The role of cell‐free DNA in non‐invasive diagnosis of urinary tract infection

Abstract

Urinary tract infection (UTI) constitutes a pervasive health concern. UTIs are dichotomously classified into upper and lower strata, and further categorized as either complicated or uncomplicated. Upper UTIs predominantly afflict the renal and ureteral domains, typified by conditions exemplified in pyelonephritis, whereas lower UTIs manifest within the confines of the urethra and bladder. The conventional diagnosis of UTIs relies upon clinical manifestations and urine culture. Common symptoms encompass dysuria, frequent micturition, hematuria, and suprapubic discomfort. Urine culture serves to identify the specific pathogens instigating the infection and assess their antibiotic susceptibility. However, this procedural protocol generally necessitates an approximate duration of 24 h, coupled with an additional 24‐h interval for antibiotic susceptibility testing. In contradistinction, the detection of cell‐free DNA (cfDNA) in the circulatory system presents a potential avenue for non‐invasive diagnostic modalities. Notwithstanding, cfDNA emanates from deteriorating cells, affording insights into the extant cellular demise within the organism. Extensive scholarly inquiry has established a positive correlation between cfDNA concentration in the bloodstream and the incidence of cell death in conditions, such as severe traumas, sepsis, aseptic inflammation, myocardial infarction, and stroke. However, limited investigative effort has been devoted to elucidating the diagnostic potential of cfDNA in the context of UTIs. Consequently, the concentration and constitution of plasma cfDNA harbor substantial promise for non‐invasively diagnosing UTIs. In summation, the utilization of cfDNA in UTI diagnosis remains an incipient area of scholarly pursuit, underscoring the imperative for further research to elucidate the prospective role of plasma cfDNA in non‐intrusively discerning UTIs.

Key words： cell‐free DNA; diagnosis; DNA methylation; urinary tract infection

References

1 Foxman B . Urinary tract infection syndromes. Infect Dis Clin North Am. 2014; 28 (1): 1- 13.

2 Tambyah PA , Maki DG , Tambyah PA , Maki DG . Catheter-associated urinary tract infection is rarely symptomatic: a prospective study of 1,497 catheterized patients. Arch Intern Med. 2000; 160 (5): 678- 82.

3 Schmiemann G , Kniehl E , Gebhardt K , Matejczyk MM , Hummers-Pradier E . The diagnosis of urinary tract infection: a systematic review. Dtsch Arztebl Int. 2010; 107 (21): 361- 7.

4 Wan JCM , Massie C , Garcia-Corbacho J , Mouliere F , Brenton JD , Caldas C , et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017; 17 (4): 223- 38.

5 Mandel P , Metais P . Nuclear acids in human blood plasma. C R Seances Soc Biol Fil. 1948; 142 (3-4): 241- 3.

6 Tan EM , Schur PH , Carr RI , Kunkel HG . Deoxybonucleic acid (DNA) and antibodies to DNA in the serum of patients with systemic lupus erythematosus. J Clin Invest. 1966; 45 (11): 1732- 40.

7 Leon SA , Shapiro B , Sklaroff DM , Yaros MJ . Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977; 37 (3): 646- 50.

8 Stroun M , Anker P , Maurice P , Lyautey J , Lederrey C , Beljanski M . Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology. 1989; 46 (5): 318- 22.

9 Vasioukhin V , Anker P , Maurice P , Lyautey J , Lederrey C , Stroun M . Point mutations of the N-ras gene in the blood plasma DNA of patients with myelodysplastic syndrome or acute myelogenous leukaemia. Br J Haematol. 1994; 86 (4): 774- 9.

10 Sorenson GD , Pribish DM , Valone FH , Memoli VA , Bzik DJ , Yao SL . Soluble normal and mutated DNA sequences from single-copy genes in human blood. Cancer Epidemiol Biomarkers Prev. 1994; 3 (1): 67- 71.

11 Qi Chen X , Stroun M , Magnenat JL , Nicod LP , Kurt AM , Lyautey J , et al. Microsatellite alterations in plasma DNA of small cell lung cancer patients. Nat Med. 1996; 2 (9): 1033- 5.

12 Nawroz H , Koch W , Anker P , Stroun M , Sidransky D . Microsatellite alterations in serum DNA of head and neck cancer patients. Nat Med. 1996; 2 (9): 1035- 7.

13 Esteller M , Sanchez-Cespedes M , Rosell R , Sidransky D , Baylin SB , Herman JG . Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients. Cancer Res. 1999; 59 (1): 67- 70.

14 Wong IH , Lo YM , Zhang J , Liew CT , Ng MH , Wong N , et al. Detection of aberrant p16 methylation in the plasma and serum of liver cancer patients. Cancer Res. 1999; 59 (1): 71- 3.

15 Silva JM , Dominguez G , Villanueva MJ , Gonzalez R , Garcia JM , Corbacho C , et al. Aberrant DNA methylation of the p16INK4a gene in plasma DNA of breast cancer patients. Br J Cancer. 1999; 80 (8): 1262- 4.

16 Lo YMD , Corbetta N , Chamberlain PF , Rai V , Sargent IL , Redman CW , et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997; 350 (9076): 485- 7.

17 Fan HC , Blumenfeld YJ , Chitkara U , Hudgins L , Quake SR . Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci. 2008; 105 (42): 16266- 71.

18 De Vlaminck I , Valantine HA , Snyder TM , Strehl C , Cohen G , Luikart H , et al. Circulating cell-free DNA enables noninvasive diagnosis of heart transplant rejection. Sci Transl Med. 2014; 6 (241): 241ra77.

19 Bettegowda C , Sausen M , Leary RJ , Kinde I , Wang Y , Agrawal N , et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014; 6 (224): 224ra24.

20 De Vlaminck I , Martin L , Kertesz M , Patel K , Kowarsky M , Strehl C , et al. Noninvasive monitoring of infection and rejection after lung transplantation. Proc Natl Acad Sci. 2015; 112 (43): 13336- 41.

21 Abbosh C , Birkbak NJ , Wilson GA , Jamal-Hanjani M , Constantin T , Salari R , et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature. 2017; 545 (7655): 446- 51.

22 Butt AN , Swaminathan R . Overview of circulating nucleic acids in plasma/serum. Ann NY Acad Sci. 2008; 1137: 236- 42.

23 Kaur R , Kaur R . Symptoms, risk factors, diagnosis and treatment of urinary tract infections. Postgrad Med J. 2021; 97 (1154): 803- 12.

24 Salvatore S , Salvatore S , Cattoni E , Siesto G , Serati M , Sorice P , et al. Urinary tract infections in women. Eur J Obstet Gynecol Reprod Biol. 2011; 156 (2): 131- 6.

25 Hooton TM . Uncomplicated urinary tract infection. N Engl J Med. 2012; 366 (11): 1028- 37.

26 Brubaker L , Carberry C , Nardos R , Carter-Brooks C , Lowder JL . American Urogynecologic Society best-practice statement: recurrent urinary tract infection in adult women. Female Pelvic Med Reconstr Surg. 2018; 24 (5): 321- 35.

27 Kodner CM , Thomas Gupton EK . Recurrent urinary tract infections in women: diagnosis and management. Am Fam Physician. 2010; 82 (6): 638- 43.

28 Anger J , Lee U , Ackerman AL , Chou R , Chughtai B , Clemens JQ , et al. Recurrent uncomplicated urinary tract infections in women: AUA/CUA/SUFU guideline. J Urol. 2019; 202 (2): 282- 9.

29 Peck J , Shepherd JP . Recurrent urinary tract infections. Obstet Gynecol Clin North Am. 2021; 48 (3): 501- 13.

30 Betschart C , Albrich WC , Brandner S , Faltin D , Kuhn A , Surbek D , et al. Guideline of the Swiss Society of Gynaecology and Obstetrics (SSGO) on acute and recurrent urinary tract infections in women, including pregnancy. Swiss Med Wkly. 2020; 150: w20236.

31 Arnold JJ , Hehn LE , Klein DA . Common questions about recurrent urinary tract infections in women. Am Fam Physician. 2016; 93 (7): 560- 9.

32 Neugent ML , Hulyalkar NV , Nguyen VH , Zimmern PE , De Nisco NJ . Advances in understanding the human urinary microbiome and its potential role in urinary tract infection. mBio. 2020; 11 (2): e00218- 20.

33 Gupta K , Hooton TM , Naber KG , Wullt B , Colgan R , Miller LG , et al. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: a 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin Infect Dis. 2011; 52 (5): e103- 20.

34 Price TK , Wolff B , Halverson T , Limeira R , Brubaker L , Dong Q , et al. Temporal dynamics of the adult female lower urinary tract microbiota. mBio. 2020; 11 (2): e00475- 20.

35 Sihra N , Goodman A , Zakri R , Sahai A , Malde S . Nonantibiotic prevention and management of recurrent urinary tract infection. Nat Rev Urol. 2018; 15 (12): 750- 76.

36 van der Vaart M , Pretorius PJ . Circulating DNA. Its origin and fluctuation. Ann NY Acad Sci. 2008; 1137: 18- 26.

37 Thierry AR , Mouliere F , Gongora C , Ollier J , Robert B , Ychou M , et al. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res. 2010; 38 (18): 6159- 75.

38 Jung K , Fleischhacker M , Rabien A . Cell‐free DNA in the blood as a solid tumor biomarker—a critical appraisal of the literature. Clin Chim Acta. 2010; 411 (21-22): 1611- 24.

39 Dong X , Hou Q , Chen Y , Wang X . Diagnostic value of the methylation of multiple gene promoters in serum in hepatitis B virus-related hepatocellular carcinoma. Dis Markers. 2017; 2017: 1- 6.

40 Sozzi G , Conte D , Leon M , Cirincione R , Roz L , Ratcliffe C , et al. Quantification of free circulating DNA as a diagnostic marker in lung cancer. J Clin Oncol. 2003; 21 (21): 3902- 8.

41 Widschwendter M , Evans I , Jones A , Ghazali S , Reisel D , Ryan A , et al. Methylation patterns in serum DNA for early identification of disseminated breast cancer. Genome Med. 2017; 9 (1): 115.

42 Widschwendter M , Zikan M , Wahl B , Lempiäinen H , Paprotka T , Evans I , et al. The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer. Genome Med. 2017; 9 (1): 116.

43 Cohen JD , Li L , Wang Y , Thoburn C , Afsari B , Danilova L , et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018; 359 (6378): 926- 30.

44 Snyder MW , Kircher M , Hill AJ , Daza RM , Shendure J . Cell‐free DNA comprises an in vivo nucleosome footprint that informs its tissues‐of‐origin. Cell. 2016; 164 (1-2): 57- 68.

45 Abelson S , Collord G , Ng SWK , Weissbrod O , Mendelson Cohen N , Niemeyer E , et al. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature. 2018; 559 (7714): 400- 4.

46 Lanman RB , Mortimer SA , Zill OA , Sebisanovic D , Lopez R , Blau S , et al. Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PLoS ONE. 2015; 10 (10): e0140712.

47 Newman AM , Lovejoy AF , Klass DM , Kurtz DM , Chabon JJ , Scherer F , et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat Biotechnol. 2016; 34 (5): 547- 55.

48 Murtaza M , Dawson SJ , Tsui DWY , Gale D , Forshew T , Piskorz AM , et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013; 497 (7447): 108- 12.

49 Peng X , Li HD , Wu FX , Wang J . Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics. Brief Bioinf. 2021; 22 (3): bbaa060.

50 Dor Y , Cedar H . Principles of DNA methylation and their implications for biology and medicine. Lancet. 2018; 392 (10149): 777- 86.

51 Smith ZD , Chan MM , Humm KC , Karnik R , Mekhoubad S , Regev A , et al. DNA methylation dynamics of the human preimplantation embryo. Nature. 2014; 511 (7511): 611- 5.

52 Smith ZD , Chan MM , Mikkelsen TS , Gu H , Gnirke A , Regev A , et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012; 484 (7394): 339- 44.

53 Kang S , Li Q , Chen Q , Zhou Y , Park S , Lee G , et al. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol. 2017; 18 (1): 53.

54 Kundaje A , Meuleman W , Ernst J , Bilenky M , Yen A , Heravi-Moussavi A , et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518 (7539): 317- 30.

55 Bergman Y , Cedar H . DNA methylation dynamics in health and disease. Nat Struct Mol Biol. 2013; 20 (3): 274- 81.

56 Lo YMD , Tein MSC , Lau TK , Haines CJ , Leung TN , Poon PMK , et al. Quantitative analysis of fetal DNA in maternal plasma and serum: implications for noninvasive prenatal diagnosis. Am J Hum Genet. 1998; 62 (4): 768- 75.

57 Jiang P , Lo YMD . The long and short of circulating cell-free DNA and the ins and outs of molecular diagnostics. Trends Genet. 2016; 32 (6): 360- 71.

58 Fan HC , Gu W , Wang J , Blumenfeld YJ , El-Sayed YY , Quake SR . Non-invasive prenatal measurement of the fetal genome. Nature. 2012; 487 (7407): 320- 4.

59 Crowley E , Di Nicolantonio F , Loupakis F , Bardelli A . Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013; 10 (8): 472- 84.

60 Dawson SJ , Tsui DWY , Murtaza M , Biggs H , Rueda OM , Chin SF , et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013; 368 (13): 1199- 209.

61 Akirav EM , Lebastchi J , Galvan EM , Henegariu O , Akirav M , Ablamunits V , et al. Detection of β cell death in diabetes using differentially methylated circulating DNA. Proc Natl Acad Sci. 2011; 108 (47): 19018- 23.

62 Lehmann-Werman R , Neiman D , Zemmour H , Moss J , Magenheim J , Vaknin-Dembinsky A , et al. Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc Natl Acad Sci. 2016; 113 (13): E1826- 34.

63 Sun K , Jiang P , Chan KCA , Wong J , Cheng YKY , Liang RHS , et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci. 2015; 112 (40): E5503- 12.

64 Lun FMF , Tsui NBY , Chan KCA , Leung TY , Lau TK , Charoenkwan P , et al. Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma. Proc Natl Acad Sci. 2008; 105 (50): 19920- 5.

65 Lo YMD , Chan KCA , Sun H , Chen EZ , Jiang P , Lun FMF , et al. Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med. 2010; 2 (61): 61ra91.

66 Chiu RWK , Chan KCA , Gao Y , Lau VYM , Zheng W , Leung TY , et al. Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci. 2008; 105 (51): 20458- 63.

67 Chiu RWK , Akolekar R , Zheng YWL , Leung TY , Sun H , Chan KCA , et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ. 2011; 342: c7401.

68 Tsui NBY , Kadir RA , Chan KCA , Chi C , Mellars G , Tuddenham EG , et al. Noninvasive prenatal diagnosis of hemophilia by microfluidics digital PCR analysis of maternal plasma DNA. Blood. 2011; 117 (13): 3684- 91.

69 Butler TM , Johnson-Camacho K , Peto M , Wang NJ , Macey TA , Korkola JE , et al. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease. PLoS ONE. 2015; 10 (8): e0136407.

70 New MI , Tong YK , Yuen T , Jiang P , Pina C , Chan KCA , et al. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab. 2014; 99 (6): E1022- 30.

71 Saito H , Sekizawa A , Morimoto T , Suzuki M , Yanaihara T . Prenatal DNA diagnosis of a single-gene disorder from maternal plasma. Lancet. 2000; 356 (9236): 1170.

72 Hui WWI , Jiang P , Tong YK , Lee WS , Cheng YKY , New MI , et al. Universal haplotype-based noninvasive prenatal testing for single gene diseases. Clin Chem. 2017; 63 (2): 513- 24.

73 Palomaki GE , Deciu C , Kloza EM , Lambert-Messerlian GM , Haddow JE , Neveux LM , et al. DNA sequencing of maternal plasma reliably identifies trisomy 18 and trisomy 13 as well as Down syndrome: an international collaborative study. Genet Med. 2012; 14 (3): 296- 305.

74 Bianchi DW , Parker RL , Wentworth J , Madankumar R , Saffer C , Das AF , et al. DNA sequencing versus standard prenatal aneuploidy screening. N Engl J Med. 2014; 370 (9): 799- 808.

75 Chen EZ , Chiu RWK , Sun H , Akolekar R , Chan KCA , Leung TY , et al. Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS ONE. 2011; 6 (7): e21791.

76 Liang D , Lv W , Wang H , Xu L , Liu J , Li H , et al. Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing. Prenatal Diagn. 2013; 33 (5): 409- 15.

77 Sparks AB , Wang ET , Struble CA , Barrett W , Stokowski R , McBride C , et al. Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenatal Diagn. 2012; 32 (1): 3- 9.

78 Snyder TM , Khush KK , Valantine HA , Quake SR . Universal noninvasive detection of solid organ transplant rejection. Proc Natl Acad Sci. 2011; 108 (15): 6229- 34.

79 Lee H , Park YM , We YM , Han DJ , Seo JW , Moon H , et al. Evaluation of digital PCR as a technique for monitoring acute rejection in kidney transplantation. Genomics Inf. 2017; 15 (1): 2- 10.

80 Baraquin A , Hervouet E , Richou C , Flori P , Peixoto P , Azizi A , et al. Circulating cell-free DNA in patients with alveolar echinococcosis. Mol Biochem Parasitol. 2018; 222: 14- 20.

81 Wan Z , Peng X , Ma L , Tian Q , Wu S , Li J , et al. Targeted sequencing of genomic repeat regions detects circulating cell-free Echinococcus DNA. PLoS Neglected Trop Dis. 2020; 14 (3): e0008147.

82 Wichmann D , Panning M , Quack T , Kramme S , Burchard GD , Grevelding C , et al. Diagnosing schistosomiasis by detection of cell-free parasite DNA in human plasma. PLoS Neglected Trop Dis. 2009; 3 (4): e422.

83 Cheng AP , Burnham P , Lee JR , Cheng MP , Suthanthiran M , Dadhania D , et al. A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection. Proc Natl Acad Sci. 2019; 116 (37): 18738- 44.

84 Burnham P , Dadhania D , Heyang M , Chen F , Westblade LF , Suthanthiran M , et al. Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract. Nat Commun. 2018; 9 (1): 2412.

85 Blauwkamp TA , Thair S , Rosen MJ , Blair L , Lindner MS , Vilfan ID , et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019; 4 (4): 663- 74.

86 Arshad A , Anderson B , Sharif A . Comparison of organ donation and transplantation rates between opt-out and opt-in systems. Kidney Int. 2019; 95 (6): 1453- 60.

87 Beck J , Oellerich M , Schulz U , Schauerte V , Reinhard L , Fuchs U , et al. Donor-derived cell-free DNA Is a novel universal biomarker for allograft rejection in solid organ transplantation. Transplant Proc. 2015; 47 (8): 2400- 3.

88 Zhou Y , Yang G , Liu H , Chen Y , Li X , Ge J , et al. A noninvasive and donor-independent method simultaneously monitors rejection and infection in patients with organ transplant. Transplant Proc. 2019; 51 (6): 1699- 705.

89 Foxman B , Barlow R , D'Arcy H , Gillespie B , Sobel JD . Urinary tract infection. Ann Epidemiol. 2000; 10 (8): 509- 15.