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 genes that are involved in transfer and maintenance than other plasmids. Hence, the proportion of genes that can be readily exchanged is much smaller than suggested by the entire genome size. Additionally, we note that different plasmid types have very different biology, and hence the plasmid type is an important category to test for.