A urine culture is a laboratory test designed to identify and quantify microorganisms, such as bacteria or fungi, present in a urine sample. The test helps healthcare providers determine if a person has a urinary tract infection (UTI) and, if so, what specific microbe is causing it. When a culture result contains “positive flora,” it simply means that bacteria were found growing on the culture plate. However, this finding alone does not automatically confirm an active and clinically significant infection, which is why the results require careful interpretation.
The Purpose of a Urine Culture
The primary reason a urine culture is ordered is to diagnose a suspected urinary tract infection (UTI). Symptoms often include painful urination, increased frequency, or lower abdominal discomfort. The urinary tract above the urethra, including the bladder and kidneys, is typically sterile and should not contain microorganisms. However, the lower urinary tract and surrounding skin naturally host a community of microorganisms, referred to as “flora” or the microbiome.
The test involves spreading a measured amount of the urine sample onto a nutrient-containing plate, called a culture medium, to encourage microbial growth. The plate is then placed in an incubator for 24 to 48 hours. If bacteria or yeast are present, they multiply and form visible clusters called colonies. Lab technicians count these colonies to determine the concentration of microorganisms in the original sample.
What Makes a Culture Result “Positive”
A culture result is deemed “positive” when the number of bacteria grown reaches a threshold high enough to indicate a true infection rather than contamination. This quantification is measured in Colony Forming Units per milliliter (CFU/mL), representing the number of viable bacterial cells present. For a clean-catch, midstream sample, the standard threshold is typically 100,000 CFU/mL of a single organism.
This high number is used as a cutoff because it suggests the bacteria are actively multiplying within the urinary tract, characteristic of an infection. Counts significantly lower than 100,000 CFU/mL, such as 10,000 CFU/mL, are often considered clinically insignificant or suggestive of contamination. However, these results are always interpreted alongside the patient’s symptoms. The type of organism is also a factor; the presence of species like the Gram-negative rod Escherichia coli is highly indicative of a UTI, sometimes even at lower colony counts.
Infection Versus Sample Contamination
Interpreting a positive culture requires distinguishing between a genuine infection and simple sample contamination. The external genital area and surrounding skin contain natural flora, such as non-pathogenic Staphylococcus species or Lactobacillus. These external bacteria can easily be introduced into the urine cup during collection. If these external bacteria are the source of growth, the result is considered contamination, and the patient does not have a true UTI.
A key indicator of contamination is the presence of three or more different bacterial species in the culture, especially at low colony counts. To minimize this risk, patients are instructed to perform a “clean-catch” midstream collection. This involves thoroughly cleansing the genital area, voiding a small amount of urine, and then collecting the middle portion of the stream. A high number of squamous epithelial cells in the lab report also suggests the sample was contaminated with external flora and may necessitate a retest.
Identifying the Organism and Next Steps
Once a positive culture is confirmed to represent a true infection, the laboratory identifies the specific microorganism and determines the most effective treatment. Escherichia coli (E. coli) is the most frequent causative agent, responsible for 65% to 75% of community-acquired UTIs. Other common pathogens include Klebsiella pneumoniae and Staphylococcus saprophyticus.
To guide treatment, the lab performs an Antibiotic Sensitivity Test (AST), also called a susceptibility test. This process exposes the isolated bacteria to various antibiotics to see which ones inhibit growth. Results are reported as Susceptible (S), Intermediate (I), or Resistant (R) for each medication. This allows the healthcare provider to prescribe a targeted antibiotic highly likely to eradicate the specific bacteria. This targeted approach ensures effective treatment and helps mitigate the development of antibiotic resistance.