Kramer Holly, Kuffel Gina, Thomas-White Krystal, Wolfe Alan J, Vellanki Kavitha, Leehey David J, Bansal Vinod K, Brubaker Linda, Flanigan Robert, Koval Julia, Wadhwa Anuradha, Zilliox Michael J
Department of Public Health Sciences, Loyola University Chicago, 2160 S. First Avenue, Maywood, IL, 60153, USA.
Medicine, Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA.
Int Urol Nephrol. 2018 Jun;50(6):1123-1130. doi: 10.1007/s11255-018-1860-7. Epub 2018 Apr 12.
To examine the characteristics of the midstream urine microbiome in adults with stage 3-5 non-dialysis-dependent chronic kidney disease (CKD).
Patients with non-dialysis-dependent CKD (estimated glomerular filtration rate [eGFR] < 60 ml/min/1.73 m) and diuretic use were recruited from outpatient nephrology clinics. Midstream voided urine specimens were collected using the clean-catch method. The bacterial composition was determined by sequencing the hypervariable (V4) region of the bacterial 16S ribosomal RNA gene. Extraction negative controls (no urine) were included to assess the contribution of extraneous DNA from possible sources of contamination. Midstream urine microbiome diversity was assessed with the inverse Simpson, Chao and Shannon indices. The diversity measures were further examined by demographic characteristics and by comorbidities.
The cohort of 41 women and 36 men with detectable bacterial DNA in their urine samples had a mean age of 71.5 years (standard deviation [SD] 7.9) years (range 60-91 years). The majority were white (68.0%) and a substantial minority were African-American (29.3%) The mean eGFR was 27.2 (SD 13.6) ml/min/1.73 m. Most men (72.2%) were circumcised and 16.6% reported a remote history of prostate cancer. Many midstream voided urine specimens were dominated (> 50% reads) by the genera Corynebacterium (n = 11), Staphylococcus (n = 9), Streptococcus (n = 7), Lactobacillus (n = 7), Gardnerella (n = 7), Prevotella (n = 4), Escherichia_Shigella (n = 3), and Enterobacteriaceae (n = 2); the rest lacked a dominant genus. The samples had high levels of diversity, as measured by the inverse Simpson [7.24 (95% CI 6.76, 7.81)], Chao [558.24 (95% CI 381.70, 879.35)], and Shannon indices [2.60 (95% CI 2.51, 2.69)]. Diversity measures were generally higher in participants with urgency urinary incontinence and higher estimated glomerular filtration rate (eGFR). After controlling for demographics and diabetes status, microbiome diversity was significantly associated with estimated eGFR (P < 0.05).
The midstream voided urine microbiome of older adults with stage 3-5 non-dialysis-dependent CKD is diverse. Greater microbiome diversity is associated with higher eGFR.
研究3 - 5期非透析依赖型慢性肾脏病（CKD）成人患者的中段尿微生物群特征。
从门诊肾病诊所招募非透析依赖型CKD患者（估计肾小球滤过率[eGFR]<60 ml/min/1.73 m²）且正在使用利尿剂的患者。采用清洁中段尿法收集尿液标本。通过对细菌16S核糖体RNA基因的高变区（V4）进行测序来确定细菌组成。纳入提取阴性对照（无尿液）以评估可能污染源的外来DNA的影响。用逆辛普森指数、Chao指数和香农指数评估中段尿微生物群多样性。通过人口统计学特征和合并症进一步研究多样性指标。
41名女性和36名男性的尿液样本中可检测到细菌DNA，平均年龄为71.5岁（标准差[SD]7.9岁，范围60 - 91岁）。大多数为白人（68.0%），相当少数为非裔美国人（29.3%）。平均eGFR为27.2（SD 13.6）ml/min/1.73 m²。大多数男性（72.2%）行包皮环切术，16.6%报告有前列腺癌既往史。许多清洁中段尿标本以棒状杆菌属（n = 11）、葡萄球菌属（n = 9）、链球菌属（n = 7）、乳杆菌属（n = 7）、加德纳菌属（n = 7）、普雷沃菌属（n = 4）、埃希菌属 - 志贺菌属（n = 3）和肠杆菌科（n = 2）为主（>50%读数）；其余样本缺乏优势菌属。用逆辛普森指数[7.24（95%CI 6.76，7.81）]、Chao指数[558.24（95%CI 381.70，879.35）]和香农指数[2.60（95%CI 2.51，2.69）]衡量，样本具有高度多样性。急迫性尿失禁患者和估计肾小球滤过率（eGFR）较高的参与者的多样性指标通常更高。在控制人口统计学和糖尿病状态后，微生物群多样性与估计的eGFR显著相关（P<0.05）。
3 - 5期非透析依赖型CKD老年患者的清洁中段尿微生物群具有多样性。微生物群多样性越高，eGFR越高。
