Universal PCR for bacteria, mycobacteria, and fungi: a 10-year retrospective review of clinical indications and patient outcomes

Jeffrey Kubiak, Alexandra Morgan, Andrea Kirmaier, Ramy Arnaout, Stefan Riedel

Research output: Contribution to journalReview articlepeer-review


Universal PCR for bacteria, mycobacteria, and fungi can aid in the diagnosis of occult infections, especially in the case of fastidious organisms or when prior antimicrobial treatment compromises culture growth. However, the limitations of this technology, including lack of specificity,high cost, long turnaround time, and lack of susceptibility data, may limit its effecton clinical outcomes. We performed a retrospective analysis of all specimens sent for universal PCR over a 10-year period from 2013 to 2022, focusing on clinical indications for test utilization and patient outcomes. All specimens required approval by a microbiology laboratory director prior to testing. A total of 708 specimens were sent from 638 patients. Of these specimens, 163 were positive, with an overall positivity rate of 23%. Pre-analytic factors associated with a positive universal PCR result were the presence of organisms on Gram stain or histology, the presence of neutrophils on Gram stain, and growth on culture. Positivity rates varied significantlyby specimen type. A total of 20% of all organisms detected were deemed clinically irrelevant by the clinical services. A positive universal PCR led to a change in antibiotic management in 29% of cases. Positive fungal universal PCR results sent from hospitalized patients were associated with worse outcomes, including increased hospital mortality. Our findingssuggest that factors such as the presence of organisms or neutrophils on Gram stain, specimen source/clinical context, and anticipated changes in management based on results should be strongly considered when making stewardship decisions regarding the appropriateness of this testing modality.

Original languageEnglish (US)
JournalJournal of clinical microbiology
Issue number12
StatePublished - Dec 2023
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2023 American Society for Microbiology.


  • laboratory utilization
  • molecular diagnostics
  • outcomes
  • universal PCR

PubMed: MeSH publication types

  • Journal Article
  • Research Support, Non-U.S. Gov't


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