Urine Is Not Sterile: Use of Enhanced Urine Culture Techniques To Detect Resident Bacterial Flora in the Adult Female Bladder

TLDR

Prior 16S rRNA sequencing studies have shown that bacterial genomes can be detected in urine from both symptomatic and asymptomatic patients even when standard cultures are negative. This study aimed to show that many of the organisms identified by 16S rRNA sequencing are cultivable using an expanded quantitative urine culture (EQUC) protocol. The authors applied EQUC, which involves plating larger urine volumes, varied atmospheric conditions, and prolonged incubation, to 65 specimens from 41 overactive bladder patients and 24 controls, comparing results to standard culture. EQUC detected bacterial growth in 80% of samples, identifying 35 genera and 85 species—most frequently Lactobacillus, Corynebacterium, Streptococcus, Actinomyces, and Staphylococcus—whereas standard culture reported no growth in 92% of those cases, demonstrating that the adult female bladder harbors a resident microbiota.

Abstract

ABSTRACT Our previous study showed that bacterial genomes can be identified using 16S rRNA sequencing in urine specimens of both symptomatic and asymptomatic patients who are culture negative according to standard urine culture protocols. In the present study, we used a modified culture protocol that included plating larger volumes of urine, incubation under varied atmospheric conditions, and prolonged incubation times to demonstrate that many of the organisms identified in urine by 16S rRNA gene sequencing are, in fact, cultivable using an expanded quantitative urine culture (EQUC) protocol. Sixty-five urine specimens (from 41 patients with overactive bladder and 24 controls) were examined using both the standard and EQUC culture techniques. Fifty-two of the 65 urine samples (80%) grew bacterial species using EQUC, while the majority of these (48/52 [92%]) were reported as no growth at 10 3 CFU/ml by the clinical microbiology laboratory using the standard urine culture protocol. Thirty-five different genera and 85 different species were identified by EQUC. The most prevalent genera isolated were Lactobacillus (15%), followed by Corynebacterium (14.2%), Streptococcus (11.9%), Actinomyces (6.9%), and Staphylococcus (6.9%). Other genera commonly isolated include Aerococcus , Gardnerella , Bifidobacterium , and Actinobaculum . Our current study demonstrates that urine contains communities of living bacteria that comprise a resident female urine microbiota.