Study in infants identifies key species among abundant population.

Following research in other specialties to understand relevant microbiomes in their fields, urology studies are revealing a surprising abundance of microorganisms in the bladders of healthy infants. 

“Once we understand what is living inside the bladder, we may be able to come up with better ways to treat urinary-tract infections and move past our dependence on antibiotics, which can create so many problems,” said Douglass Clayton, M.D., an associate professor of urology at Vanderbilt.

“Antibiotics only treat the acute symptoms and they breed resistance. We don’t have good non-antibiotic treatments to reduce recurrent infections yet, and we really need them.”

Treatments Cry Out for Improvement

Clayton cares for many children who have recurrent UTIs despite taking antibiotics daily, and for others who have spina bifida and require intermittent catheterization for bladder management. “These children are chronically colonized with bacteria always present in their urine, and take antibiotics frequently and for long periods,” he said.

Clayton works on bladder microbiome research with partners including Maria Hadjifrangiskou, Ph.D., an associate director of the Vanderbilt Institute for Infection, Immunology and Inflammation, and Viktor Flores, M.D., who is completing a two-year pediatric urology fellowship at Vanderbilt.

The new research builds on existing expertise at Monroe Carell Children’s Hospital at Vanderbilt and could inform alternative UTI treatment strategies. Clayton’s previous work focused on ways to improve and expand treatment options for children with urinary disorders.

Shaking Up Traditional Thinking

While the Human Microbiome Project, begun in 2007, has revealed several microbiomes across various bodily systems, no one looked at the bladder, Clayton explained.

“Back then, the technology wasn’t there to study the bladder microbiome. We hadn’t figured out the culture environment that was needed, and there was a presumption for many years that the bladder was a sterile environment.”

If a urine sample from a patient with no symptoms is placed on a traditional culture environment, nothing grows, he explained. New technical approaches were necessary to study bladder-dwelling microorganisms.

“We may be able to come up with better ways to treat urinary-tract infections and move past our dependence on antibiotics.”

Developing New Techniques

The research team decided to work with infants to explore how early microorganisms inhabit the bladder and to investigate the nature of these microorganisms. They recruited 50 male infant patients who were going to be circumcised under anesthesia and obtained the parents’ permission to catheterize the infants while they were already sedated.

Torres took samples in conjunction with Hadjifrangiskou’s laboratory.

“We dove into the technical aspects of the work. How do we handle the samples? How much urine do we need? What do we do with it? How do we identify the bacteria?” Clayton said.

Innovative Approaches

Until now, urology researchers have taken a one-size-fits-all approach to culturing bacteria in urine to find which microorganism is causing disease, Hadjifrangiskou explained.

“We did two things differently,” she said. “First, we obtained urine that hadn’t left the body and wasn’t contaminated by bacteria outside the bladder. Second, we changed the food we provided and the growing conditions, and so many microbes grew.”

The research team also developed controls to account for environmental contamination.

Their approach is expected to serve as a protocol for future research.

The Eureka Moment

Ultimately, the team observed many bacteria not previously identified in pediatric urine.

“More than 50 percent of our samples from healthy children grew dozens of different bacteria,” Clayton said.

Based on sequencing, the outlines of a pediatric urobiome began to emerge.

Standard laboratory conditions were learned to be ineffective at culturing many of the microbes identified through sequencing. By altering these standards, the researchers were able to culture key members of the male pediatric urobiome.

Notably, 36 percent of the samples yielded microorganisms Actinotignum schaalii, which seems to be associated with prostate inflammation in adult men, Hadjifrangiskou said. The researchers went on to sequence the genomes of the Actinotignum schaalii strains they collected, aiming to dissect the biology of this understudied bacterium.

Hopes for Better Prevention and Treatment

The study offers a springboard to understand the influence of antibiotic use on the urobiome.

Pediatric urologists prescribe many antibiotics to prevent recurring UTIs, although the drugs’ long-term effects are unclear.

“If you take 14 days of a strong antibiotic, that can permanently wipe out certain good bacteria in the gut for life,” Clayton said.

No one knows what this practice may ultimately mean for the bladder, because study of the bladder microbiome is still in its infancy.

“Understanding what happens in the bladder is a huge step to identifying ways to prevent recurrent infections,” he said.

About the Expert

Douglass Clayton, M.D.

Douglass Clayton, M.D., is an associate professor of urology in Vanderbilt University Medical Center’s Division of Pediatric Urology. His care emphasizes management of children with myelomeningocele, the fetal diagnosis of urologic anomalies, and minimally invasive surgeries. His research interest is the role of hypoxic signaling in the bladder and the therapeutic effects of acute activation of the hypoxia inducible factor pathway in the bladder.

Maria Hadjifrangiskou, Ph.D.

Maria Hadjifrangiskou, Ph.D., is an associate professor of urology, pathology, microbiology and immunology at Vanderbilt University Medical Center. Her research centers around how bacteria that cause urinary tract infections sense and respond to environmental signals.