Abstract:
Stenotrophomonas maltophilia is an emerging multidrug-resistant opportunistic pathogen
associated with high morbidity in hospitalized patients. This study presents the
comprehensive genomic characterization of 57 clinical S. maltophilia isolates collected
from a tertiary care hospital in Lebanon. Whole-genome sequencing (WGS) and
bioinformatic analyses were conducted to determine antimicrobial resistance profiles,
virulence factors, and mobile genetic elements. Multilocus sequence typing (MLST)
revealed high genetic diversity, with isolates distributed across 12 known sequence types
(STs), and over half (56%) assigned to novel or untypeable STs. Five isolates (ST138) were
recovered from respiratory samples in critical care units, suggesting potential nosocomial
transmission. Resistance to key antimicrobials was observed: 28.1% of isolates were
resistant to levofloxacin, 3.5% to trimethoprim-sulfamethoxazole (TMP-SMX), and 71.9%
to colistin. While TMP-SMX resistance was limited, it was not always linked to common
resistance genes (e.g., sul1, sul2), suggesting alternative mechanisms. Similarly,
fluoroquinolone resistance was only partially associated with the presence of smeD,
pointing to multifactorial resistance pathways. Genomic screening showed that all isolates
harbored the efflux pump genes phoP, macA, macB, emrA, and emrB, which may
contribute to intrinsic resistance. Virulence-related genes such as fliC, smf-1, and katA were widely distributed, while biofilm assays revealed phenotypic heterogeneity despite
conserved genetic markers. Seventeen isolates carried Tn3-family transposons associated
with metal resistance genes, emphasizing the role of mobile genetic elements in adaptation
and survival. These findings reveal the complexity of S. maltophilia as a nosocomial
pathogen and highlight the need for further functional studies to elucidate resistance
mechanisms. Enhanced molecular surveillance and targeted infection control strategies are
critical to managing the spread of this highly adaptable organism in healthcare settings.
