Urinary cfDNA Analysis Valuable for Urinary Tract Infections

Sequencing of urinary cell-free DNA (cfDNA) offers a comprehensive examination of bacterial and viral infections of the urinary tract and could be a valuable diagnostic tool for both kidney transplant patients, as well as in the general population, according to a study published June 20 in Nature Communications. Analysis of cfDNA improves clinical practice by identifying bacteria and viruses that may be clinically relevant but not routinely detected in current screening protocols.

Urinary tract infections (UTI) are one of the most commonly diagnosed infections and occur at even a higher rate among kidney transplant recipients. UTIs in kidney transplant recipients can lead to serious complications, including graft loss and death. In vitro urine culture is the gold standard for diagnosis of bacterial UTI, but is of limited utility because of the relatively few cultivable organisms.

Isolated cfDNA from 141 urine samples from 82 kidney transplant patients were sequenced. The researchers applied a single-stranded library preparation technique in order to create diverse sequencing libraries that capture short, highly degraded cfDNA. The assay performed well even from just 1 mL of urine supernatant and had a turnaround time of 1 to 2 days.

Overall, the researchers found that urinary cfDNA sequencing agrees in the vast majority of cases with conventional diagnostic testing, but can uncover bacteria and viruses that remain undetected in conventional diagnostic protocols.

Among patients with a diagnosed bacterial UTI, cfDNA fragments accounted for more than one-third of raw sequencing reads. For 41 of the 43 positive urine specimens, sequencing of urinary cfDNA detected the clinically reported organisms to the species level. However, only in 26 of the 43 UTI cases was the organism identified in culture the most prevalent organism detected by cfDNA. Finally, for 42 of the 43 UTI samples, researchers were able to determine the relative abundance of genes conferring antibiotic resistance.

Additionally, nearly half of the samples had detectable levels potentially clinically relevant viruses on cfDNA analysis. Findings support the utility of urinary cfDNA sequencing for the detection of both common and uncommon viral agents, particularly among kidney transplant recipients.

“Different layers of clinical information are accessible from a single assay that are either inaccessible using current diagnostic protocols or require parallel implementation of a multitude of different tests,” write the authors led by Philip Burnham, from Cornell University, Ithaca, N.Y. “The assay we present has the potential to become a valuable tool to monitor bacteriuria and viruria in kidney transplant cohorts and to ascertain their potential impact on allograft health.”

Takeaway: Urinary cfDNA as a highly versatile analyte to monitor infections of the urinary tract and can reveal the viral or bacterial source of infections that may be undetected with conventional diagnostics. Additionally, urinary cfDNA can predict antimicrobial susceptibility in a timely manner.