ABSTRACT Stenotrophomonas is a significant opportunistic pathogen associated with high attributable mortality. Notably high isolation rates and species diversity have been observed among tuberculosis patients in Beijing, China. To determine its infection/colonization rate and characteristics in non-TB patients, we conducted a study utilizing a sensitive pre-enrichment PCR assay on pharyngeal swabs from inpatients in the Department of Infectious Diseases. Three Stenotrophomonas strains were isolated from 143 samples (2.10%), and positive cases shared common characteristics—advanced age, invasive procedures, repeated hospitalizations, and broad-spectrum antimicrobial exposure—which are established risk factors for Stenotrophomonas maltophilia infection. Both the isolation rate and common characteristics differed from those of TB patients. Notably, three isolates were identified via average nucleotide identity (ANI) as S. geniculate and S. muris , but both species were misidentified as S. maltophilia by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, despite achieving reliable identification scores (≥2.0). This misidentification likely explains the exclusive focus on S. maltophilia and the underestimation of other species absent from MALDI-TOF databases. Antibiotic susceptibility testing showed general susceptibility to quinolones, tigecycline, chloramphenicol, and trimethoprim-sulfamethoxazole and partial susceptibility to ceftazidime and ceftazidime/avibactam. Notably, a strain susceptible to ceftazidime and moxifloxacin was isolated from a patient treated with these agents. In conclusion, this study underscores the necessity of developing alternative rapid molecular methods with ANI-equivalent resolution for Stenotrophomonas , alongside expanding mass spectral databases and reevaluating the clinical significance and resistance profiles of the Stenotrophomonas species. IMPORTANCE Compounding its inherent pathogenicity, Stenotrophomonas adversely impacts co-infecting pathogens and is associated with high attributable mortality and multidrug resistance. This study demonstrates that through enrichment and PCR of throat swab samples, this elusive pathogen—frequently undetected in routine clinical testing—can be identified with high sensitivity, providing crucial diagnostic alerts for clinicians, particularly in critically ill and etiology-unknown patients. Our analysis reveals that the risk factors for Stenotrophomonas positivity differ between general infectious disease inpatients and tuberculosis patients. Furthermore, our findings highlight a critical issue of species misidentification by routine microbiological methods, which has obscured the true clinical significance and resistance profiles of Stenotrophomonas species.
Xu et al. (Wed,) studied this question.