Search

Background: Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies., Results: We find that all methods that rely on differential lysis of host and microbial cells introduce substantial biases as assessed by 16 S rRNA gene amplicon profiling. However, ChIP enables 10-fold enrichment of microbial DNA while introducing less bias, sufficient to make assessment possible against background, in both pigs and humans., Conclusions: We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias., Conclusions: We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias., Competing Interests: Declarations. Ethics approval and consent to participate: Human colon samples were procured from UCSD’s Moores Cancer Center biorepository. All procedures performed on animals were in accordance with regulations and established guidelines and were reviewed and approved by UC San Diego’s Institutional Animal Care and Use Committee (protocol S21167). Consent for publication: Not applicable. Competing interests: S.L. and M.G.R. are employed by Pfizer, Inc., who funded this study. R. K. is a scientific advisory board member, and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant and scientific advisory board member for DayTwo, and receives income. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc., and has equity. He is a cofounder of Micronoma, and has equity and is a scientific advisory board member. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. A.B. is a founder of Guilden Corporation and is an equity owner. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. All other authors declare no conflicts., (© 2025. The Author(s).)

Objective Design: In June of 2024, Becton Dickinson experienced a blood culture bottle shortage for their BACTEC system, forcing health systems to reduce usage or risk exhausting their supply. Virginia Commonwealth University Health System (VCUHS) in Richmond, VA decided that it was necessary to implement austerity measures to preserve the blood culture bottle supply., Setting: VCUHS includes a main campus in Richmond, VA as well as two affiliate hospitals in South Hill, VA (Community Memorial Hospital (CMH)) and Tappahannock Hospital in Tappahannock, VA. It also includes a free-standing Emergency Department in New Kent, VA., Patients: Blood cultures from both pediatric and adult patients were included in this study., Interventions: VCUHS intervened to decrease blood culture utilization across the entire health system. Interventions included communication of blood culture guidance as well as an electronic health record order designed to guide providers and discourage wasteful ordering., Results: Post-implementation analyses showed that interventions reduced overall usage by 35.6% ( P < .0001) and by greater than 40% in the Emergency Departments. The impact of these changes in utilization on positivity were analyzed, and it was found that the overall positivity rate increased post-intervention from 8.8% to 12.1% ( P = .0115) and in the ED specifically from 10.2% to 19.5% ( P < .0001)., Conclusions: These findings strongly suggest that some basic stewardship interventions can significantly change blood culture practice in a manner that minimizes the impact on patient care., Competing Interests: MD, GB, HD, MV, FP, MW, AH, DF, AB, SR, SL, JK, HM, JW, RM, AJ, FP, JP, RF– No conflicts. CD – Karius., (© The Author(s) 2025.)