resistancebank.org, an open-access repository for surveys of antimicrobial resistance in animals

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Abstract

Antimicrobial resistance (AMR) is a growing threat to the health of humans and animals that requires global actions. In high-income countries, surveillance systems helped inform policies to curb AMR in animals. In low- and middle-income countries (LMICs), demand for meat is rising, and developing policies against AMR is urgent. However, surveillance of AMR is at best nascent, and the current evidence base to inform policymakers is geographically heterogeneous. We present resistancebank.org, an online platform that centralizes information on AMR in animals from 1,285 surveys from LMICs. Surveys were conducted between 2000 and 2019 and include 22,403 resistance rates for pathogens isolated from chickens, cattle, sheep, and pigs. The platform is built as a shiny application that provides access to individual surveys, country-level reports, and maps of AMR at 10 × 10 kilometers resolution. The platform is accessed via any internet browser and enables users to upload surveys to strengthen a global database. resistancebank.org aims to be a focal point for sharing AMR data in LMICs and to help international funders prioritize their actions.

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Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.

A-P Magiorakos, A. Srinivasan, R.B. Carey … (2012)

Many different definitions for multidrug-resistant (MDR), extensively drug-resistant (XDR) and pandrug-resistant (PDR) bacteria are being used in the medical literature to characterize the different patterns of resistance found in healthcare-associated, antimicrobial-resistant bacteria. A group of international experts came together through a joint initiative by the European Centre for Disease Prevention and Control (ECDC) and the Centers for Disease Control and Prevention (CDC), to create a standardized international terminology with which to describe acquired resistance profiles in Staphylococcus aureus, Enterococcus spp., Enterobacteriaceae (other than Salmonella and Shigella), Pseudomonas aeruginosa and Acinetobacter spp., all bacteria often responsible for healthcare-associated infections and prone to multidrug resistance. Epidemiologically significant antimicrobial categories were constructed for each bacterium. Lists of antimicrobial categories proposed for antimicrobial susceptibility testing were created using documents and breakpoints from the Clinical Laboratory Standards Institute (CLSI), the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the United States Food and Drug Administration (FDA). MDR was defined as acquired non-susceptibility to at least one agent in three or more antimicrobial categories, XDR was defined as non-susceptibility to at least one agent in all but two or fewer antimicrobial categories (i.e. bacterial isolates remain susceptible to only one or two categories) and PDR was defined as non-susceptibility to all agents in all antimicrobial categories. To ensure correct application of these definitions, bacterial isolates should be tested against all or nearly all of the antimicrobial agents within the antimicrobial categories and selective reporting and suppression of results should be avoided. © 2011 European Society of Clinical Microbiology and Infectious Diseases. No claim to original US government works.

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The global distribution and burden of dengue

Samir Bhatt, Peter W. Gething, Oliver J Brady … (2013)

Dengue is a systemic viral infection transmitted between humans by Aedes mosquitoes 1 . For some patients dengue is a life-threatening illness 2 . There are currently no licensed vaccines or specific therapeutics, and substantial vector control efforts have not stopped its rapid emergence and global spread 3 . The contemporary worldwide distribution of the risk of dengue virus infection 4 and its public health burden are poorly known 2,5 . Here we undertake an exhaustive assembly of known records of dengue occurrence worldwide, and use a formal modelling framework to map the global distribution of dengue risk. We then pair the resulting risk map with detailed longitudinal information from dengue cohort studies and population surfaces to infer the public health burden of dengue in 2010. We predict dengue to be ubiquitous throughout the tropics, with local spatial variations in risk influenced strongly by rainfall, temperature and the degree of urbanisation. Using cartographic approaches, we estimate there to be 390 million (95 percent credible interval 284-528) dengue infections per year, of which 96 million (67-136) manifest apparently (any level of clinical or sub-clinical severity). This infection total is more than three times the dengue burden estimate of the World Health Organization 2 . Stratification of our estimates by country allows comparison with national dengue reporting, after taking into account the probability of an apparent infection being formally reported. The most notable differences are discussed. These new risk maps and infection estimates provide novel insights into the global, regional and national public health burden imposed by dengue. We anticipate that they will provide a starting point for a wider discussion about the global impact of this disease and will help guide improvements in disease control strategies using vaccine, drug and vector control methods and in their economic evaluation. [285]

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Nextstrain: real-time tracking of pathogen evolution

James Hadfield, Colin Megill, Sidney Bell … (2018)

Abstract Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualization platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, open to health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

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Author and article information

Contributors

Nicola G. Criscuolo:

ORCID: http://orcid.org/0000-0002-0394-0888

nicola.criscuolo@usys.ethz.ch

Journal

Journal ID (nlm-ta): Sci Data

Journal ID (iso-abbrev): Sci Data

Title: Scientific Data

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2052-4463

Publication date (Electronic): 22 July 2021

Publication date PMC-release: 22 July 2021

Publication date Collection: 2021

Volume: 8

Electronic Location Identifier: 189

Affiliations

[1 ]GRID grid.5801.c, ISNI 0000 0001 2156 2780, Institute for Environmental Decisions, ETH Zürich, ; Zurich, Switzerland

[2 ]GRID grid.511514.5, Center for Disease Dynamics, Economics and Policy, ; New Delhi, India

Author information

Nicola G. Criscuolo http://orcid.org/0000-0002-0394-0888

João Pires http://orcid.org/0000-0001-9738-4423

Cheng Zhao http://orcid.org/0000-0002-3176-0593

Thomas P. Van Boeckel http://orcid.org/0000-0002-6556-0952

Article

Publisher ID: 978

DOI: 10.1038/s41597-021-00978-9

PMC ID: 8298417

PubMed ID: 34294731

SO-VID: 348cf93b-7a75-46d3-814b-3dfcdde1786a

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 25 September 2020

Date accepted : 29 June 2021

Funding

Funded by: Branco Weiss Fellowship

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Keywords: epidemiology,antimicrobial resistance,bacterial infection,health policy

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Keywords: epidemiology, antimicrobial resistance, bacterial infection, health policy

resistancebank.org, an open-access repository for surveys of antimicrobial resistance in animals

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Most cited references 53

Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.

The global distribution and burden of dengue

Nextstrain: real-time tracking of pathogen evolution

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