plsMD：一种基于短读组装的质粒重建工具
plsMD: a plasmid reconstruction tool from short-read assemblies.
摘要(中文译文)
尽管全基因组测序已成为抗菌药物耐药性监测的基石，但由于重复序列和组装片段化的问题，从短读长数据中重建质粒序列仍然是一项挑战。当前用于质粒识别和分箱的计算工具在重建完整质粒序列方面存在局限，阻碍了系统发育研究和抗菌药物耐药基因追踪等下游分析。我们提出了plsMD，一种专为从短读长组装结果中进行完整质粒重建而设计的工具。plsMD将Unicycler组装结果与复制子和完整质粒序列数据库相结合，通过一系列重叠群操作指导质粒重建。使用两个数据集——一个既往基准研究中使用的成熟基准数据集和一个由新测序细菌分离株组成的新数据集——plsMD在两个数据集上均优于现有工具。在基准数据集中，其召回率、精确率和F1分数分别达到91.3%、95.5%和92.0%，表现优异。在新数据集中，其召回率、精确率和F1分数分别为77.6%、88.9%和74.5%。plsMD支持两种使用模式：用于质粒重建和基因注释的单样本分析，以及用于质粒传播系统发育研究的批样本分析。plsMD代表了质粒分析领域的重大进步，为利用现有短读长全基因组测序数据研究质粒介导的抗菌药物耐药性传播和进化提供了稳健的解决方案。
Abstract
While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tools for plasmid identification and binning have limitations in reconstructing full plasmid sequences, hindering downstream analyses like phylogenetic studies and antimicrobial resistance gene tracking. We present plsMD, a tool designed for full plasmid reconstruction from short-read assemblies. plsMD integrates Unicycler assemblies with replicon and full plasmid sequence databases to guide plasmid reconstruction through a series of contig manipulations. Using two datasets - an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates - plsMD outperformed existing tools in both. In the benchmark dataset, it achieved excellent recall, precision, and F1 scores of 91.3%, 95.5%, and 92.0%, respectively. In the novel dataset, it achieved recall, precision, and F1 scores of 77.6, 88.9 and 74.5%, respectively. plsMD supports two usage modalities: single-sample analysis for plasmid reconstruction and gene annotation, and batch-sample analysis for phylogenetic investigations of plasmid transmission. plsMD represents a significant advancement in plasmid analysis, offering a robust solution for utilizing existing short-read whole genome sequencing data to study plasmid-mediated antimicrobial resistance spread and evolution.
如何引用
AMA
Maryam Lotfi, Deena Jalal, Ahmed A Sayed. plsMD: a plasmid reconstruction tool from short-read assemblies.. BMC bioinformatics. 2026; doi:10.1186/s12859-026-06585-y.
APA
Maryam Lotfi, Deena Jalal, Ahmed A Sayed (2026). plsMD: a plasmid reconstruction tool from short-read assemblies.. BMC bioinformatics. https://doi.org/10.1186/s12859-026-06585-y
GB/T 7714
Maryam Lotfi, Deena Jalal, Ahmed A Sayed. plsMD: a plasmid reconstruction tool from short-read assemblies.[J]. BMC bioinformatics, 2026 doi:10.1186/s12859-026-06585-y.
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