Utility of Broad-Range PCR Sequencing for Infectious Diseases Clinical Decision Making: a Pediatric Center Experience

Broad-range PCR (BRPCR) sequencing is a promising tool for diagnosis of infectious conditions when traditional microbiologic strategies fail to identify a pathogen. Data on the optimal clinical scenarios in which to use this tool are limited. We assessed, via retrospective chart review, the rate of organism identification and impact on clinical management from BRPCR testing sent from our quaternary care children's hospital between February 2010 and June 2020. A total of 382 samples were sent from 269 individual patients. A total of 200 (74.3%) patients were immunocompromised. Median age at time of sample collection was 10.0 years (interquartile range, 4.2 to 15.8). A total of 254/377 (64.7%) samples were from patients known to be on ≥1 antimicrobial in the 24 h prior to sample collection. A total of 112/382 (29.3%) samples were from patients ultimately diagnosed with a bacterial or fungal infection by another testing modality. The most common sample types were bronchoalveolar lavage (BAL) fluid (45), lung tissue (41), and bone (39). An organism was identified from 83 (21.7%) samples, but results from only 19 (5.0%) samples led to a change in management. Organisms were identified from 18 (40%) BAL samples; only 2 (4.4%) were judged to be clinically significant. A total of 4/12 (33.3%) samples from cardiac hardware changed clinical management. We found that only 5% of BRPCR results influenced antimicrobial management in a diverse pediatric cohort. Our findings suggest that the impact on clinical management varied widely by sample type. Additional work is necessary to characterize the ideal clinical scenarios in which BRPCR should be used.