Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis

被引：7

作者：

Burnham, Philip ^{[1
,8
]}

Chen, Fanny ^{[1
]}

Cheng, Alexandre P. ^{[1
]}

Srivatana, Vesh ^{[2
]}

Zhang, Lisa T. ^{[3
]}

Edusei, Emmanuel ^{[3
]}

Albakry, Shady ^{[3
]}

Botticelli, Brittany ^{[3
]}

Guo, Xunxi ^{[3
]}

Renaghan, Amanda ^{[3
]}

Silberzweig, Jeffrey ^{[2
]}

Dadhania, Darshana M. ^{[3
,4
]}

Lenz, Joan S. ^{[1
]}

Heyang, Michael ^{[1
]}

Iliev, Iliyan D. ^{[5
]}

Hayden, Joshua A. ^{[6
,9
]}

Westblade, Lars F. ^{[6
,7
]}

De Vlaminck, Iwijn ^{[1
]}

Lee, John R. ^{[3
,4
]}

机构：

[1] Cornell Univ, Meinig Sch Biomed Engn, Weill Hall Room 301, Ithaca, NY 14853 USA

[2] Rogosin Inst, New York, NY USA

[3] Weill Cornell Med, Div Nephrol & Hypertens, Dept Med, 525 E 68th St Box 3, New York, NY 10065 USA

[4] New York Presbyterian Hosp, Dept Transplantat Med, Weill Cornell Med Ctr, New York, NY USA

[5] Weill Cornell Med, Div Gastroenterol & Hepatol, Dept Med, New York, NY 10065 USA

[6] Weill Cornell Med, Dept Pathol & Lab Med, New York, NY 10065 USA

[7] Weill Cornell Med, Div Infect Dis, Dept Med, New York, NY 10065 USA

[8] Univ Penn, Dept Bioengn, Philadelphia, PA 19104 USA

[9] Norton Healthcare, Dept Chem, Louisville, KY USA

来源：

KIDNEY MEDICINE | 2022年 / 4卷 / 01期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

ALIGNMENT;

D O I：

10.1016/j.xkme.2021.08.017

中图分类号：

R5 [内科学]; R69 [泌尿科学（泌尿生殖系疾病）];

学科分类号：

1002 ; 100201 ;

摘要：

Rationale & Objective: Conventional culture can be insensitive for the detection of rare infections and for the detection of common infections in the setting of recent antibiotic usage. Patients receiving peritoneal dialysis (PD) with suspected peritonitis have a significant proportion of negative conventional cultures. This study examines the utility of metagenomic sequencing of peritoneal effluent cell-free DNA (cfDNA) for evaluating the peritoneal effluent in PD patients with and without peritonitis. Study Design: Prospective cohort study. Setting & Participants: We prospectively characterized cfDNA in 68 peritoneal effluent samples obtained from 33 patients receiving PD at a single center from September 2016 to July 2018. Outcomes: Peritoneal effluent, microbial, and human cfDNA characteristics were evaluated in culture-confirmed peritonitis and culture-negative peritonitis. Analytical Approach: Descriptive statistics were analyzed and microbial cfDNA was detected in culture-confirmed peritonitis and culture-negative peritonitis. Results: Metagenomic sequencing of cfDNA was able to detect and identify bacterial, viral, and eukaryotic pathogens in the peritoneal effluent from PD patients with culture-confirmed peritonitis, as well as patients with recent antibiotic usage and in cases of culture-negative peritonitis. Limitations: Parallel cultures were not obtained in all the peritoneal effluent specimens. Conclusions: Metagenomic cfDNA sequencing of the peritoneal effluent can identify pathogens in PD patients with peritonitis, including culture-negative peritonitis.

引用

页数：9

共 17 条

[1] CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database [J].

Alcock, Brian P. ;

Raphenya, Amogelang R. ;

Lau, Tammy T. Y. ;

Tsang, Kara K. ;

Bouchard, Megane ;

Edalatmand, Arman ;

Huynh, William ;

Nguyen, Anna-Lisa, V ;

Cheng, Annie A. ;

Liu, Sihan ;

Min, Sally Y. ;

Miroshnichenko, Anatoly ;

Tran, Hiu-Ki ;

Werfalli, Rafik E. ;

Nasir, Jalees A. ;

Oloni, Martins ;

Speicher, David J. ;

Florescu, Alexandra ;

Singh, Bhavya ;

Faltyn, Mateusz ;

Hernandez-Koutoucheva, Anastasia ;

Sharma, Arjun N. ;

Bordeleau, Emily ;

Pawlowski, Andrew C. ;

Zubyk, Haley L. ;

Dooley, Damion ;

Griffiths, Emma ;

Maguire, Finlay ;

Winsor, Geoff L. ;

Beiko, Robert G. ;

Brinkman, Fiona S. L. ;

Hsiao, William W. L. ;

Domselaar, Gary, V ;

McArthur, Andrew G. .

NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) :D517-D525

[2]

ALTSCHUL SF, 1990, J MOL BIOL, V215, P403, DOI 10.1006/jmbi.1990.9999

[3] Separating the signal from the noise in metagenomic cell-free DNA sequencing [J].

Burnham, Philip ;

Gomez-Lopez, Nardhy ;

Heyang, Michael ;

Cheng, Alexandre Pellan ;

Lenz, Joan Sesing ;

Dadhania, Darshana M. ;

Lee, John Richard ;

Suthanthiran, Manikkam ;

Romero, Roberto ;

De Vlaminck, Iwijn .

MICROBIOME, 2020, 8 (01)

[4] Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract [J].

Burnham, Philip ;

Dadhania, Darshana ;

Heyang, Michael ;

Chen, Fanny ;

Westblade, Lars F. ;

Suthanthiran, Manikkam ;

Lee, John Richard ;

De Vlaminck, Iwijn .

NATURE COMMUNICATIONS, 2018, 9

[5] Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma [J].

Burnham, Philip ;

Kim, Min Seong ;

Agbor-Enoh, Sean ;

Luikart, Helen ;

Valantine, Hannah A. ;

Khush, Kiran K. ;

De Vlaminck, Iwijn .

SCIENTIFIC REPORTS, 2016, 6

[6] A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection [J].

Cheng, Alexandre Pellan ;

Burnham, Philip ;

Lee, John Richard ;

Cheng, Matthew Pellan ;

Suthanthiran, Manikkam ;

Dadhania, Darshana ;

De Vlaminck, Iwijn .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2019, 116 (37) :18738-18744

[7] Recognizing the reagent microbiome [J].

de Goffau, Marcus C. ;

Lager, Susanne ;

Salter, Susannah J. ;

Wagner, Josef ;

Kronbichler, Andreas ;

Charnock-Jones, D. Stephen ;

Peacock, Sharon J. ;

Smith, Gordon C. S. ;

Parkhill, Julian .

NATURE MICROBIOLOGY, 2018, 3 (08) :851-853

[8] Circulating Cell-Free DNA Enables Noninvasive Diagnosis of Heart Transplant Rejection [J].

De Vlaminck, Iwijn ;

Valantine, Hannah A. ;

Snyder, Thomas M. ;

Strehl, Calvin ;

Cohen, Garrett ;

Luikart, Helen ;

Neff, Norma F. ;

Okamoto, Jennifer ;

Bernstein, Daniel ;

Weisshaar, Dana ;

Quake, Stephen R. ;

Khush, Kiran K. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (241)

[9] Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy [J].

De Vlaminck, Iwijn ;

Khush, Kiran K. ;

Strehl, Calvin ;

Kohli, Bitika ;

Luikart, Helen ;

Neff, Norma F. ;

Okamoto, Jennifer ;

Snyder, Thomas M. ;

Cornfield, David N. ;

Nicolls, Mark R. ;

Weill, David ;

Bernstein, Daniel ;

Valantine, Hannah A. ;

Quake, Stephen R. .

CELL, 2013, 155 (05) :1178-1187

[10] Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids [J].

Gu, Wei ;

Deng, Xianding ;

Lee, Marco ;

Sucu, Yasemin D. ;

Arevalo, Shaun ;

Stryke, Doug ;

Federman, Scot ;

Gopez, Allan ;

Reyes, Kevin ;

Zorn, Kelsey ;

Sample, Hannah ;

Yu, Guixia ;

Ishpuniani, Gurpreet ;

Briggs, Benjamin ;

Chow, Eric D. ;

Berger, Amy ;

Wilson, Michael R. ;

Wang, Candace ;

Hsu, Elaine ;

Miller, Steve ;

DeRisi, Joseph L. ;

Chiu, Charles Y. .

NATURE MEDICINE, 2021, 27 (01) :115-+

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