Impact of direct from clinical sample sequencing assays for infectious diseases diagnostics: A single-centre retrospective cohort study

Background: The analytical performance of bacterial targeted sequencing (BTS), fungal targeted/panfungal sequencing (FTS), and metagenomic next-generation sequencing (mNGS) assays has been previously evaluated and their clinical use is increasing. Limited evidence is available on their true clinical impact on infectious disease diagnosis and treatment. Methods: We conducted a 3-year retrospective cohort study including all patients for whom broad-range sequencing assays were performed directly from clinical samples for the detection of bacterial and fungal pathogens. The operational characteristics, diagnostic and therapeutic impacts of the assays were assessed by reviewing patient clinical files and laboratory information system charts. Results: 279 samples from 185 patients were included. The positivity rates for BTS, FTS, and mNGS were respectively 20.5% (47/229), 20% (9/45), and 20% (1/5). Of these 279 samples, 40 (14.3%) had an impact on patient management. The test results helped to establish a diagnosis in 26 (9.3%) cases and led to treatment modifications in 14 (5%). FTS achieved higher impact rates (26.7%) than both BTS (12.2%) and mNGS (0%). Short turnaround times increase impact rates, and the most impactful tests were those performed on bone and intervertebral disc samples, or in patients with negative culture results due to prior antibiotic administration. Conclusion: In this study, the overall diagnostic impact of BTS and FTS was high. Both the diagnostic and treatment impact of those assays can be increased if prescribed in well-selected clinical syndromes and performed on well-selected clinical samples.