Structure and diversity of urinary cell-free DNA informative of host-pathogen interactions in human urinary tract infection

The risk of acquiring urinary tract infection (UTI) is very high for patients who have received kidney transplants; nearly half will develop bacteriuria and an eighth viruria via BK polyomavirus in the first three years following transplantation. Current methodology for diagnosing viral and bacterial infections, while well practiced, is often limited in scope. The advent of next generation sequencing of cell-free DNA has shown promise in its ability to capture multiple perspectives of human health from discovering the origin of cell-free DNA in plasma; such a diagnostic has not been readily applied to urinary cell-free DNA. In this study we selected 141 urine samples from a cohort of kidney transplant patients, collected and stored at Weill Cornell Medical College - New York Presbyterian Hospital. Of these samples, 43 samples were determined to be culture positive (> 10,000 CFU) for one or more bacterial species (including E. coli, Enterococcus, Klebsiella, Haemophilus, and Raoultella). A separate 23 samples were confirmed for BK virus nephropathy, with presence of BK polyomavirus confirmed via qPCR. We also included 29 samples from fourteen patients who did not develop UTIs in the three months following transplantation, and 11 samples that were negative for BK virus nephropathy. For a full description of samples, please see the following link and download the supplemental data table (https://www.biorxiv.org/content/10.1101/177402v2). From these urine samples, we aimed to capture and sequence urinary cell-free DNA using a single-stranded library preparation.

• Study Design:
  • Case-Control
• Study Type:
  • Case-Control
• Subject Sample Telemetry Report (SSTR)

For urinary cell-free DNA:
Inclusion criteria: age range of 18 to 90 years old, sex being either male or female, kidney transplant recipient, and ability to provide informed consent.
Exclusion criteria: inability to provide informed consent. Children were not included in this study.

For amniotic fluid cell-free NDA:
Inclusion criteria: pregnant mothers with or without chorioamnionitis determined a time of amniocentesis.
Exclusion criteria: inability to provide informed consent. Children were not included in this study.

Frozen urine samples from the past several years were acquired. Samples were processed (DNA extracted and corresponding libraries prepared and sequenced) from June 2016 to December 2017.

Amniotic fluid samples collected during amniocentesis and stored at -80⁰C. Samples were processed (DNA extracted and corresponding libraries prepared and sequenced) from January 2017 to January 2019.

• Primary Phenotype: Bacteriuria
• BK Virus
• Control Groups

• BioProject
• PubMed
• Sequence Read Archive
• BioSample
• MeSH
• PMC

• Principal Investigator
  • Iwijn De Vlaminck, PhD. Cornell University, Ithaca, NY, USA.
• Co-Investigator
  • John Richard Lee, MD. Weill Cornell Medicine, New York, NY, USA.
• Funding Source
  • R21AI133331. National Institutes of Health, Bethesda, MD, USA.
  • R21AI124237. National Institutes of Health, Bethesda, MD, USA.
  • DP2AI138242. National Institutes of Health, Bethesda, MD, USA.
  • K23AI124464. National Institutes of Health, Bethesda, MD, USA.
  • R37AI051652. National Institutes of Health, Bethesda, MD, USA.