Genomic Diversity, Antimicrobial Resistance, and Mobile Genetic Elements in Clinical Isolates of the Stenotrophomonas maltophilia Complex from a University Hospital in Thailand: A Whole-Genome Sequencing Study

Background/Objectives: The Stenotrophomonas maltophilia complex (Smc) comprises opportunistic bacteria with substantial antimicrobial resistance and genomic diversity. This study investigated the antimicrobial susceptibility and genomic characteristics of clinical Smc isolates from a university hospital in Thailand. Methods: Fifty clinical isolates underwent broth microdilution susceptibility testing and whole-genome sequencing. Analyses included average nucleotide identity, digital DNA–DNA hybridization, multilocus sequence typing, screening for resistance- and virulence-associated genes, prediction of mobile genetic elements, and SNP-based phylogenetic analysis. Results: Forty-nine isolates were assigned to eight species, and the remaining isolate, which could not be resolved at the species level, was designated Stenotrophomonas sp. The predominant groups were S. maltophilia and S. sepilia (n = 14 each), followed by S. hibiscicola (n = 12). Resistance to trimethoprim–sulfamethoxazole and levofloxacin was detected in 14% and 16% of isolates, respectively. Thirty-six isolates (72%) were not assigned to an existing sequence type by seven-locus MLST. Phylogenetic analysis resolved eight major clades corresponding to the reported species. Resistance-associated annotations included aminoglycoside-modifying enzymes, β-lactamases, and efflux-associated proteins. Predicted mobile genetic elements varied among isolates. Conclusions: These findings describe genomic diversity and antimicrobial susceptibility in a single-hospital collection of clinical Smc isolates from Thailand. They provide a foundation for genomic surveillance and the investigation of resistance-associated features. Broader sampling and functional validation are needed to establish the clinical significance of the predicted genomic features.