Potential clinical actionability of metagenomic next-generation sequencing for antimicrobial stewardship for urinary tract infections: a retrospective, single-centre, BI-Biotia UTI cohort study.

OBJECTIVES

Culture and antimicrobial susceptibility testing (AST) take 48-72 hours, leaving empirical therapy for urinary tract infections (UTIs) without resistance data. Metagenomic next-generation sequencing (mNGS) reports resistance within hours, but its potential clinical actionability for prescribing is underexplored.

METHODS

In a retrospective single-centre cohort (Bangkok tertiary hospital, 2018-2020), BIOTIA-DX results were compared with culture and AST in 251 culture-paired samples. Potential clinical actionability was assessed for 54 same-day empirical prescriptions and a post hoc ablation estimated what a rule-based policy would have prescribed under different information from mNGS.

RESULTS

Twenty-two of 54 prescriptions (40·7%, 95% CI 28·7-54·0) were potentially actionable: treatment failure prevention 9 (16·7%) and de-escalation 13 (24·1%). Excluding blaEC and blaACT raised cephalosporin specificity from 25·6% to 78·9% with a small tradeoff in sensitivity. NPVs were at least 89·7% for carbapenems, cephalosporins, trimethoprim/sulfamethoxazole, aminoglycosides and the fluoroquinolone classifier reached 100·0% PPV in Escherichia coli. Our refined resistance classification rules achieved a good tradeoff between the risk of ineffective antibiotics and the use of broad-spectrum carbapenem, compared with observed prescribing.

CONCLUSIONS

In a high-resistance setting, a same-day mNGS report was potentially actionable for two in five empirical prescriptions, mainly through resistance calling. However, the findings rest on a small number of cases.