Extended Quantitative Urine Culture Characterizes the Urinary Microbiome in Infant Males
Viktor Xavier Flores, MD, Seth Reasoner, BS, Benjamin Abelson, MD, Carmila Manuel, BS, Abby S. Taylor, MD, John C. Thomas, MD, Cyrus M. Adams, MD, Mark C. Adams, MD, Grace Morales, BS, Gerald T. Van Horn, PhD, Jonathan E. Schmitz, MD, PhD, Maria Hadjifrangiskou, PhD, Douglass Clayton, MD.
Vanderbilt University Medical Center, Nashville, TN, USA.
BACKGROUND: Interest in exploring the urinary microbiome has increased in our field. Expanded quantitative urine culture (EQUC) is a new and more sensitive culturing method that can be applied when standard urine culture fails to detect fastidious uropathogens. EQUC has been used along with more traditional methods of microbiome assessment such as 16s rRNA sequencing to prove the existence of a urinary microbiome. To date, EQUC has not been used to study the pediatric urinary microbiome of asymptomatic healthy infants. We hypothesized that EQUC can be used to profile the urinary microbiome in infant males.
METHODS: IRB approval was obtained to collect sterile catheterized urine samples from healthy infants less than 12 months of age undergoing an elective circumcision under general anesthesia. Exclusion criteria included prior history of UTI, genitourinary anomaly, urethral catheterization or receiving preoperative antibiotics. Urine aliquots were plated using a modified EQUC protocol consisting of 5% Sheep's Blood and Brucella agars, incubated anaerobically and aerobically at 5% at CO2 for 2 to 5 days. Speciation of facultative and obligate anaerobic bacterial isolates were verified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF). Our primary endpoint was to characterize the type of organisms that could be captured using EQUC in healthy infant males. Our Secondary endpoint was to determine if race, gestational term at birth, type of delivery, or prior antibiotic exposure was associated with EQUC detection.
RESULTS: Fifty patients consented to participate in this study. The mean age at the time of surgery was 231 days old (range 180 to 348 days). Thirty-six percent of patients did not grow organisms using EQUC, 24% grew at least one organism, 22% grew two different organisms, and 18% grew 3 to 5 different organisms. Infants born full term (≥ 37 weeks gestation) or via cesarean section were more likely to grow an organism using EQUC (p≤0.05) (table 1). Overall, there were 39 different isolates identified, with the highest representation in the Actinomycetaceae (17%) and Enterobacteriaceae (12%) Family (figure 1). The most common species was Actinotignum schaalii seen in 18% of infants and Enterobacter faecalis in 12%.
CONCLUSIONS:
Using EQUC, we identified bacterial isolates in 64% of healthy infants, with 39 distinct organisms identified. We identified Actinotignum schaalii as a common organism in 18% of patients. The role of this bacteria in the urinary tract will require further study. Our results demonstrate that a urinary microbiome can be detected in a significant number of healthy male infants using enhanced culturing methods. 
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