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Abstract: FR-PO801

Metagenomic Detection of Clinical and Potentially Undiagnosed Infections in Kidney Transplant Recipients

Session Information

Category: Transplantation

  • 2002 Transplantation: Clinical

Authors

  • Kleiboeker, Steven, Eurofins Viracor Inc, Lee's Summit, Missouri, United States
  • Miller, Mikaela A., Eurofins Viracor Inc, Lee's Summit, Missouri, United States
  • Sinha, Rohita, Eurofins Viracor Inc, Lee's Summit, Missouri, United States
  • Park, Sookhyeon, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
  • Rebello, Christabel, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
  • Kinsella, Bradley M., Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
  • Friedewald, John J., Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States
Background

Kidney transplant recipients are immunosuppressed and predisposed to infections. Current diagnostics detect single pathogens, often by qPCR. Unbiased detection of common viruses with sensitivity and specificity comparable to qPCR allows more comprehensive diagnosis or surveillance. Quantification of donor-derived cell-free DNA (dd cfDNA) is an established method for diagnosis of allograft rejection. Combining dd cfDNA and pathogen detection by sequencing (mNGS) into one test represents an opportunity to screen for both infection and rejection.

Methods

A total of 1,980 plasma samples from 256 CTOT-08 study subjects were tested by whole genome sequencing, with dd cfDNA analyzed as described (CJASN 16:1539). Non-human reads underwent reference-assisted assembly and taxonomic annotation using KrakenUneq (K-mers of 16, 21, and 31) trained on ~12,000 viral genomes. Final predictions were made with a majority-wins rule.

Results

For transplant viruses, BK virus (BKV) was most often detected (11.5% of samples), followed by cytomegalovirus (CMV, 8.3%), adenovirus (ADV, 2.6%), Epstein Barr virus (EBV, 2.6%) and JC virus (JCV, 2.0%). Concordance with qPCR results was 97.7%. Clinical infections of BKV, CMV and EBV were reported, and a total of 62 samples collected up to 60 days prior to the onset of infection were tested by mNGS (Table 1). The pathogen diagnosed clinically was detected by mNGS for 32 of 33 samples collected at infection onset to 10 days prior to onset. From 11 to 60 days prior to onset, detection ranged from 31% to 50% of samples. Additionally, 19 BKV infections >10,000 copies/mL and 10 CMV infections >1,000 IU/mL, all from different subjects, were detected by mNGS but not reported as clinical infections, suggesting under-diagnosis or lack of reporting for these viruses.

Conclusion

Viral detection by sequencing demonstrated sensitive and specific detection of key viral pathogens which correlated with clinical diagnoses, as well as suggested an unrecognized pathogen burden. Prospective studies will assess the clinical utility of combined metagenomic and dd cfDNA analysis.

Funding

  • Commercial Support