Utility of direct microorganism species identification and antimicrobial susceptibility tests in urine samples

Introduction: Urinary tract infections (UTIs) are one of the most common bacterial infections and a major cause of sepsis. It is important to promptly diagnose and treat UTIs.

Method: We found that a Gram-staining score of ≥2+ could be substituted for a colony-forming unit value of ≥10,000/mL. Using this criterion, we evaluated the performance of direct species identification (ID) and antimicrobial susceptibility testing (AST) using 233 isolates from urine.

Results: Of the 212 monomicrobial isolates, 159 (75.0%) showed spectral scores of ≥1.7 using the direct ID. Of these, 135 isolates (135/159: 84.9%) were correctly identified at the species level (spectral score ≥2.0) and 153 isolates (153/159: 96.2%) were correctly identified at the genus level (spectral score ≥1.7), indicating that direct ID may be reliable for urine samples when the spectral score is ≥1.7. GNR were identified with higher accuracy compared with GPC. The ID results of 21 polymicrobial samples were not fully consistent with the conventional method. Of the direct AST results obtained from 146 isolates, there was 97.7% (1,501/1,537) categorical agreement (CA), 0.07% (1/1,537) very major errors, 0.7% (11/1,537) major errors, and 1.4% (22/1,537) minor errors, indicating high AST capability among the various isolates, including resistant strains. Twelve extended-spectrum beta-lactamase-producing bacteria were detected in 12 isolates, indicating high CA (99.2%) with direct AST.

Conclusions: Direct ID and AST may be reliable for urine samples, but further improvements are required in order to realize accurate diagnosis and treatment, especially, for Gram-positive cocci and polymicrobial samples.