Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial-resistance genes. Here, we present Flanker, a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as ‘flank patterns’ (FPs), are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterized to fine-tune outputs by characterizing upstream and downstream regions separately, and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (bla OXA-48 and bla KPC-2/3) and show that it successfully identifies distinct clusters of FPs, including both known and previously uncharacterized structural variants. For example, Flanker identified four Tn4401 profiles that could not be sufficiently characterized using TETyper or MobileElementFinder, demonstrating the utility of Flanker for flanking-gene characterization. Similarly, using a large (n=226) European isolate dataset, we confirm findings from a previous smaller study demonstrating association between Tn1999.2 and bla OXA-48 upregulation and demonstrate 17 FPs (compared to the 5 previously identified). More generally, the demonstration in this study that FPs are associated with geographical regions and antibiotic-susceptibility phenotypes suggests that they may be useful as epidemiological markers. Flanker is freely available under an MIT license at https://github.com/wtmatlock/flanker.

中文翻译：

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Flanker：基因侧翼区域比较基因组学工具


分析感兴趣基因周围的侧翼序列通常与理解移动遗传元件 (MGE) 在水平基因转移中的作用高度相关，特别是对于抗菌素耐药基因。在这里，我们介绍了 Flanker，一个 Python 包，它以一致的格式对基因侧翼序列进行免比对聚类，允许在不事先了解 MGE 结构的情况下研究 MGE。这些簇称为“侧翼模式”(FP)，基于 Mash 距离，可以轻松比较序列之间的相似性。此外，Flanker 可以灵活地参数化，通过分别表征上游和下游区域并研究侧翼序列的可变长度来微调输出。我们将 Flanker 应用于两个最近的数据集，这些数据集描述了重要碳青霉烯酶基因（ bla OXA-48和bla KPC-2/3 ）的质粒相关携带，并表明它成功识别了不同的 FP 簇，包括已知的和以前未表征的结构变体。例如，Flanker 鉴定了四个无法使用 TETyper 或 MobileElementFinder 充分表征的 Tn 4401配置文件，这证明了 Flanker 在侧翼基因表征方面的实用性。同样，使用大型 ( n = 226) 欧洲分离株数据集，我们证实了之前一项小型研究的结果，证明了 Tn 1999.2和bla OXA-48上调之间的关联，并展示了 17 个 FP（与之前确定的 5 个相比）。 更一般地说，本研究证明 FP 与地理区域和抗生素敏感性表型相关，表明它们可能可用作流行病学标记。 Flanker 可在 MIT 许可下免费使用，网址为 https://github.com/wtmatlock/flanker。