{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T09:31:13Z","timestamp":1787909473653,"version":"build-2784847793"},"reference-count":104,"publisher":"MDPI AG","issue":"21","license":[{"start":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:00:00Z","timestamp":1761609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Stenotrophomonas maltophilia (S. maltophilia) is a multidrug-resistant opportunistic pathogen. There are an increasing number of case reports on S. maltophilia infections in recent years, and the species is becoming a public health concern. Many studies have focused on profiling and pangenome of the species, particularly on their antibiotic resistance and virulence genes. However, there is a lack of studies on mobile genetic elements (MGEs), a subset of pangenome that significantly contributes to the diversity, stability, and plasticity of a population. In this study, 20 genomes of S. maltophilia were downloaded from the NCBI Genome database. The genomes were subjected to profiling of MGEs, their impact on the population structures, and the evaluation of evolutionary trends of the core genomes. The cataloguing of MGEs indicated active horizontal gene transfer events in the S. maltophilia\u2019s population. Multiple virulence and drug resistance genes were predicted within and outside of the MGEs. We observed multiple chromosomal rearrangements in the genomes, most likely caused by MGEs, affecting up to approximately 50% of a single genome sequence. A high number of linkage disequilibrium sites were also predicted in the core genomes. This study provides insights into stability in the core and plasticity in the accessory regions in the S. maltophilia population.<\/jats:p>","DOI":"10.3390\/ijms262110477","type":"journal-article","created":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T17:02:01Z","timestamp":1761670921000},"page":"10477","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Comparative Analyses Suggest Genome Stability and Plasticity in Stenotrophomonas maltophilia"],"prefix":"10.3390","volume":"26","author":[{"given":"Danny Khar Chen","family":"Sum","sequence":"first","affiliation":[{"name":"Faculty of Information Science and Technology, Multimedia University, Melaka 75450, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yee Yee","family":"Chong","sequence":"additional","affiliation":[{"name":"Faculty of Information Science and Technology, Multimedia University, Melaka 75450, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8241-1879","authenticated-orcid":false,"given":"Joon Liang","family":"Tan","sequence":"additional","affiliation":[{"name":"Faculty of Information Science and Technology, Multimedia University, Melaka 75450, Malaysia"},{"name":"Center for Intelligent Cloud Computing, CoE for Advanced Cloud, Multimedia University, Melaka 75450, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1136\/bmj.a226","article-title":"The Emergence of Stenotrophomonas Maltophilia","volume":"336","author":"Johnson","year":"2008","journal-title":"BMJ"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"986","DOI":"10.1111\/j.1469-0691.2006.01511.x","article-title":"Central Venous Catheter-Related Stenotrophomonas Maltophilia Bacteraemia and Associated Relapsing Bacteraemia in Haematology and Oncology Patients","volume":"12","author":"Lai","year":"2006","journal-title":"Clin. 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