{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T06:09:48Z","timestamp":1783922988131,"version":"3.55.0"},"reference-count":119,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Stenotrophomonas<\/jats:italic>\n                      spp. are increasingly recognized opportunistic pathogens characterized by intrinsic multidrug resistance. Despite recent taxonomic reclassification and the delineation of new species within the\n                      <jats:italic>S. maltophilia<\/jats:italic>\n                      complex (Smc), routine diagnostics often misidentify these species, and their distinctive antibiotic resistance traits and genetic makeup remain underexplored. We aimed to characterize the phylogenomic diversity, genotypic and phenotypic antibiotic resistance traits, virulence markers and horizontally transferrable elements in a large national cohort of clinical\n                      <jats:italic>Stenotrophomonas<\/jats:italic>\n                      isolates.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We analyzed 323 clinical isolates from the Russian sentinel surveillance program (2002\u20132021). Analysis included MALDI-TOF MS identification, broth microdilution susceptibility testing to six agents [aztreonam-avibactam, colistin, levofloxacin, minocycline, tigecycline, and trimethoprim-sulfamethoxazole (TMP-SMX)], and long-read Nanopore WGS with hybrid polishing. We performed average nucleotide identity (ANI)-based classification, core- and accessory-genome comparisons, and comprehensive profiling of antibiotic resistance genes (ARGs), virulence factors (VFs), plasmids, and prophages.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      While MALDI-TOF MS identified all isolates as\n                      <jats:italic>S. maltophilia<\/jats:italic>\n                      , ANI (\u226595% threshold) and core-genome phylogeny revealed 17 distinct species: 52%\n                      <jats:italic>S. maltophilia<\/jats:italic>\n                      sensu stricto, 36.8% across eight other ICNP-named Smc species, and 11.2% within eight \u201cnovel\u201d genomic lineages identified elsewhere. Pan-genome comprised 24,815 genes (9.6% core genes), with accessory genes showing robust species-level clustering in UMAP. TMP-SMX resistance was prevalent (40.2%) among all species, though only 13.1% of resistant isolates harbored\n                      <jats:italic>sul<\/jats:italic>\n                      genes. Intrinsic \u03b2-lactamase genes (\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>L1<\/jats:sub>\n                      - and\n                      <jats:italic>bla<\/jats:italic>\n                      <jats:sub>L2<\/jats:sub>\n                      -like) were ubiquitous but exhibited high sequence variability (up to 20.6% and 25.1%) and evidence of inter-species exchange. Phosphoethanolamine transferase genes (\n                      <jats:italic>mcr<\/jats:italic>\n                      -5- and\n                      <jats:italic>mcr<\/jats:italic>\n                      -8-like) were identified as intrinsic chromosomal components. Acquired ARGs were primarily associated with chromosomal integrative conjugative and mobilizable elements (ICEs\/IMEs). Plasmids (2.5 to &amp;gt;334 kb) were identified in 8% of isolates across 10 species, including a cluster of eight nearly identical replicons distributed among five species despite lacking canonical mobilization genes. Prophages were ubiquitous (median: 4 per genome), dominated by\n                      <jats:italic>Caudoviricetes<\/jats:italic>\n                      and\n                      <jats:italic>Inoviridae<\/jats:italic>\n                      . Several VFs linked to motility, capsule formation, and invasion\/toxicity were universally present across the genus.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Our findings demonstrate that current routine diagnostics fail to resolve the significant taxonomic diversity within clinical\n                      <jats:italic>Stenotrophomonas<\/jats:italic>\n                      isolates, leading to widespread species misidentification. Integrating the genomic and phenotypic insights from this study into routine surveillance is essential to overcome these diagnostic limitations and to modernize the clinical management of infections caused by this formidable genus.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1854839","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T05:32:53Z","timestamp":1783920773000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic phylogeny, taxonomic classification, genetic landscape, and antibiotic resistance of clinical Stenotrophomonas isolates"],"prefix":"10.3389","volume":"17","author":[{"given":"Valery V.","family":"Shapovalova","sequence":"first","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elvira R.","family":"Shaidullina","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natali V.","family":"Ivanchik","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Igor V.","family":"Chebotar","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna V.","family":"Mikotina","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aida N.","family":"Chagaryan","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena Y.","family":"Skleenova","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilya S.","family":"Azizov","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey V.","family":"Romanov","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrey V.","family":"Dekhnich","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roman S.","family":"Kozlov","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikhail V.","family":"Edelstein","sequence":"additional","affiliation":[{"name":"Institute of Antimicrobial Chemotherapy, Smolensk State Medical University","place":["Smolensk, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/nar\/gkac920","article-title":"CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database","volume":"51","author":"Alcock","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"B2","unstructured":"Andrews\n              S.\n            \n          \n          FastQC\n          \n          2010"},{"key":"B3","doi-asserted-by":"publisher","first-page":"e000093","DOI":"10.1099\/mgen.0.000093","article-title":"Microreact: visualizing and sharing data for genomic epidemiology and phylogeography","volume":"2","author":"Argim\u00f3n","year":"2016","journal-title":"Microb. 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