Targeted next-generation sequencing in lower respiratory tract infections: scope-matched comparison with conventional microbiological testing and antimicrobial regimen adjustments

Targeted next-generation sequencing (tNGS) may broaden reported organism detection in lower respiratory tract infections (LRTIs). However, conventional microbiological testing (CMT) is selectively ordered and has variable target coverage in routine care. The incremental detection yield of tNGS is therefore difficult to estimate, and how tNGS findings are incorporated into antimicrobial prescribing remains incompletely characterized. This single-center retrospective study included 404 hospitalized adults with clinically diagnosed LRTIs who underwent tNGS. Reported organism detection with tNGS and available CMT was summarized in the overall routine-care cohort. The paired comparison subcohort included 156 patients who completed all CMT components required for scope matching during the same diagnostic episode; patient-level comparisons were restricted to corresponding CMT-covered targets. The antimicrobial-adjustment analysis included 125 patients with a tNGS-positive final clinical report after excluding tuberculosis. In the overall routine-care cohort, tNGS and available CMT were positive in 337/404 patients (83.4%) and 183/404 patients (45.3%), respectively. After scope matching, tNGS positivity remained higher than CMT positivity in the paired comparison subcohort (75.0% versus 58.3%; p < 0.001). Among 44 retained CMT-covered targets, at least one positive result was observed for 40 by tNGS and 24 by CMT. In addition, tNGS detected 17 distinct organism types outside the corresponding CMT scope. Among the 125 patients in the antimicrobial-adjustment analysis, 78 (62.4%) underwent a tNGS-informed antimicrobial regimen adjustment, and 73 (93.6%) adjustments occurred on the report date or the following calendar day. In hospitalized adults with LRTIs, tNGS showed a higher patient-level positivity rate than corresponding CMT after scope matching, and its findings frequently informed antimicrobial regimen decisions. These findings support tNGS as a complement to CMT and clinical assessment, but do not establish diagnostic accuracy or treatment benefit. Not applicable.