{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T13:09:26Z","timestamp":1789736966389,"version":"4.0.1"},"reference-count":61,"publisher":"American Society for Microbiology","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Stenotrophomonas maltophilia<\/jats:italic>\n                      is an emerging multidrug-resistant opportunistic pathogen associated with high morbidity and mortality in hospitalized patients. We present an integrated genomic and phenotypic characterization of 57 clinical\n                      <jats:italic toggle=\"yes\">S. maltophilia<\/jats:italic>\n                      isolates from a tertiary care hospital in Lebanon. Whole-genome sequencing defined resistance profiles, virulence traits, and mobile genetic elements. Multilocus sequence typing revealed marked diversity across 12 known sequence types, with more than half (56%) of isolates assigned to novel or untypable STs. Five ST138 isolates were recovered from respiratory samples in critical care units, a pattern consistent with nosocomial transmission. Phenotypically, 28.1% and 3.5% of isolates were resistant to levofloxacin and trimethoprim\u2013sulfamethoxazole, respectively; 71.9% were non-susceptible to colistin; and one (1.8%) was non-susceptible to minocycline. Trimethoprim\u2013sulfamethoxazole resistance was not associated with\n                      <jats:italic toggle=\"yes\">sul1<\/jats:italic>\n                      or\n                      <jats:italic toggle=\"yes\">sul2<\/jats:italic>\n                      , and fluoroquinolone resistance was only partially explained by\n                      <jats:italic toggle=\"yes\">smeD<\/jats:italic>\n                      , pointing to multifactorial mechanisms. Virulence genes\n                      <jats:italic toggle=\"yes\">fliC<\/jats:italic>\n                      ,\n                      <jats:italic toggle=\"yes\">smf-1<\/jats:italic>\n                      , and\n                      <jats:italic toggle=\"yes\">katA<\/jats:italic>\n                      were broadly conserved, whereas biofilm formation varied markedly. Type I secretion system components\n                      <jats:italic toggle=\"yes\">hlyB<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">hlyD<\/jats:italic>\n                      occurred in a minority of isolates, with\n                      <jats:italic toggle=\"yes\">hlyD<\/jats:italic>\n                      detected on both chromosomal and plasmid loci in three. A complete type VI secretion system (T6SS) core was identified in four isolates, with VipA subtyping placing most in i4b and a divergent CASM6 variant in i3. Tn\n                      <jats:italic toggle=\"yes\">3<\/jats:italic>\n                      family transposons linked to metal resistance genes were carried by 17 isolates. Together, these findings reveal a genetically diverse population in which multifactorial resistance, heterogeneous T6SS carriage, variable biofilm capacity, and transposon-linked metal resistance converge to shape clinical adaptability, emphasizing the need for integrated surveillance to guide treatment and infection control.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Stenotrophomonas maltophilia<\/jats:italic>\n                        has emerged as an important cause of infections globally. This is largely due to its intrinsic resistance and genomic plasticity. Through integrated genomic and phenotypic characterization of 57 clinical isolates, this study reveals a highly diverse population with a stable core genome and a dynamic accessory genome shaped by mobile genetic elements. The combination of widespread intrinsic resistance, variable acquired resistance traits, and virulence factors highlights the adaptive pathogenic capacity of this organism. These results highlight the importance of combining genomic data with phenotypic analysis to better understand pathogen evolution and transmission. By providing the first comprehensive molecular overview of clinical\n                        <jats:italic toggle=\"yes\">S. maltophilia<\/jats:italic>\n                        isolates from Lebanon, this study supports the implementation of genomic surveillance frameworks and informed infection control strategies to limit the spread of this multidrug-resistant pathogen.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01344-26","type":"journal-article","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T13:00:12Z","timestamp":1789736412000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Whole-genome characterization of clinical\n                    <i>Stenotrophomonas maltophilia<\/i>\n                    in Lebanon: sequence types, resistome, and T6SS diversity"],"prefix":"10.1128","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-4029-4026","authenticated-orcid":true,"given":"Carmen","family":"Adam","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rayane","family":"Adam","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Saba","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rita","family":"Menhem","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Computer Science and Mathematics, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nareg","family":"Assadourian","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Gebrayel","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0977-1242","authenticated-orcid":true,"given":"Charbel","family":"Al Khoury","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, School of Arts and Sciences, Lebanese American University","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George F.","family":"Araj","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/04pznsd21","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology and Laboratory Medicine, American University of Beirut, Medical Center","place":["Beirut, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3653-8940","authenticated-orcid":true,"given":"Sima","family":"Tokajian","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00hqkan37","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Biological Sciences, School of Arts and Sciences, Lebanese American University","place":["Byblos, Lebanon"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/asmcr.00005-25"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmed.2023.1163439"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1155\/1996\/585141"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2163"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00019-11"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-018-3428-y"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-007-0279-3"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0153753"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-023-02950-6"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1586\/14787210.2014.864553"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.3343\/alm.2015.35.2.246"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1080\/14787210.2020.1730178"},{"key":"e_1_3_5_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01094-21"},{"key":"e_1_3_5_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.45.2.413-419.2001"},{"key":"e_1_3_5_16_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2015.00893"},{"key":"e_1_3_5_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00777-17"},{"key":"e_1_3_5_18_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2015.00041"},{"key":"e_1_3_5_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-15123-0"},{"key":"e_1_3_5_20_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.diagmicrobio.2014.11.005"},{"key":"e_1_3_5_21_2","volume-title":"Performance standards for antimicrobial susceptibility testing: 30th informational supplement","author":"Clinical and Laboratory Standards Institute","year":"2020","unstructured":"Clinical and Laboratory Standards Institute. 2020. Performance standards for antimicrobial susceptibility testing: 30th informational supplement. Clinical and Laboratory Standards Institute, Wayne, PA."},{"key":"e_1_3_5_22_2","doi-asserted-by":"publisher","DOI":"10.3791\/2437-v"},{"key":"e_1_3_5_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-0463.2007.apm_630.x"},{"key":"e_1_3_5_24_2","doi-asserted-by":"publisher","DOI":"10.3855\/jidc.17168"},{"key":"e_1_3_5_25_2","unstructured":"Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics Babraham Institute. Available from: https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc"},{"key":"e_1_3_5_26_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_3_5_27_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_5_28_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0072-8"},{"key":"e_1_3_5_29_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty266"},{"key":"e_1_3_5_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpz1.323"},{"key":"e_1_3_5_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_5_32_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_5_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02452-13"},{"key":"e_1_3_5_34_2","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11091169"},{"key":"e_1_3_5_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btab007"},{"key":"e_1_3_5_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv421"},{"key":"e_1_3_5_37_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0009490"},{"key":"e_1_3_5_38_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"key":"e_1_3_5_39_2","doi-asserted-by":"publisher","DOI":"10.1002\/cpbi.40"},{"key":"e_1_3_5_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_3_5_41_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msaa015"},{"key":"e_1_3_5_42_2","doi-asserted-by":"publisher","DOI":"10.1007\/s11427-022-2172-x"},{"key":"e_1_3_5_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.infpip.2020.100097"},{"key":"e_1_3_5_44_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2020.00411"},{"key":"e_1_3_5_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00405-19"},{"key":"e_1_3_5_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgar.2018.07.009"},{"key":"e_1_3_5_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00714-15"},{"key":"e_1_3_5_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dkt148"},{"key":"e_1_3_5_49_2","doi-asserted-by":"publisher","DOI":"10.7883\/yoken.JJID.2023.389"},{"key":"e_1_3_5_50_2","doi-asserted-by":"publisher","DOI":"10.1089\/mdr.2015.0228"},{"key":"e_1_3_5_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00496-09"},{"key":"e_1_3_5_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01981-23"},{"key":"e_1_3_5_53_2","doi-asserted-by":"publisher","DOI":"10.1503\/cmaj.111152"},{"key":"e_1_3_5_54_2","doi-asserted-by":"publisher","DOI":"10.1093\/jacamr\/dlac040"},{"key":"e_1_3_5_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/jac\/dku317"},{"key":"e_1_3_5_56_2","doi-asserted-by":"publisher","DOI":"10.1155\/2023\/8873948"},{"key":"e_1_3_5_57_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00284-022-02869-7"},{"key":"e_1_3_5_58_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0108409"},{"key":"e_1_3_5_59_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00283268"},{"key":"e_1_3_5_60_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02770-24"},{"key":"e_1_3_5_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/msphere.00584-23"},{"key":"e_1_3_5_62_2","doi-asserted-by":"publisher","DOI":"10.1139\/cjm-2018-0379"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01344-26","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.01344-26","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T13:00:14Z","timestamp":1789736414000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.01344-26"}},"subtitle":[],"editor":[{"given":"Dhammika H.","family":"Navarathna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":61,"alternative-id":["10.1128\/spectrum.01344-26"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.01344-26","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,18]]},"assertion":[{"value":"2026-04-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-08-19","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-18","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e01344-26"}}