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Diversity of the midstream urine microbiome in adults with chronic kidney disease

International Urology and Nephrology Apr 18, 2018

Kramer H, et al. - The characteristics of the midstream urine microbiome were investigated in adults with stage 3–5 non-dialysis-dependent chronic kidney disease (CKD). The midstream voided urine microbiome is diverse among the older adults with stage 3–5 non-dialysis-dependent CKD. Greater microbiome diversity was observed in association with higher estimated glomerular filtration rate [eGFR].

Methods

  • From outpatient nephrology clinics, researchers recruited patients with non-dialysis-dependent CKD (estimated glomerular filtration rate [eGFR] < 60 ml/min/1.73 m2) and diuretic use.
  • Using the clean-catch method, they collected midstream voided urine specimens.
  • Determination of the bacterial composition was performed via sequencing the hypervariable (V4) region of the bacterial 16S ribosomal RNA gene.
  • Inclusion of extraction negative controls (no urine) was performed to assess the contribution of extraneous DNA from possible sources of contamination.
  • With the inverse Simpson, Chao and Shannon indices, they determined midstream urine microbiome diversity.
  • Further examination of the diversity measures was performed via demographic characteristics and via comorbidities.

Results

  • The cohort included 41 women and 36 men with detectable bacterial DNA in their urine samples [mean age was 71.5 years (standard deviation [SD] 7.9 years) (range 60–91 years)].
  • White (68.0%) comprised the majority of the cohort; a substantial minority of the cohort consisted of African-American (29.3%).
  • Findings revealed the mean eGFR of 27.2 (SD 13.6) ml/min/1.73 m2.
  • Circumcision was noted in most men (72.2%) and 16.6% reported a remote history of prostate cancer.
  • In this study, 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.
  • High levels of diversity was noted in the samples, 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)].
  • In participants with urgency urinary incontinence and higher estimated glomerular filtration rate (eGFR), higher diversity measures were generally noted.
  • Microbiome diversity was significantly associated with estimated eGFR after controlling for demographics and diabetes status(P < 0.05).

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