Application of artificial intelligence to the
antimicrobial resistance
bacterial pathogens
machine learning
predictive genomics
whole genome sequence
Journal
Canada communicable disease report = Releve des maladies transmissibles au Canada
ISSN: 1188-4169
Titre abrégé: Can Commun Dis Rep
Pays: Canada
ID NLM: 9303729
Informations de publication
Date de publication:
04 Jun 2020
04 Jun 2020
Historique:
entrez:
17
7
2020
pubmed:
17
7
2020
medline:
17
7
2020
Statut:
epublish
Résumé
Each year, approximately one in eight Canadians are affected by foodborne illness, either through outbreaks or sporadic illness, with animals being the major reservoir for the pathogens. Whole genome sequence analyses are now routinely implemented by public and animal health laboratories to define epidemiological disease clusters and to identify potential sources of infection. Similarly, a number of bioinformatics tools can be used to identify virulence and antimicrobial resistance (AMR) determinants in the genomes of pathogenic strains. Many important clinical and phenotypic characteristics of these pathogens can now be predicted using machine learning algorithms applied to whole genome sequence data. In this overview, we compare the ability of support vector machines, gradient-boosted decision trees and artificial neural networks to predict the levels of AMR within
Identifiants
pubmed: 32673383
doi: 10.14745/ccdr.v46i06a05
pii: 460605
pmc: PMC7343051
doi:
Types de publication
Journal Article
Langues
eng
Pagination
180-185Déclaration de conflit d'intérêts
Conflict of interest: None.
Références
Nat Rev Genet. 2018 Sep;19(9):549-565
pubmed: 29973680
J Biol Chem. 2018 Mar 30;293(13):4913-4927
pubmed: 29378850
BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):420
pubmed: 30453987
Front Public Health. 2019 Sep 04;7:242
pubmed: 31552211
J Antimicrob Chemother. 2001 Jul;48 Suppl 1:5-16
pubmed: 11420333
Front Pharmacol. 2019 Aug 27;10:913
pubmed: 31507413
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42
pubmed: 23193287
PLoS Comput Biol. 2019 Sep 3;15(9):e1007349
pubmed: 31479500
Microb Genom. 2019 Dec;5(12):
pubmed: 31778355
Elife. 2019 Feb 12;8:
pubmed: 30744806
Genome Med. 2017 Sep 6;9(1):81
pubmed: 28877757
Sci Rep. 2019 Mar 11;9(1):4071
pubmed: 30858411
J Clin Microbiol. 2019 Jan 30;57(2):
pubmed: 30333126
PLoS Comput Biol. 2018 Dec 14;14(12):e1006258
pubmed: 30550564
Nat Commun. 2018 Oct 17;9(1):4306
pubmed: 30333483
PLoS Comput Biol. 2017 Aug 2;13(8):e1005677
pubmed: 28767643
Microb Genom. 2017 Oct 3;3(10):e000135
pubmed: 29177093
J Hosp Infect. 2016 Jan;92(1):33-41
pubmed: 26597637
Nat Commun. 2019 Sep 25;10(1):4354
pubmed: 31554788
Bioinformatics. 2011 Mar 15;27(6):764-70
pubmed: 21217122
Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11312-11317
pubmed: 27647883
Genome Res. 2017 Jul 18;:
pubmed: 28720578
Eur J Clin Microbiol Infect Dis. 2018 Feb;37(2):187-208
pubmed: 28871407
Foodborne Pathog Dis. 2019 Jul;16(7):504-512
pubmed: 31246502
Front Microbiol. 2019 May 21;10:1107
pubmed: 31231317