{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T05:07:11Z","timestamp":1789103231617,"version":"build-2803163510"},"reference-count":42,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005322","name":"Recep Tayyip Erdogan \u00dcniversitesi","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"\n Background<\/jats:title>\n \n Stenotrophomonas maltophilia<\/jats:italic>\n is an opportunistic nosocomial pathogen with intrinsic multidrug resistance and limited therapeutic options. This study integrated phenotypic susceptibility testing, targeted molecular screening, PFGE and short-read whole-genome sequencing (WGS) to characterize resistance determinants and their local genomic context in clinical-culture isolates.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n Thirty-four non-duplicate clinical-culture isolates were analyzed. Susceptibility to trimethoprim-sulfamethoxazole (TMP-SMX), levofloxacin and minocycline was determined by disk diffusion. Minocycline testing was repeated with acceptable quality control, and the repeat-run zone records were reassessed using current CLSI breakpoints. A predefined, hypothesis-driven PCR panel was used to screen selected resistance-, efflux- and biofilm-associated targets, and\n gyrA<\/jats:italic>\n ,\n gyrB<\/jats:italic>\n ,\n parC<\/jats:italic>\n and\n parE<\/jats:italic>\n were sequenced. Genetic relatedness was assessed by\n Xba<\/jats:italic>\n I-PFGE. Three selected isolates (S05, S08 and S25) underwent WGS as a targeted genomic-context analysis rather than a whole-collection population-genomic study.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n Resistance rates were 5.9% for TMP-SMX, 8.8% for levofloxacin and 11.8% for minocycline after reassessment using current CLSI minocycline breakpoints.\n Smqnr<\/jats:italic>\n - and\n sul1<\/jats:italic>\n -target PCR positivity was observed in 61.8% and 8.8% of isolates, respectively. A\n dfrA27<\/jats:italic>\n -target PCR amplicon was observed in 82.4% of isolates but was not associated with TMP-SMX resistance and was not confirmed in the three sequenced genomes. No QRDR hotspot mutations were identified. The two TMP-SMX-resistant isolates, S05 and S08, shared the same PFGE genotype. Short-read WGS identified an identical 19,361-bp mobile-element-associated resistance region in these isolates, containing a putative Sul-family\/\n folP<\/jats:italic>\n -like dihydropteroate synthase (DHPS) annotation, two assembly-predicted hits each of\n \n bla\n OXA-2<\/jats:sub>\n <\/jats:italic>\n and\n ant(3\u2019\u2019)<\/jats:italic>\n , multiple insertion sequences and a mercury-resistance module; the region was absent from S25.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusions<\/jats:title>\n \n The identical resistance region in two TMP-SMX-resistant isolates sharing the same PFGE genotype is compatible with shared ancestry, vertical inheritance or persistence of an island-carrying PFGE-defined genotype; horizontal transfer was not demonstrated. The discordance between\n dfrA27<\/jats:italic>\n -target PCR positivity, phenotype and WGS highlights the need to interpret molecular screening together with phenotypic susceptibility and orthogonal confirmation. The WGS component provides a local genomic-context characterization rather than evidence of cross-genotype dissemination.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.3389\/fcimb.2026.1926102","type":"journal-article","created":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T04:35:41Z","timestamp":1789101341000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic characterization of a mobile-element-associated resistance island in trimethoprim-sulfamethoxazole-resistant Stenotrophomonas maltophilia isolates sharing the same PFGE genotype"],"prefix":"10.3389","volume":"16","author":[{"given":"G\u00fcl\u015fah","family":"Altan","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology, Faculty of Medicine, Kocaeli University","place":["Kocaeli, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erva","family":"Rak\u0131c\u0131","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdo\u011fan University","place":["Rize, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devrim","family":"D\u00fcndar","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Faculty of Medicine, Kocaeli University","place":["Kocaeli, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osman Birol","family":"\u00d6zg\u00fcm\u00fc\u015f","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Faculty of Medicine, Recep Tayyip Erdo\u011fan University","place":["Rize, T\u00fcrkiye"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2023.1163439","article-title":"Global prevalence and antibiotic resistance in clinical isolates of Stenotrophomonas maltophilia: a systematic review and meta-analysis","volume":"10","author":"Banar","year":"2023","journal-title":"Front. 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