Molecular Pathology Abstracts

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Use of urinary cell-free DNA for monitoring infections of the urinary tract

While there is an abundance of literature about the use of plasma circulating cell-free DNA in diagnostic assays, data on the use of urinary cell-free DNA (cfDNA) are limited. The authors conducted a study in which they tested the utility of urinary cfDNA to monitor host and pathogen interactions in bacterial and viral urinary tract infections. Urinary cfDNA is primarily composed of DNA released from host cells and microbes in the urinary tract and has a lesser contribution from plasma cfDNA that is filtered into urine. The authors extracted cfDNA from as little as 1 mL of urine and processed it using a single-stranded library preparation protocol followed by next-generation sequencing. Urine samples for cfDNA analysis collected from 82 kidney transplant recipients were assayed for varying metrics that included the use of host and microbe cfDNA. This was a particularly relevant cohort as more than 15,000 patients receive renal transplants in the United States annually, and bacterial and viral infections are a significant cause of morbidity and mortality in this cohort. The authors profiled the urinary microbiome in patients without urinary tract infection (UTI) and showed a gender-specific signature that corresponded to transplant recipient gender. For instance, female recipients had significantly higher cfDNA from Gardnerella, Ureaplasma, and Lactobacillus compared with male recipients. Using relative genome equivalents (RGE), by normalizing microbial genome copies to human genome copies, the authors identified causative organisms for UTI using conventional culture and identification methods, with a high degree of sensitivity and specificity. This assay was also used to establish the nature of polymicrobial bacterial infections as well as to identify causative organisms in culture-negative cases. This technique was equally effective for viral identification, such as detecting BK polyomavirus (BKV), as well as detecting parvovirus B19 in the preclinical phase. Furthermore, estimation of bacterial replication index, based on sequencing coverage signatures and antimicrobial resistance profiles, could be further exploited to guide clinical decision-making. Assessment of host cfDNA revealed elevated donor-derived cfDNA, particularly in the setting of BKV nephropathy, while this metric was not informative in the setting of bacterial UTI, suggesting that donor-specific urinary cfDNA correlates with graft tissue injury in the setting of BKV nephropathy. In summary, this study shows that urinary cfDNA is a highly versatile analyte and may have immediate application in monitoring bacterial and viral infections and in allograft health in patients with renal transplants.

Burnham P, Dadhania D, Heyang M, et al. Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nat Commun. 2018;9:2412. doi:10.1038/541467-018-04745-0.

Correspondence: Dr. John Richard Lee at jrl2002@med.cornell.edu