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      KCI등재

      Microbiome Analysis Using Next-Generation Sequencing in Urinary Tract Infections

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      https://www.riss.kr/link?id=A108118462

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      다국어 초록 (Multilingual Abstract)

      In recent decades, the understanding of the genetic information of microbes and hosts has advanced considerably with the development of next-generation sequencing (NGS). For infectious diseases, genomic analysis can provide valuable information on the...

      In recent decades, the understanding of the genetic information of microbes and hosts has advanced considerably with the development of next-generation sequencing (NGS). For infectious diseases, genomic analysis can provide valuable information on the host disease susceptibility, microbial pathogenicity, and drug sensitivity. For urinary tract infections (UTI), NGS can reveal the pathogenic microbe and the dysbiosis of the urinary microbiome, which is a crucial factor in the pathogenesis of UTI and other urinary tract disorders. This review outlines the role of urinary microbiome dysbiosis in UTI, urinary stone disease, and cancer.
      Furthermore, the recent advances in NGS technologies for future applications in infectious disease research are described in detail.

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      참고문헌 (Reference)

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      2 Bundgaard-Nielsen C, "Voided urinary microbiota is stable over time but impacted by post void storage" 10 : 435-, 2020

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      4 Subashchandrabose S, "Virulence and fitness determinants of uropathogenic Escherichia coli" 3 : 2015

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      8 Rani A, "Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance" 181 : 59-70, 2017

      9 Burnham P, "Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract" 9 : 2412-, 2018

      10 Al KF, "Ureteral stent microbiota is associated with patient comorbidities but not antibiotic exposure" 1 : 100094-, 2020

      1 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" 23 : 647-652, 2017

      2 Bundgaard-Nielsen C, "Voided urinary microbiota is stable over time but impacted by post void storage" 10 : 435-, 2020

      3 Hull RA, "Virulence properties of Escherichia coli 83972, a prototype strain associated with asymptomatic bacteriuria" 67 : 429-432, 1999

      4 Subashchandrabose S, "Virulence and fitness determinants of uropathogenic Escherichia coli" 3 : 2015

      5 Hilt EE, "Urine is not sterile : use of enhanced urine culture techniques to detect resident bacterial flora in the adult female bladder" 52 : 871-876, 2014

      6 Salabura A, "Urinary tract virome as an urgent target for metagenomics" 11 : 1264-, 2021

      7 Vitko D, "Urinary tract infections in children with vesicoureteral reflux are accompanied by alterations in urinary microbiota and metabolome profiles" 81 : 151-154, 2022

      8 Rani A, "Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance" 181 : 59-70, 2017

      9 Burnham P, "Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract" 9 : 2412-, 2018

      10 Al KF, "Ureteral stent microbiota is associated with patient comorbidities but not antibiotic exposure" 1 : 100094-, 2020

      11 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" 12 : 9-, 2017

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      14 Gottschick C, "The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment" 5 : 99-, 2017

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      18 Dornbier RA, "The microbiome of calcium-based urinary stones" 48 : 191-199, 2020

      19 Jones-Freeman B, "The microbiome and host mucosal interactions in urinary tract diseases" 14 : 779-792, 2021

      20 Santiago-Rodriguez TM, "The human urine virome in association with urinary tract infections" 6 : 14-, 2015

      21 Lewis DA, "The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults" 3 : 41-, 2013

      22 Mulder M, "The effect of antimicrobial drug use on the composition of the genitourinary microbiota in an elderly population" 19 : 9-, 2019

      23 Ackerman AL, "The bladder is not sterile : an update on the urinary microbiome" 14 : 331-341, 2019

      24 Roos V, "The asymptomatic bacteriuria Escherichia coli strain 83972 outcompetes uropathogenic E. coli strains in human urine" 74 : 615-624, 2006

      25 Pearman WS, "Testing the advantages and disadvantages of short-and long-read eukaryotic metagenomics using simulated reads" 21 : 220-, 2020

      26 Kuleshov V, "Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome" 34 : 64-69, 2016

      27 Plante JA, "Spike mutation D614G alters SARS-CoV-2 fitness" 592 : 116-121, 2021

      28 Toma I, "Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia" 52 : 3913-3921, 2014

      29 Flannigan R, "Renal struvite stones--pathogenesis, microbiology, and management strategies" 11 : 333-341, 2014

      30 Glover M, "Recurrent urinary tract infections in healthy and nonpregnant women" 25 : 1-8, 2014

      31 Josephs-Spaulding J, "Recurrent urinary tract infections : unraveling the complicated environment of uncomplicated rUTIs" 11 : 562525-, 2021

      32 Kai S, "Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer" 9 : 548-557, 2019

      33 Fischer H, "Pathogen specific, IRF3-dependent signaling and innate resistance to human kidney infection" 6 : e1001109-, 2010

      34 Plenge RM, "Molecular underpinnings of severe coronavirus disease 2019" 324 : 638-639, 2020

      35 Ambite I, "Molecular determinants of disease severity in urinary tract infection" 18 : 468-486, 2021

      36 Moustafa A, "Microbial metagenome of urinary tract infection" 8 : 4333-, 2018

      37 Schreiber PW, "Metagenomic virome sequencing in living donor and recipient kidney transplant pairs revealed JC polyomavirus transmission" 69 : 987-994, 2019

      38 Bajic P, "Male bladder microbiome relates to lower urinary tract symptoms" 6 : 376-382, 2020

      39 Warwick-Dugdale J, "Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands" 7 : e6800-, 2019

      40 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" 58 : 650-660, 2020

      41 Yahara K, "Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria" 12 : 27-, 2021

      42 Cuscó A, "Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces" 22 : 330-, 2021

      43 Van Goethem MW, "Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics" 4 : 1302-, 2021

      44 Kiguchi Y, "Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads" 28 : dsab019-, 2021

      45 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" 10 : 174-, 2012

      46 Zhang Q, "Inborn errors of type I IFN immunity in patients with life-threatening COVID-19" 370 : eabd4570-, 2020

      47 Marotz CA, "Improving saliva shotgun metagenomics by chemical host DNA depletion" 6 : 42-, 2018

      48 Pickard JM, "Gut microbiota : role in pathogen colonization, immune responses, and inflammatory disease" 279 : 70-89, 2017

      49 Garretto A, "Genomic survey of E. coli from the bladders of women with and without lower urinary tract symptoms" 11 : 2094-, 2020

      50 Chen SL, "Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection" 5 : 184ra60-, 2013

      51 Pairo-Castineira E, "Genetic mechanisms of critical illness in COVID-19" 591 : 92-98, 2021

      52 Matsuo Y, "Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution" 21 : 35-, 2021

      53 Wolfe AJ, "Evidence of uncultivated bacteria in the adult female bladder" 50 : 1376-1383, 2012

      54 Sundén F, "Escherichia coli 83972 bacteriuria protects against recurrent lower urinary tract infections in patients with incomplete bladder emptying" 184 : 179-185, 2010

      55 Schilling JD, "Effect of trimethoprim-sulfamethoxazole on recurrent bacteriuria and bacterial persistence in mice infected with uropathogenic Escherichia coli" 70 : 7042-7049, 2002

      56 Fredsgaard L, "Description of the voided urinary microbiota in asymptomatic prepubertal children-a pilot study" 17 : 545.e1-545.e8, 2021

      57 Hasan MR, "Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing" 54 : 919-927, 2016

      58 Lukjancenko O, "Comparison of 61sequenced Escherichia coli genomes" 60 : 708-720, 2010

      59 van der Loos L, "Characterizing the ulva microbiome with long-reads from nanopore sequencing" 38-, 2021

      60 Wei PL, "Characterization of fecal microbiota with clinical specimen using long-read and short-read sequencing platform" 21 : 7110-, 2020

      61 Cai T, "Asymptomatic bacteriuria in recurrent UTI-to treat or not to treat" 5 : Doc09-, 2017

      62 Cai T, "Asymptomatic bacteriuria in clinical urological practice : preoperative control of bacteriuria and management of recurrent UTI" 5 : 4-, 2016

      63 Siddiqui H, "Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons" 11 : 244-, 2011

      64 Beaulaurier J, "Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities" 30 : 437-446, 2020

      65 Mayne AIW, "Antibiotic treatment of asymptomatic bacteriuria prior to hip and knee arthroplasty; a systematic review of the literature" 16 : 176-182, 2018

      66 Siddiqui H, "Alterations of microbiota in urine from women with interstitial cystitis" 12 : 205-, 2012

      67 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" 19 : 213-220, 2017

      68 Oberle A, "16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis" 42 : 1097-1107, 2021

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      학술지 이력

      학술지 이력
      연월일 이력구분 이력상세 등재구분
      2023 평가예정 재인증평가 신청대상 (재인증)
      2020-01-01 평가 등재학술지 선정 (재인증) KCI등재
      2019-12-01 평가 등재후보로 하락 (계속평가) KCI등재후보
      2016-01-01 평가 등재학술지 선정 (계속평가) KCI등재
      2015-10-12 학술지명변경 한글명 : 대한요로생식기감염학회지 -> Urogenital Tract Infection
      외국어명 : The Korean Journal of Urogenital Tract Infection and Inflammation -> Urogenital Tract Infection
      KCI등재후보
      2015-01-01 평가 등재후보학술지 유지 (계속평가) KCI등재후보
      2013-01-01 평가 등재후보학술지 유지 (기타) KCI등재후보
      2011-01-01 평가 등재후보학술지 선정 (신규평가) KCI등재후보
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      학술지 인용정보

      학술지 인용정보
      기준연도 WOS-KCI 통합IF(2년) KCIF(2년) KCIF(3년)
      2016 0.07 0.07 0.06
      KCIF(4년) KCIF(5년) 중심성지수(3년) 즉시성지수
      0.04 0.03 0.28 0.04
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