljana Petrovska; Richard J Ellis; Richard Elson; Anthony Underwood; Jonathan Green; William P Hanage; Claire Jenkins; Kathie Grant; John Wain
Journal:  Clin Infect Dis       Date:  2015-04-17       Impact factor: 9.079

3.  Universal influenza B virus genomic amplification facilitates sequencing, diagnostics, and reverse genetics.

Authors:  Bin Zhou; Xudong Lin; Wei Wang; Rebecca A Halpin; Jayati Bera; Timothy B Stockwell; Ian G Barr; David E Wentworth
Journal:  J Clin Microbiol       Date:  2014-02-05       Impact factor: 5.948

Review 4.  Whole genome sequencing of Mycobacterium tuberculosis for detection of drug resistance: a systematic review.

Authors:  D Papaventsis; N Casali; I Kontsevaya; F Drobniewski; D M Cirillo; V Nikolayevskyy
Journal:  Clin Microbiol Infect       Date:  2016-09-22       Impact factor: 8.067

5.  Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States.

Authors:  B J Metcalf; S Chochua; R E Gertz; Z Li; H Walker; T Tran; P A Hawkins; A Glennen; R Lynfield; Y Li; L McGee; B Beall
Journal:  Clin Microbiol Infect       Date:  2016-08-17       Impact factor: 8.067

Review 6.  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

7.  Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.

Authors:  Ivica Letunic; Peer Bork
Journal:  Nucleic Acids Res       Date:  2016-04-19       Impact factor: 16.971

8.  Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing.

Authors:  Laila Parvaresh; Taryn Crighton; Elena Martinez; Andrea Bustamante; Sharon Chen; Vitali Sintchenko
Journal:  BMC Infect Dis       Date:  2018-06-07       Impact factor: 3.090

Review 9.  Next-generation sequencing technologies and their application to the study and control of bacterial infections.

Authors:  J Besser; H A Carleton; P Gerner-Smidt; R L Lindsey; E Trees
Journal:  Clin Microbiol Infect       Date:  2017-10-23       Impact factor: 8.067

10.  Inference of genetic relatedness between viral quasispecies from sequencing data.

Authors:  Olga Glebova; Sergey Knyazev; Andrew Melnyk; Alexander Artyomenko; Yury Khudyakov; Alex Zelikovsky; Pavel Skums
Journal:  BMC Genomics       Date:  2017-12-06       Impact factor: 3.969
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  58 in total

1.  Insights into health and disease from ancient biomolecules.

Authors:  Anne C Stone; Cecil M Lewis; Verena J Schuenemann
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-10-05       Impact factor: 6.237

2.  Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.

Authors:  Christina Yek; Andrea R Pacheco; Manu Vanaerschot; Jennifer A Bohl; Elizabeth Fahsbender; Andrés Aranda-Díaz; Sreyngim Lay; Sophana Chea; Meng Heng Oum; Chanthap Lon; Cristina M Tato; Jessica E Manning
Journal:  Front Epidemiol       Date:  2022-08-15

Review 3.  Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective.

Authors:  Jee In Kim; Finlay Maguire; Kara K Tsang; Theodore Gouliouris; Sharon J Peacock; Tim A McAllister; Andrew G McArthur; Robert G Beiko
Journal:  Clin Microbiol Rev       Date:  2022-05-25       Impact factor: 50.129

4.  Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol.

Authors:  Alfredo Mayor; Clemente da Silva; Eduard Rovira-Vallbona; Arantxa Roca-Feltrer; Craig Bonnington; Alexandra Wharton-Smith; Bryan Greenhouse; Caitlin Bever; Arlindo Chidimatembue; Caterina Guinovart; Joshua L Proctor; Maria Rodrigues; Neide Canana; Paulo Arnaldo; Simone Boene; Pedro Aide; Sonia Enosse; Francisco Saute; Baltazar Candrinho
Journal:  BMJ Open       Date:  2022-07-12       Impact factor: 3.006

5.  Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia.

Authors:  Jessica E Manning; Jennifer A Bohl; Sreyngim Lay; Sophana Chea; Ly Sovann; Yi Sengdoeurn; Seng Heng; Chan Vuthy; Katrina Kalantar; Vida Ahyong; Michelle Tan; Jonathan Sheu; Cristina M Tato; Joseph L DeRisi; Laurence Baril; Veasna Duong; Philippe Dussart; Erik A Karlsson
Journal:  bioRxiv       Date:  2020-03-05

6.  Design of Multidrug-Resistant Tuberculosis Treatment Regimens Based on DNA Sequencing.

Authors:  Hans-Peter Grobbel; Matthias Merker; Niklas Köhler; Sönke Andres; Harald Hoffmann; Jan Heyckendorf; Maja Reimann; Ivan Barilar; Viola Dreyer; Doris Hillemann; Barbara Kalsdorf; Thomas A Kohl; Patricia Sanchez Carballo; Dagmar Schaub; Katharina Todt; Christian Utpatel; Florian P Maurer; Christoph Lange; Stefan Niemann
Journal:  Clin Infect Dis       Date:  2021-10-05       Impact factor: 9.079

7.  Genomics of Environmental Salmonella: Engaging Students in the Microbiology and Bioinformatics of Foodborne Pathogens.

Authors:  Noah A Greenman; Sophie K Jurgensen; Charles P Holmes; Curtis J Kapsak; Raechel E Davis; William M Maza; Desiree Edemba; Bethany A Esser; Selena M Hise; Tara N Keen; Hunter G Larson; Dominique J Lockwood; Brian Wang; Joseph A Harsh; James B Herrick
Journal:  Front Microbiol       Date:  2021-04-22       Impact factor: 5.640

8.  Global transmission network of SARS-CoV-2: from outbreak to pandemic.

Authors:  Pavel Skums; Alexander Kirpich; Pelin Icer Baykal; Alex Zelikovsky; Gerardo Chowell
Journal:  medRxiv       Date:  2020-03-27

9.  Logically Inferred Tuberculosis Transmission (LITT): A Data Integration Algorithm to Rank Potential Source Cases.

Authors:  Kathryn Winglee; Clinton J McDaniel; Lauren Linde; Steve Kammerer; Martin Cilnis; Kala M Raz; Wendy Noboa; Jillian Knorr; Lauren Cowan; Sue Reynolds; James Posey; Jeanne Sullivan Meissner; Shameer Poonja; Tambi Shaw; Sarah Talarico; Benjamin J Silk
Journal:  Front Public Health       Date:  2021-06-21

10.  Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions.

Authors:  Kentaro Tohma; Michael Kulka; Suzie Coughlan; Kim Y Green; Gabriel I Parra
Journal:  Viruses       Date:  2020-05-07       Impact factor: 5.048
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