ACORN: A Clinically Oriented antimicrobial Resistance Network - 2020 Shiny Contest Submission

ACORN: A Clinically Oriented antimicrobial Resistance Network

Authors: Olivier Celhay
Working with Shiny more than 1 year

Abstract: Antimicrobial resistance (AMR) threatens the effective prevention and treatment of an ever-increasing range of infections caused by bacteria, parasites, viruses and fungi. A Clinically Oriented antimicrobial Resistance Network (ACORN) is a Wellcome funded project led by the Mahidol-Oxford Tropical Medicine Research Unit and the Oxford University of Oxford Clinical Research Unit. Sensitive data can't be shared but the option of using a "Demo Dataset" is provided in the App.

Full Description: What is ACORN? ACORN is a Wellcome funded project led by the Mahidol-Oxford Tropical Medicine Research Unit (MORU) and the Oxford University of Oxford Clinical Research Unit (OUCRU). The pilot phase of ACORN will focus on development, implementation and assessment of enhanced antimicrobial resistance (AMR) surveillance, including collection of relevant clinical metadata and denominators, as part of routine clinical care in three hospitals in southeast Asia.

Why is ACORN needed? Existing AMR surveillance systems are based mostly on diagnostic microbiology laboratory antimicrobial susceptibility testing results alone, which limits interpretability of resistant proportions. Resulting data fail to give relevant feedback for treatment decisions for local clinicians and do not allow for direct assessment and subsequent modelling of the clinically relevant impacts and burden of drug resistant infections (DRI). Tools to capture and analyse AMR data in low- and middle-income countries (LMIC) are scarce, which hinders engagement with and use of available data.
To fill these gaps, the major aim of ACORN is to develop and test a comprehensive data capture system for patient-focussed AMR surveillance in LMIC settings. Surveillance will include diagnostic stewardship activities. Data collected will harmonise with and expand on the pathogen-focussed WHO Global Antimicrobial Resistance Surveillance System to enable accurate classification of infection syndromes and patient outcomes. These data will be of critical importance to estimate syndromic and/or pathogen outcomes and associated costs: i.e. how many people die from DRIs and how much does AMR cost?

Where is ACORN surveillance being done? The ACORN pilot will occur at Angkor Hospital for Children (Siem Reap, Cambodia), Mahosot Hospital (Vientiane, Lao PDR), and the National Hospital for Tropical Diseases (Hanoi, Vietnam).

Reason for not providing URL of RStudio Cloud project with app:
ACORN requires R >= 3.6 while RStudio Cloud is running R version 3.5.3
ERROR: this R is version 3.5.3, package 'ACORN' requires R >= 3.6


Category: Healthcare
Keywords: Public Health, Antimicrobial
Shiny app: https://moru.shinyapps.io/acornamr/
Repo: https://github.com/ocelhay/ACORN
RStudio Cloud: https://rstudio.cloud/project/197815

Thumbnail:

Full image: