Abstract
BackgroundThe urinary tract is inhabited by a diversity of microorganisms, known as the genitourinary microbiota. Here, we investigated the association between the use of antimicrobial drugs and the composition of the genitourinary microbiota.ResultsClean-catch urinary samples were collected from 27 participants of the Rotterdam Study. Bacterial DNA was extracted and the 16S ribosomal RNA gene variable regions V3 and V4 were analyzed using Illumina sequencing. 23 of the 27 participants were included in the analysis. The population consisted of 10 men and 13 women with a mean age of 75 ± 3 years. The time between the last prescription of an antimicrobial drug and sampling was determined and categorized. The use of antimicrobial drugs prior to urine sampling was associated with statistically significant differences in the beta-diversity of the genitourinary microbiota. No association was found between antimicrobial drug use and the alpha-diversity of the genitourinary microbiota. Operational Taxonomic Units (OTUs) that were lowest in participants who used antimicrobial drug belonged to Lactobacillus and Finegoldia. In contrast, an OTU belonging to the genus Parabacteroides had higher abundances. Also, an OTU belonging to the species E.coli was higher in the participants who used antimicrobial drugs.ConclusionPrior use of antimicrobial drugs is associated with a different composition of the genitourinary microbiota. Our results might indicate a persisting effect of antimicrobial drugs on the composition of the microbiota, but reverse causality cannot be ruled out. Future studies are needed to differentiate between two possibilities. Genitourinary dysbiosis could be the result of antimicrobial drug use or genitourinary dysbiosis could be a risk factor for urinary tract infections resulting in increased use of antimicrobial drugs. This may have important implications for treatment and prevention of (recurrent) UTIs.
Highlights
The urinary tract is inhabited by a diversity of microorganisms, known as the genitourinary microbiota
In 1979, it was recognized that slow-growing micro-organisms were missed when standard culturing techniques were used [3]. It was only with the development of 16S ribosomal Ribonucleic acid (RNA) sequencing that it was established that most body sites are colonized with bacteria, but the urinary tract was not tested in the Human Microbiome
We do not know whether she had symptoms indicating a Urinary tract infection (UTI), we could not exclude a UTI at the time of sampling
Summary
The urinary tract is inhabited by a diversity of microorganisms, known as the genitourinary microbiota. In 1979, it was recognized that slow-growing micro-organisms were missed when standard culturing techniques were used [3]. It was only with the development of 16S ribosomal RNA sequencing that it was established that most body sites are colonized with bacteria, but the urinary tract was not tested in the Human Microbiome (2019) 19:9. The microbiota seem to be more complex with higher interindividual variability than in males [7], but no clear relation with urinary tract infections (UTIs) has been demonstrated until now. No evident core microbiota have been found yet, this could possibly be present when grouping by age [7, 8]
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