Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study

Abstract

We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.

Keywords: DNA sequencing; broad-range universal PCR; molecular diagnostics; pathogen identification.

Figure 1.

A, The clinical utility of universal broad-range polymerase chain reaction amplicon sequencing (uPCR) by clinical specimen type. The bars are overlapping and the 3 horizontal, dashed lines represent the overall proportion of all samples with corresponding positive uPCR results (16.5%), positive uPCR results that were clinically significant (10.1%), and positive uPCR results that changed clinical management (4.1%). B, The clinical utility of uPCR by clinical sample type: fresh tissue, formalin-fixed paraffin-embedded tissue, or fluid sample. C, The proportion of clinical samples, stratified by sample type, that have a corresponding positive microbiological or pathology result. Abbreviations: BAL, bronchoalveolar lavage; CSF, cerebrospinalfluid; FFPE, formalin-fixed paraffin-embedded; PMN, polymorphonuclear neutrophil.