• AMRnet: a data visualization p...

Treffer: AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance.

Title:
AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance.
Authors:
Cerdeira LT; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom., Dyson ZA; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom., Sharma V; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom., Maranga M; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom., Foster-Nyarko E; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom., Carey ME; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom., Holt KE; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom.; Department of Infectious Diseases, School of Translational Medicine, Monash University, Melbourne, Victoria 3004, Australia.
Source:
Nucleic acids research [Nucleic Acids Res] 2026 Jan 06; Vol. 54 (D1), pp. D691-D702.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
Imprint Name(s):
Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.
MeSH Terms:
Software* , Drug Resistance, Bacterial*/genetics , Bacteria*/genetics , Bacteria*/drug effects , Data Visualization*, Humans ; Databases, Genetic ; Genome, Bacterial ; Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Internet
References:
Nat Commun. 2023 Oct 23;14(1):6392. (PMID: 37872141)
Nat Commun. 2021 May 17;12(1):2879. (PMID: 34001879)
Nat Commun. 2021 Jul 7;12(1):4188. (PMID: 34234121)
Clin Infect Dis. 2021 Dec 1;73(Suppl_4):S325-S335. (PMID: 34850838)
Nucleic Acids Res. 2025 Jan 6;53(D1):D757-D762. (PMID: 39441072)
Lancet Infect Dis. 2022 Mar;22(3):401-412. (PMID: 34767753)
Front Public Health. 2019 Sep 04;7:242. (PMID: 31552211)
J Clin Microbiol. 2005 Aug;43(8):4178-82. (PMID: 16081970)
Genome Med. 2020 Jan 16;12(1):11. (PMID: 31948471)
Lancet Infect Dis. 2019 Jan;19(1):56-66. (PMID: 30409683)
BMC Biol. 2007 Sep 07;5:35. (PMID: 17825091)
Nat Commun. 2016 Oct 05;7:12827. (PMID: 27703135)
Wellcome Open Res. 2018 Sep 24;3:124. (PMID: 30345391)
NPJ Antimicrob Resist. 2025 May 9;3(1):37. (PMID: 40346194)
Nucleic Acids Res. 2025 Jan 6;53(D1):D62-D66. (PMID: 39535044)
Lancet Infect Dis. 2022 May;22(5):692-705. (PMID: 35114140)
Nat Commun. 2023 Apr 8;14(1):1983. (PMID: 37031199)
Lancet Infect Dis. 2025 Sep;25(9):1033-1043. (PMID: 40245910)
Lancet. 2024 Sep 28;404(10459):1199-1226. (PMID: 39299261)
Nucleic Acids Res. 2023 Jan 6;51(D1):D29-D38. (PMID: 36370100)
Genome Med. 2025 May 9;17(1):51. (PMID: 40346656)
Microb Genom. 2023 May;9(5):. (PMID: 37219927)
Lancet Reg Health West Pac. 2022 Apr 12;23:100446. (PMID: 35465046)
Lancet Microbe. 2023 Dec;4(12):e1035-e1039. (PMID: 37977164)
PLOS Glob Public Health. 2025 Nov 24;5(11):e0005256. (PMID: 41284650)
Sex Health. 2019 Sep;16(5):412-425. (PMID: 31437420)
Front Public Health. 2019 Nov 21;7:317. (PMID: 31824904)
Philos Trans R Soc Lond B Biol Sci. 2022 Oct 10;377(1861):20210240. (PMID: 35989609)
Genome Res. 2020 Jan;30(1):138-152. (PMID: 31809257)
Mol Biol Evol. 2022 Jul 2;39(7):. (PMID: 35700230)
Genome Med. 2021 Apr 19;13(1):61. (PMID: 33875000)
Front Cell Infect Microbiol. 2016 Nov 18;6:141. (PMID: 27917373)
Elife. 2023 Sep 12;12:. (PMID: 37697804)
Sci Rep. 2021 Jun 16;11(1):12728. (PMID: 34135355)
Science. 2018 May 18;360(6390):733-738. (PMID: 29773743)
J Antimicrob Chemother. 2018 Mar 1;73(suppl_3):iii2-iii78. (PMID: 29514274)
Genome Med. 2025 Oct 24;17(1):130. (PMID: 41327441)
mBio. 2023 Aug 31;14(4):e0088223. (PMID: 37255304)
J Clin Microbiol. 2018 Aug 27;56(9):. (PMID: 29925638)
Nat Rev Dis Primers. 2023 Dec 14;9(1):71. (PMID: 38097589)
J Infect Dis. 2021 Dec 20;224(12 Suppl 2):S775-S780. (PMID: 34453548)
J Infect Dis. 2004 Apr 15;189(8):1497-505. (PMID: 15073688)
Nat Microbiol. 2019 Nov;4(11):1919-1929. (PMID: 31358985)
Grant Information:
United Kingdom WT_ Wellcome Trust; 226432/Z/22/Z United Kingdom WT_ Wellcome Trust
Substance Nomenclature:
0 (Anti-Bacterial Agents)
Entry Date(s):
Date Created: 20251109 Date Completed: 20260117 Latest Revision: 20260119
Update Code:
20260119
PubMed Central ID:
PMC12807673
DOI:
10.1093/nar/gkaf1101
PMID:
41206476
Database:
MEDLINE

Weitere Informationen

Antimicrobial resistance (AMR) poses a substantial threat to global public health. Whole genome sequencing is increasingly used as a core method for pathogen characterization to support AMR surveillance. As a result, a vast amount of bacterial sequence data are available in public archives, yet the AMR-related information they encode is not readily accessible to those without bioinformatics expertise and is essentially invisible to policy makers. The AMRnet platform aims to make publicly available genome-derived AMR data accessible to a diverse user base. The underlying data are drawn from public genomic databases and used to calculate pooled estimates of national annual prevalence that can be visualized interactively, and broken down and explored in terms of underlying pathogen variants, resistance mechanisms, and geographic and temporal distributions. Users can download dynamically generated reports, summary and line-list data from the web-based dashboard (https://www.amrnet.org), and query the database via application programming interface. For selected organisms, data are curated for purpose of sampling, to reduce the public data bias towards sequencing of resistant or severe infections. By improving the accessibility and utility of publicly archived data, AMRnet aims to encourage wider sequencing initiatives and collaborative data-sharing efforts while providing crucial data insights for researchers and policy makers.
(© The Author(s) 2025. Published by Oxford University Press.)