Whole-genome characterization of clinical Stenotrophomonas maltophilia in Lebanon: sequence types, resistome, and T6SS diversity

ABSTRACT Stenotrophomonas maltophilia 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 S. maltophilia 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–sulfamethoxazole, respectively; 71.9% were non-susceptible to colistin; and one (1.8%) was non-susceptible to minocycline. Trimethoprim–sulfamethoxazole resistance was not associated with sul1 or sul2 , and fluoroquinolone resistance was only partially explained by smeD , pointing to multifactorial mechanisms. Virulence genes fliC , smf-1 , and katA were broadly conserved, whereas biofilm formation varied markedly. Type I secretion system components hlyB and hlyD occurred in a minority of isolates, with hlyD 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 3 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. IMPORTANCE Stenotrophomonas maltophilia 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 S. maltophilia 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.