Phylogenetic divergence drives distinct antimicrobial susceptibility profiles and resistomes in Stenotrophomonas

Stenotrophomonas is a genus of increasing clinical and industrial importance, yet comprehensive antimicrobial susceptibility data and the major influencing factors are lacking, especially for species beyond Stenotrophomonas maltophilia.

In this study, the antibiotic susceptibility of 21 average nucleotide identity (ANI) species that were relatively evenly distributed across the genus-level ANI clustering tree was tested, and the relationship between the antibiotic resistance gene profiles and phylogenetic divergence was investigated.

Among the 17 drugs tested, tigecycline showed 100% susceptibility, followed by chloramphenicol and trimethoprim-sulfamethoxazole (7.69% resistance). Cefotaxime had the highest resistance (97.44%), while ceftazidime and ceftazidime/avibactam showed 41.03% resistance. The overall multidrug resistance (MDR) rate was 74.36%. All strains harbored the SmeTDEF and AdeFGH multidrug efflux systems, while Smc-sgn strains commonly carried class A and B β-lactamases (blaL1 and blaL2), aminoglycoside resistance genes aph(3')-IIc_1, aph(6)-Smalt, aph(9)-Ic), and quaternary ammonium compound resistance genes (qacG/J). MDR phenotypes, resistance gene distributions, and integrity of the smeTDEF operon differed significantly between Smc-sgn and non-Smc-sgn strains, aligning closely with the clades resolved in the ANI-based phylogenetic tree.

Based on this study, preliminary insights into the comprehensive antibiotic resistance profiles and genetic mechanisms of Stenotrophomonas have been gained. Unlike S. maltophilia, MDR and resistance to β-lactam antibiotics are not universal characteristics across the genus. Genetic clade background may serve as the primary determinant and driving force of multidrug resistance within this genus. Tigecycline, chloramphenicol, and SXT can be considered as broad-spectrum options for emergency or empirical treatment of Stenotrophomonas infections and should be prioritized in future clinical data collection to inform antibiotic treatment guidelines.