Microbiome Analysis Using Next-Generation Sequencing in Urinary Tract Infections

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참고문헌 (68)

1. Pairo-Castineira E, "Genetic mechanisms of critical illness in COVID-19", Nature, 591, pp.92~98 (2021)
2. Plenge RM, "Molecular underpinnings of severe coronavirus disease 2019", JAMA, 324, pp.638~639 (2020)
3. Zhang Q, "Inborn errors of type I IFN immunity in patients with life-threatening COVID-19", Science, 370, pp.eabd4570~ (2020)
4. Plante JA, "Spike mutation D614G alters SARS-CoV-2 fitness", Nature, 592, pp.116~121 (2021)
5. Abraham SN, "The nature of immune responses to urinary tract infections", Nat Rev Immunol, 15, pp.655~663 (2015)
6. Ambite I, "Molecular determinants of disease severity in urinary tract infection", Nat Rev Urol, 18, pp.468~486 (2021)
7. Fischer H, "Pathogen specific, IRF3-dependent signaling and innate resistance to human kidney infection", PLoS Pathog, 6, pp.e1001109~ (2010)
8. Hawn TR, "Toll-like receptor polymorphisms and susceptibility to urinary tract infections in adult women", PLoS One, 4, pp.e5990~ (2009)
9. Subashchandrabose S, "Virulence and fitness determinants of uropathogenic Escherichia coli", Microbiol Spectr, 3 (2015)[DOI]
10. Hull RA, "Virulence properties of Escherichia coli 83972, a prototype strain associated with asymptomatic bacteriuria", Infect Immun, 67, pp.429~432 (1999)
11. Sundén F, "Escherichia coli 83972 bacteriuria protects against recurrent lower urinary tract infections in patients with incomplete bladder emptying", J Urol, 184, pp.179~185 (2010)
12. Roos V, "The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine", Infect Immun, 74, pp.615~624 (2006)
13. Heytens S, "Women with symptoms of a urinary tract infection but a negative urine culture : PCR-based quantification of Escherichia coli suggests infection in most cases", Clin Microbiol Infect, 23, pp.647~652 (2017)
14. Mayne AIW, "Antibiotic treatment of asymptomatic bacteriuria prior to hip and knee arthroplasty; a systematic review of the literature", Surgeon, 16, pp.176~182 (2018)
15. Garretto A, "Genomic survey of E. coli from the bladders of women with and without lower urinary tract symptoms", Front Microbiol, 11, pp.2094~ (2020)
16. Ackerman AL, "The bladder is not sterile : an update on the urinary microbiome", Curr Bladder Dysfunct Rep, 14, pp.331~341 (2019)
17. McDonald M, "A head-to-head comparative phase II study of standard urine culture and sensitivity versus DNA next-generation sequencing testing for urinary tract infections", Rev Urol, 19, pp.213~220 (2017)
18. Dornbier RA, "The microbiome of calcium-based urinary stones", Urolithiasis, 48, pp.191~199 (2020)
19. Flannigan R, "Renal struvite stones--pathogenesis, microbiology, and management strategies", Nat Rev Urol, 11, pp.333~341 (2014)
20. Bajic P, "The urinary microbiome : implications in bladder cancer pathogenesis and therapeutics", Urology, 126, pp.10~15 (2019)
21. DeMasi M, "The role of the urinary, fecal, and prostatic microbiome in prostate cancer : a systematic review", J Urol, 203, pp.e970~ (2020)
22. Kuleshov V, "Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome", Nat Biotechnol, 34, pp.64~69 (2016)
23. Oberle A, "16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis", Reprod Biomed Online, 42, pp.1097~1107 (2021)
24. Toma I, "Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia", J Clin Microbiol, 52, pp.3913~3921 (2014)
25. Wolfe AJ, "Evidence of uncultivated bacteria in the adult female bladder", J Clin Microbiol, 50, pp.1376~1383 (2012)
26. Siddiqui H, "Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons", BMC Microbiol, 11, pp.244~ (2011)
27. Lewis DA, "The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults", Front Cell Infect Microbiol, 3, pp.41~ (2013)
28. Pickard JM, "Gut microbiota : role in pathogen colonization, immune responses, and inflammatory disease", Immunol Rev, 279, pp.70~89 (2017)
29. Hilt EE, "Urine is not sterile : use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder", J Clin Microbiol, 52, pp.871~876 (2014)
30. Bajic P, "Male bladder microbiome relates to lower urinary tract symptoms", Eur Urol Focus, 6, pp.376~382 (2020)
31. Siddiqui H, "Alterations of microbiota in urine from women with interstitial cystitis", BMC Microbiol, 12, pp.205~ (2012)
32. Adebayo AS, "The urinary tract microbiome in older women exhibits host genetic and environmental influences", Cell Host Microbe, 28, pp.298~305.e3 (2020)
33. Fouts DE, "Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury", J Transl Med, 10, pp.174~ (2012)
34. Fredsgaard L, "Description of the voided urinary microbiota in asymptomatic prepubertal children-a pilot study", J Pediatr Urol, 17, pp.545.e1~545.e8 (2021)
35. Glover M, "Recurrent urinary tract infections in healthy and nonpregnant women", Urol Sci, 25, pp.1~8 (2014)
36. Chen SL, "Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection", Sci Transl Med, 5, pp.184ra60~ (2013)
37. Mulder M, "The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population", BMC Microbiol, 19, pp.9~ (2019)
38. Gottschick C, "The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment", Microbiome, 5, pp.99~ (2017)
39. Rani A, "Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance", Transl Res, 181, pp.59~70 (2017)
40. Josephs-Spaulding J, "Recurrent urinary tract infections : unraveling the complicated environment of uncomplicated rUTIs", Front Cell Infect Microbiol, 11, pp.562525~ (2021)
41. Schilling JD, "Effect of trimethoprim-sulfamethoxazole on recurrent bacteriuria and bacterial persistence in mice infected with uropathogenic Escherichia coli", Infect Immun, 70, pp.7042~7049 (2002)
42. Cai T, "Asymptomatic bacteriuria in recurrent UTI-to treat or not to treat", GMS Infect Dis, 5, pp.Doc09~ (2017)
43. Cai T, "Asymptomatic bacteriuria in clinical urological practice : preoperative control of bacteriuria and management of recurrent UTI", Pathogens, 5, pp.4~ (2016)
44. Marotz CA, "Improving saliva shotgun metagenomics by chemical host DNA depletion", Microbiome, 6, pp.42~ (2018)
45. Hasan MR, "Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing", J Clin Microbiol, 54, pp.919~927 (2016)
46. Bundgaard-Nielsen C, "Voided urinary microbiota is stable over time but impacted by post void storage", Front Cell Infect Microbiol, 10, pp.435~ (2020)
47. Vitko D, "Urinary tract infections in children with vesicoureteral reflux are accompanied by alterations in urinary microbiota and metabolome profiles", Eur Urol, 81, pp.151~154 (2022)
48. Al KF, "Ureteral stent microbiota is associated with patient comorbidities but not antibiotic exposure", Cell Rep Med, 1, pp.100094~ (2020)
49. Jones-Freeman B, "The microbiome and host mucosal interactions in urinary tract diseases", Mucosal Immunol, 14, pp.779~792 (2021)
50. Salabura A, "Urinary tract virome as an urgent target for metagenomics", Life(Basel), 11, pp.1264~ (2021)
51. Santiago-Rodriguez TM, "The human urine virome in association with urinary tract infections", Front Microbiol, 6, pp.14~ (2015)
52. Moustafa A, "Microbial metagenome of urinary tract infection", Sci Rep, 8, pp.4333~ (2018)
53. Schreiber PW, "Metagenomic virome sequencing in living donor and recipient kidney transplant pairs revealed JC polyomavirus transmission", Clin Infect Dis, 69, pp.987~994 (2019)
54. Burnham P, "Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract", Nat Commun, 9, pp.2412~ (2018)
55. Matsuo Y, "Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution", BMC Microbiol, 21, pp.35~ (2021)
56. van der Loos L, "Characterizing the ulva microbiome with long-reads from nanopore sequencing", Proceedings of the 12th International Phycological Congress, pp.38~ (2021)
57. Wei PL, "Characterization of fecal microbiota with clinical specimen using long-read and short-read sequencing platform", Int J Mol Sci, 21, pp.7110~ (2020)
58. Kai S, "Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer", FEBS Open Bio, 9, pp.548~557 (2019)
59. Lukjancenko O, "Comparison of 61sequenced Escherichia coli genomes", Microb Ecol, 60, pp.708~720 (2010)
60. Irinyi L, "Long-read sequencing based clinical metagenomics for the detection and confirmation of Pneumocystis jirovecii directly from clinical specimens : a paradigm shift in mycological diagnostics", Med Mycol, 58, pp.650~660 (2020)
61. Pearman WS, "Testing the advantages and disadvantages of short-and long-read eukaryotic metagenomics using simulated reads", BMC Bioinformatics, 21, pp.220~ (2020)
62. Beaulaurier J, "Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities", Genome Res, 30, pp.437~446 (2020)
63. Cuscó A, "Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces", BMC Genomics, 22, pp.330~ (2021)
64. Driscoll CB, "Towards long-read metagenomics : complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture", Stand Genomic Sci, 12, pp.9~ (2017)
65. Warwick-Dugdale J, "Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands", PeerJ, 7, pp.e6800~ (2019)
66. Kiguchi Y, "Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads", DNA Res, 28, pp.dsab019~ (2021)
67. Yahara K, "Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria", Nat Commun, 12, pp.27~ (2021)
68. Van Goethem MW, "Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics", Commun Biol, 4, pp.1302~ (2021)

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