Prophage density predicts AMR repertoire breadth

Claim

Species with higher prophage marker density tend to carry broader AMR repertoires. This makes prophage context a first-class covariate for AMR ecology, even when direct phage-mediated transfer is not proven.

Review Brief

What changed: mobile context moved from a generic AMR caveat to a measurable predictor of AMR repertoire breadth.

Why review matters: this claim is useful for modeling but easy to overread as direct phage-mediated transfer. Reviewers should confirm that the page keeps association, covariate value, and mechanism separate.

Evidence to inspect:

• Species-level association between prophage marker density and AMR breadth.
• Genome-count control in the species-level model.
• Threshold sensitivity of AMR-prophage proximity.
• Marker limitations from keyword and Pfam-based prophage detection.

Questions for reviewers:

• Should prophage density be required as a covariate in metal-AMR co-selection analyses?
• Is "predicts AMR repertoire breadth" the right wording, or should the claim be narrowed to "is associated with"?
• Which follow-up caller or distance metric would most improve confidence?
• Does this result warrant a derived mobile-context feature product?

Evidence

prophage_amr_comobilization reports that prophage density explains a substantial share of AMR breadth across thousands of species and remains associated after controlling for genome count. Gene-level proximity between AMR genes and prophage markers exists but is smaller, heterogeneous, and sensitive to the distance threshold.

Why It Matters

AMR topic pages should no longer treat "mobile context" as a generic caveat. Prophage burden is now a concrete explanatory variable and a likely confound for metal-AMR co-selection analyses.

Caveats

The project uses keyword and Pfam prophage markers rather than a dedicated prophage caller, and gene distances are ordinal gene positions rather than base-pair distances. The result supports ecological association and prioritization, not proof of transfer mechanism.

Promotion Criteria

Promote this claim if reviewers agree that the current evidence supports a predictive covariate claim. Keep it draft if the wording needs to wait for dedicated prophage calls, base-pair distances, or plasmid/ICE partitioning.