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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

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Overview

Paper Summary › Explain Like I'm Five › Conflicts of Interest › Identified Limitations › Rating Explanation › Good to know › Topic Hierarchy › File Information ›

Paper Summary

Paperzilla title
AMRFinderPlus: A Supercharged Tool to Detect Drug Resistance and More in Bacterial Baddies

This paper describes AMRFinderPlus, an enhanced tool for identifying antimicrobial resistance, stress response, and virulence genes in bacterial genomes. AMRFinderPlus uses a curated database, HMMs, and a hierarchical naming system to accurately detect and classify genes, including point mutations. Validation tests using Salmonella datasets showed high concordance with previous results and highlighted the tool's ability to analyze closed plasmid sequences and whole-genome shotgun assemblies.

Explain Like I'm Five

Scientists made a special computer tool that helps them find the hidden instructions inside tiny germs. These instructions tell the germs how to fight off medicine, handle tough times, or make people sick.

Possible Conflicts of Interest

This work was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health. The authors declare no competing interests.

Identified Limitations

Limited Validation Datasets
The validation of AMRFinderPlus was limited to two datasets, both focused on Salmonella. While the tool's performance was consistent with previous findings, a broader range of bacterial species and resistance mechanisms needs to be tested for robust validation.
Limitations of Draft Assemblies
The reliance on draft assemblies for genome analysis introduces limitations, as demonstrated by the inability to recover duplicate blaCMY-2 genes. Draft assemblies may not accurately represent the true genomic content, potentially leading to misinterpretations of resistance mechanisms.
Bias in Gene Catalog
The study primarily focuses on foodborne pathogens, leading to a bias in the virulence and stress response genes included in the Reference Gene Catalog. Expanding the catalog to encompass a wider range of bacterial species and their associated genes would enhance its applicability and utility.
Database Limitations
AMRFinderPlus relies on a manually curated protein database and HMMs, which may not capture all possible resistance mechanisms, especially novel or emerging ones. Continuous updates and refinement of the database are crucial to maintain its accuracy and comprehensiveness.

Rating Explanation

This paper presents a valuable tool, AMRFinderPlus, with enhanced capabilities for detecting antimicrobial resistance genes, stress response genes, and virulence genes. The comprehensive database and improved functionality represent a significant advancement in genomic analysis, despite a few limitations. The study is clearly described and well-executed, with rigorous methodology and appropriate validation.

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File Information

Original Title: AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
Uploaded: July 14, 2025 at 10:52 AM
Privacy: Public