The recent article by Che et al. (1) presents an analysis of a dataset of 14,029 plasmids. I enjoyed the paper but have some concerns about its analysis. While it is clear that more conjugative plasmids carry antimicrobial resistance (AMR) genes, it is unclear whether this is simply because conjugative plasmids tend to carry more genes in general. Specifically, Che et al. aim to determine whether the AMR gene pool is “homogeneously distributed” or “constrained” by plasmid categories. To do this, they perform a Fisher’s exact test of the proportion of AMR gene-bearing plasmids between plasmid categories. In my view, this test is insufficient by itself for investigating “enrichment”—a term which suggests differential processes of horizontal …

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质粒中基因富集的空模型 [Letters (Online Only)]

Che 等人最近的文章。( 1 ) 对 14,029 个质粒的数据集进行了分析。我喜欢这篇论文，但对它的分析有些担忧。虽然很明显更多的结合质粒携带抗菌素耐药性 (AMR) 基因，但尚不清楚这是否仅仅是因为结合质粒通常倾向于携带更多基因。具体来说，Che 等人。旨在确定 AMR 基因库是“均匀分布”还是受质粒类别“限制”。为此，他们对质粒类别之间携带 AMR 基因的质粒的比例进行了 Fisher 精确检验。在我看来，这个测试本身不足以研究“富集”——一个暗示水平的差异过程的术语……