Related To

• Bactopia
• Bactopia Tools

Is this related to a problem?
The current implementation of the AMRFinderPlus module in Bactopia produces different outputs compared to the standalone AMRFinderPlus tool. Specifically, there are fewer results in the Bactopia output when analyzing genomes for mutational resistance, organism-specific filtering, and the inclusion of additional genes such as virulence and stress-response factors.

For example, when analyzing Acinetobacter baumannii genomes, the standalone AMRFinderPlus tool with the -O and --plus options identified additional rows, particularly for point mutations (e.g., gyrA, parC) and virulence-associated genes, which were missing in the Bactopia output.

Is this something you would like to see added?
Yes, I would like to see the AMRFinderPlus module in Bactopia enhanced to include:

Mutational Resistance Detection: Identifying point mutations associated with antimicrobial resistance.
Organism-Specific Filtering: Supporting the -O option to refine results based on the specified organism.
Inclusion of Additional Genes: Annotating stress-response, and related genes using the --plus option.
These features would provide a more comprehensive analysis, especially for species-specific workflows like those for Acinetobacter baumannii.

Describe the solution you'd like
Enhance the AMRFinderPlus module in Bactopia to incorporate:

Support for organism-specific filtering (-O option).
Detection of point mutations for mutational resistance.
Inclusion of additional gene annotations (e.g., stress-response genes) using the --plus option.

Additional Information
This enhancement would increase the accuracy and utility of the AMRFinderPlus module for species-specific analyses. It would allow results to better match those generated by the standalone AMRFinderPlus tool, ensuring comprehensive resistance profiling.

Thank you for considering this feature request!

Best regards,
Dejenie Shiferaw