AMRsummary

What does it do?

Use AMRsummary to detect acquired antimicrobial-resistance genes in FASTA-formatted draft genome assemblies, predict plasmid contigs, and summarize whether detected AMR genes are located on a predicted plasmid or chromosome.

AMRsummary combines:

  • ResFinder — detects acquired AMR genes in draft genome assemblies;
  • MOB-suite mob_recon — reconstructs and types predicted plasmids from draft genome assemblies.

The Redmine ResFinder workflow does not detect resistance caused by chromosomal point mutations. Use PointFinder, StarAMR, or CARD-RGI when mutation-based resistance must also be assessed.

For additional MOB-suite output details, see the MOB-suite repository.

How do I use it?

Subject

In the Subject field, enter:

amr summary

Spelling matters, but matching is not case-sensitive.

Description

In the Description field, enter one SEQID per line:

2026-SEQ-0001
2026-SEQ-0002

Each requested SEQID must have a FASTA-formatted draft genome assembly available.

Attachments

No attachment is required. AMRsummary retrieves the assemblies associated with the requested SEQIDs.

Optional parameters

The supplied documentation does not identify optional parameters for the Redmine AMRsummary automator.

Example

2026-SEQ-0001
2026-SEQ-0002

See issue 14100 for an example AMRsummary request.

Interpreting results

AMRsummary uploads three reports.

resfinder_blastn.xlsx

This workbook lists acquired AMR genes detected in each sample. Review:

  • PercentIdentity — sequence identity between the detected gene and reference target;
  • PercentCovered — coverage of the reference target.

A hit with 100 for both identity and coverage provides stronger evidence that the complete acquired gene is present. Lower-identity or partially covered hits require further review. A listed gene does not by itself establish an expressed resistance phenotype.

mob_recon_summary.csv

This report lists contigs that MOB-suite predicts to be plasmid-derived. Contigs predicted to be chromosomal are omitted.

Important fields include:

  • Location — the predicted plasmid name;
  • Contig — the contig predicted to contain plasmid sequence.

A predicted plasmid can contain several contigs when it could not be circularized.

amr_summary.csv

This combined report maps the contigs containing acquired AMR-gene hits to the MOB-suite plasmid predictions. It includes the predicted location and plasmid incompatibility types when available.

The Location field reports either:

  • chromosome; or
  • the name of a predicted plasmid.

The location is a computational prediction and should be interpreted with the underlying ResFinder and MOB-suite evidence.

How long does it take?

ResFinder is fast, while MOB-suite is comparatively slower. Expect AMRsummary to take a few minutes per requested SEQID, depending on assembly size, sample count, and service workload.

What can go wrong?

A requested SEQID is unavailable

Symptom: The Redmine issue receives a warning identifying unavailable sequences.

Likely cause: AMRsummary cannot locate a draft genome assembly for the requested SEQID.

What to do: Verify each SEQID, confirm that its FASTA assembly is available, and submit a corrected request.

Expected mutation-based resistance is absent

Symptom: The report contains acquired-gene findings but not an expected chromosomal resistance mutation.

Likely cause: AMRsummary uses the Redmine ResFinder workflow, which does not detect resistance caused by chromosomal point mutations.

What to do: Use PointFinder, StarAMR, or CARD-RGI, as appropriate.

An AMR gene has an uncertain predicted location

Symptom: A detected gene cannot be confidently assigned to a predicted plasmid or chromosome.

Likely cause: Draft assemblies can fragment plasmids across contigs, and plasmid reconstruction is predictive.

What to do: Review resfinder_blastn.xlsx, mob_recon_summary.csv, and the underlying assembly evidence together before drawing conclusions.

  • ResFinder — detects acquired AMR genes in draft genome assemblies without plasmid-location summarization.
  • MobSuite — detects, reconstructs, and types predicted plasmids in draft genome assemblies.
  • Plasmid-Borne Identity — searches assemblies for user-supplied target genes and predicts whether matching targets are plasmid-borne.
  • PointFinder — detects supported chromosomal resistance mutations.