Kidney Week

Abstract: TH-PO878

Metagenomic Sequencing of Cell-Free DNA in Peritoneal Fluid: A Novel Strategy to Identify Pathogens and Characterize Bacterial Growth Dynamics and Antibiotic Resistomes in Peritonitis

Session Information

• Dialysis: Infection
  November 02, 2017 | Location: Hall H, Morial Convention Center
  Abstract Time: 10:00 AM - 10:00 AM

Category: Dialysis

• 610 Dialysis: Infection

Authors

• Lee, John Richard, Weill Cornell Medicine-, New York, New York, United States

John Richard Lee,

• Burnham, Philip, Cornell University, Ithaca, New York, United States

Philip Burnham,

• Renaghan, Amanda DeMauro, Weill Cornell Medicine-, New York, New York, United States

Amanda DeMauro Renaghan,

• Silberzweig, Jeffrey I., The Rogosin Institute, New York, New York, United States

Jeffrey I. Silberzweig,

• Srivatana, Vesh, The Rogosin Institute, New York, New York, United States

Vesh Srivatana,

• Dadhania, Darshana, Weill Cornell Medicine-, New York, New York, United States

Darshana Dadhania,

• Muthukumar, Thangamani, Weill Cornell Medicine-, New York, New York, United States

Thangamani Muthukumar,

• Suthanthiran, Manikkam, Weill Cornell Medicine-, New York, New York, United States

Manikkam Suthanthiran,

• De Vlaminck, Iwijn, Cornell University, Ithaca, New York, United States

Iwijn De Vlaminck,

Background

Peritonitis is a devastating complication in peritoneal dialysis (PD) patients. Newer techniques are needed to predict peritonitis development and to characterize pathogen dynamics.

Methods

In this first-in-kind study, we recruited 4 ESRD PD patients; 2 subjects had peritonitis at the time of recruitment and the remaining 2 did not. We collected serial peritoneal fluid (PF) specimens from these subjects. We performed metagenomic sequencing on PF under single-stranded DNA library preparation using an Illumina NextSeq platform (2x75 bp).

Results

A mean of 3.6 million cfDNA fragments was obtained per specimen (N=7 specimens) and these fragments had peaks at 65 bp and 167 bp (Fig A). cfDNA profiling confirmed 2 cases of peritonitis (Klebsiella pneumoniae, Staphylococcus epidermis). Serial profiling showed decreasing adjusted BLAST hits after antibiotic treatment (Fig. B). Alignment of cfDNA fragments to the reference genome of K. pneumoniae revealed disproportionate coverage over the replication origin, highlighting active growth of K. pneumoniae, and subsequent decrease in growth activity after antibiotic treatment (Fig. C). Antibiotic resistance determination revealed the presence of PmrE, PmrF, oqxB, mfd, FosA5, cpxAR, PatA-PatB, and msbA, which provide resistance to colistin, novobiocin, ciprofloxacin, and norfloxacin.

Conclusion

Our first-in-kind study demonstrates that cfDNA profiling of peritoneal fluid is an all-inclusive approach to comprehensively identify pathogens, bacterial growth dynamics, and antibiotic resistomes, which may be useful in culture-negative peritonitis and recurrent peritonitis.