Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids

We thank Liam Shaw for his letter (1), “Null models for gene enrichment in plasmids,” and appreciate the detailed simulation regarding the enrichment analysis of AMR genes on different types of plasmids, which confirms our original conclusions that conjugative plasmids are enriched in these genes (2). We agree that considering the plasmid size is a good point when using a null model for the enrichment analysis as it tests for a completely neutral accumulation of genes. However, using a completely neutral model for all genes on plasmids does not capture the reality of gene content constraints. Conjugative plasmids contain a much larger portion of … [↵][1]1To whom correspondence may be addressed. Email: zhangt{at}hku.hk. [1]: #xref-corresp-1-1