National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway.
J Antimicrob Chemother. 2021 Jan 1;76(1):101-109. doi: 10.1093/jac/dkaa390.
Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community.
The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids.
MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica.
MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.
临床上相关细菌的抗生素耐药性（AMR）是对全球公共健康的一个日益严重的威胁。在这些细菌中，抗生素耐药基因通常与移动遗传元件（MGEs）相关联，这些元件促进了它们的移动性，使它们能够在细菌群落中迅速传播。
开发了工具 MobileElementFinder，以实现快速检测组装序列数据中的 MGEs 及其遗传背景。MGEs 是根据与包含注释的耐药基因、毒力因子和质粒检测的 4452 个已知元件数据库的序列相似性来检测的。
MobileElementFinder 被应用于分析来自丹麦、德国和美国的 1725 株动物源沙门氏菌分离株的可移动组。我们发现，根据多位点 ST，MGEs 似乎是保守的，而不受宿主或起源国的限制。此外，我们鉴定了特定氨基糖苷类、磺胺类和四环素基因的潜在可转移单元。预测了几个潜在的复合转座子，它们可以移动 AMR、金属抗性和与巨噬细胞存活相关的磷酸二酯酶基因等。据我们所知，这是首次发现磷酸二酯酶样 pdeL 有可能被转移到沙门氏菌中。
MobileElementFinder 是一种强大的工具，可用于研究大量基因组序列中 MGEs 的流行病学，并确定细菌基因组可塑性的潜力。该网络服务提供了一种方便的方法来检测组装序列数据中的 MGEs。可以在 https://cge.cbs.dtu.dk/services/MobileElementFinder/ 访问 MobileElementFinder。
