Genetic Diversity of Stenotrophomonas spp. and Its Impact on Diagnosis and Treatment of Pediatric Infections.

Stenotrophomonas maltophilia is an opportunistic, multidrug-resistant pathogen emerging in pediatric infections. Its intrinsic resistance to multiple antibiotics and genetic diversity complicates both the identification of this species and treatment strategies. We conducted genomic and phenotypic analyses of isolates of Stenotrophomonas spp. from pediatric patients to assess species diversity through multilocus sequence typing and average nucleotide identity analyses. Antimicrobial susceptibility and resistance mechanisms, particularly the sul1 gene linked to sulfonamide resistance, were investigated. Our findings revealed multiple genomospecies. Of the isolates initially identified as S. maltophilia using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry, only 58.5% were identified as such through molecular analyses. These other Stenotrophomonas species may not be standardized for antimicrobial susceptibility testing by the Clinical and Laboratory Standards Institute and the European Committee on Antimicrobial Susceptibility and Testing. The sul1 gene, carried on a mobilized class 1 integron, emerged as the primary driver of trimethoprim-sulfamethoxazole resistance, raising concerns about the rapid dissemination of resistance traits. Our findings underscore the diagnostic and therapeutic challenges posed by Stenotrophomonas spp. infections, highlighting the urgent need for enhanced molecular diagnostics for accurate species identification and resistance profiling. Continuous surveillance and updates to clinical guidelines are essential for improving infection management in pediatric patients.