{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T07:33:41Z","timestamp":1786692821538,"version":"build-2736575974"},"reference-count":30,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T00:00:00Z","timestamp":1786579200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"57357 Hospital"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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 \u2014 an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates \u2014 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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>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.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-026-06585-y","type":"journal-article","created":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T19:13:31Z","timestamp":1786648411000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["plsMD: a plasmid reconstruction tool from short-read assemblies"],"prefix":"10.1186","volume":"27","author":[{"given":"Maryam","family":"Lotfi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deena","family":"Jalal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed A.","family":"Sayed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,13]]},"reference":[{"issue":"4","key":"6585_CR1","doi-asserted-by":"publisher","first-page":"e00088-17","DOI":"10.1128\/CMR.00088-17","volume":"31","author":"SR Partridge","year":"2018","unstructured":"Partridge SR, Kwong SM, Firth N, Jensen SO. 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