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The Use of Microbial Cell–Free DNA (mcfDNA) to Detect Infections after Pediatric Hematopoietic Stem Cell Transplant

Year: 2025

Type: article

Abstract: Background Infections are a major driver of morbidity and mortality after pediatric hematopoietic cell transplantation (HCT). Early detection and initiation of appropriate antimicrobials remains vital to reduce these risks. Standard of care (SOC) tests from blood, urine, and bronchoalveolar lavage yield pathogens in only 10-50% of cases. Data support that plasma microbial cell–free DNA next-generation sequencing (mcfDNA) tests may identify more pathogens noninvasively, but data are limited after HCT. We hypothesized that mcfDNA would identify more pathogens than SOC tests. Methods We performed a retrospective, single center, IRB approved study from August 2019 to June 2024 to determine the rate of positive mcfDNA tests obtained in children undergoing HCT as compared to SOC. McfDNA was obtained when there was new clinical or radiographic concern for high-risk infection in HCT patients (requiring intensive care, protracted oxygen, or worsening despite broad-spectrum antimicrobials). Results 91 mcfDNA tests were obtained in 55 patients; 52 patients were evaluable with at least 1 interpretable test, yielding 87 results. The average age was 9.5 years (range 8 months to 19 years). Transplant indications included malignancy (62%), immune dysregulation (21%), and non-malignant hematologic disorders (17%). 95% underwent allogeneic HCT; of these, 33% received PBSC, 6% cord, 61% marrow. Of these 6% were related haplo-identical, 29% were HLA mis-matched unrelated, and 65% were 8/8 HLA-matched. McfDNA was obtained 2 (42%), 3 (17%), and 4 times (6%), with 1 patient tested 5 times. Of the 87 mcfDNA tests, 52% were negative for pathogens. Pathogens included: mycobacteria in 2.3% (n=2), viruses in 46% (n=40), Gram negative bacteria in 30% (n=26), Gram positive bacteria in 35.6% (n=31) and fungus in 4.6% (n=4). Multiple organisms were identified in 27 tests (31%). 28% were concordant SOC results. SOC tests identified pathogens in 12.6% (n=11) in which mcfDNA was negative. 54% (28/52) of the cohort died. Discussion Our data suggest that mcfDNA detects organisms not identified by SOC testing in pediatric HCT patients, including organisms that can be challenging to diagnose via SOC testing. SOC also identified pathogens not identified by mcfDNA. McfDNA might be valuable to complement SOC testing. Future studies are needed to validate these data and determine the proportion of tests that are actionable and the optimal approach to incorporate mcfDNA testing into pediatric HCT care.

Source: Transplantation and Cellular Therapy

DOI: 10.1016/j.jtct.2025.01.821