Publication: Application of hAMRonization Tool in Investigating Anti-microbial Resistance Genes to Generate Harmonized Reports
Date
2023
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Kathmandu University
Abstract
ABSTRACT
Background
Antimicrobial resistance has become a serious threat to global public health, with the
potential to cause significant morbidity and mortality. Therefore, the detection and
surveillance of antimicrobial resistance genes are critical to monitor the prevalence
of resistance and to guide appropriate treatment decisions. Several bioinformatics
tools have been developed to facilitate the detection and investigation of
antimicrobial resistance genes from sequencing data. However, these tools often
require a significant amount of manual curation and provide results which can limit
their intra-operability, accessibility and usability. This lack of standardization in
the reporting of antimicrobial resistance genes investigation greatly hinders the
comparison of results across the public health sector.
Method
This study focuses on the application of hAMRonize tool developed by Public
Health Alliance for Genomic Epidemiology. In this study, we have implemented
hAMRonization to evaluate antimicrobial resistance genes in Salmonella and
compared to the results from other tools (ARIBA, RGI, amrfinderplus and abricate).
Result
We observed that hAMRonize was more comprehensive than other tools in
predicting genes, including information on antimicrobials, drug classes, and start and
end base pair of genes, among others. The hAMRonize tool also provided results in
an interactive Hypertext Markup Language format.
Conclusion
hAMRonization is an innovative tool for investigating and sharing antimicrobial
resistance data in the current field of research, where scientists use a plethora of
prediction tools that provide different results and subsequent interpretations.
KEY WORDS
Antimicrobial resistance, Gene-prediction, hAMRonize
Description
Katuwal N,1-3 Tamrakar D,1,3,4 Shrestha R1-3,5
1Center for Infectious Disease Research andSurveillance
Dhulikhel Hospital, Kathmandu
University Hospital, Dhulikhel, Nepal
2Molecular and Genome Sequencing Research Lab
Dhulikhel Hospital, Kathmandu University Hospital
Dhulikhel, Nepal
3Research and Development Division, Dhulikhel
Hospital, Kathmandu University Hospital, Dhulikhel
Nepal
4Department of Community Medicine, Kathmandu
University School of Medical Sciences, Dhulikhel
Nepal
5Department of Pharmacology
Kathmandu University School of Medical Sciences, Dhulikhel
Nepal
Keywords
Antimicrobial resistance, Gene-prediction, hAMRonize