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

Abstract

BackgroundClinical dogma is that healthy urine is sterile and the presence of bacteria with an inflammatory response is indicative of urinary tract infection (UTI). Asymptomatic bacteriuria (ABU) represents the state in which bacteria are present but the inflammatory response is negligible. Differentiating ABU from UTI is diagnostically challenging, but critical because overtreatment of ABU can perpetuate antimicrobial resistance while undertreatment of UTI can result in increased morbidity and mortality. In this study, we describe key characteristics of the healthy and ABU urine microbiomes utilizing 16S rRNA gene (16S rDNA) sequencing and metaproteomics, with the future goal of utilizing this information to personalize the treatment of UTI based on key individual characteristics.MethodsA cross-sectional study of 26 healthy controls and 27 healthy subjects at risk for ABU due to spinal cord injury-related neuropathic bladder (NB) was conducted. Of the 27 subjects with NB, 8 voided normally, 8 utilized intermittent catheterization, and 11 utilized indwelling Foley urethral catheterization for bladder drainage. Urine was obtained by clean catch in voiders, or directly from the catheter in subjects utilizing catheters. Urinalysis, urine culture and 16S rDNA sequencing were performed on all samples, with metaproteomic analysis performed on a subsample.ResultsA total of 589454 quality-filtered 16S rDNA sequence reads were processed through a NextGen 16S rDNA analysis pipeline. Urine microbiomes differ by normal bladder function vs. NB, gender, type of bladder catheter utilized, and duration of NB. The top ten bacterial taxa showing the most relative abundance and change among samples were Lactobacillales, Enterobacteriales, Actinomycetales, Bacillales, Clostridiales, Bacteroidales, Burkholderiales, Pseudomonadales, Bifidobacteriales and Coriobacteriales. Metaproteomics confirmed the 16S rDNA results, and functional human protein-pathogen interactions were noted in subjects where host defenses were initiated.ConclusionsCounter to clinical belief, healthy urine is not sterile. The healthy urine microbiome is characterized by a preponderance of Lactobacillales in women and Corynebacterium in men. The presence and duration of NB and method of urinary catheterization alter the healthy urine microbiome. An integrated approach of 16S rDNA sequencing with metaproteomics improves our understanding of healthy urine and facilitates a more personalized approach to prevention and treatment of infection.

Human Microbiota Characterization in the Course of Renal Transplantation

“…Diverse microbial communities were identified in all sample types, except blood, with similar compositions as previously reported for the fecal and oral (19) and urine (20) microbiota. Compared to previously reported fecal microbiota compositions, rectal swabs from several patients also contained significant fractions of Lactobacillus and Streptococcus species.…”

Urinary Bacteria in Adult Women With Urgency Urinary Incontinence

“…Studies based on DNA and culture have provided evidence of live bacteria in urine samples that are deemed "culture-negative" by standard clinical microbiological procedures [3,5].…”

“…Recent DNA and culture-based evidence suggests that even when urine cultures are negative, detectable bacterial communities (microbiota) exist in the urine of some adult women, regardless of their urinary symptoms [3][4][5][6]. In addition to broader implications of this discovery for a variety of lower urinary tract disorders, these findings may allow us to identify baseline factors that predispose or even protect women to subsequent UTI.…”

Intestinal fungi contribute to development of alcoholic liver disease

“…Sequence processing and analysis steps were performed by our open-access, mothur-based (49) workflow software, YAP (46,50). Mothur version 1.34 was used in this study.…”