A urine culture is a common diagnostic test used to determine the presence of a urinary tract infection (UTI) by growing and identifying microorganisms in a urine sample. Patients often encounter the term “resident flora” or “normal flora” on their results, which can be confusing. This terminology refers to microorganisms that naturally inhabit the body’s surfaces. Their appearance on a lab report usually indicates a collection issue, not a true disease. Interpreting the presence of this flora is necessary to distinguish between a contaminated sample and a clinically significant infection.
What is Normal Resident Flora
Normal resident flora refers to the diverse population of microorganisms that live on or within the human body without causing harm. This community is also known as the human microbiota. In the genitourinary system, the upper tract (bladder and kidneys) is typically considered sterile in healthy individuals. The lower urinary tract, specifically the distal urethra and surrounding skin, naturally hosts a variety of bacteria.
These harmless organisms are primarily a mixture of bacteria from the skin and genital area. Common examples include Lactobacillus species, coagulase-negative staphylococci, and various diphtheroids. The presence of these microbes is a normal biological phenomenon and is not associated with disease in this location.
The function of this flora is often protective; for example, Lactobacillus helps maintain an acidic environment that prevents pathogen colonization. The key distinction in a urine culture is that organisms like Escherichia coli (E. coli) are known uropathogens that cause UTIs. Resident flora, conversely, are considered non-pathogenic contaminants.
How Urine Samples Become Contaminated
Contamination occurs when resident flora from the skin or urethra enters the collection cup, mixing with the urine intended for testing. This happens when the “clean-catch midstream” collection procedure is not followed precisely. The goal of this technique is to minimize the inclusion of external bacteria.
The proper procedure requires thorough cleansing of the genital area using antiseptic wipes before collection. For females, this involves separating the labia and wiping front to back; males must wipe the head of the penis. The next step involves voiding a small amount of urine into the toilet first, which flushes out bacteria residing in the beginning of the urethra.
The actual sample is collected midstream, meaning the cup is placed into the flow after the initial urine has passed. Improper technique, such as inadequate cleaning, touching the inside of the sterile cup, or failing to collect the midstream portion, allows normal flora to enter the sample. When this occurs, the lab report shows growth originating from the patient’s skin or genital area rather than a true bladder infection.
Interpreting Culture Results
The laboratory uses specific criteria to determine if the presence of bacteria represents a true urinary tract infection or simple contamination. This interpretation hinges on three main factors: the number of bacteria, the type of organism, and the diversity of organisms present. The amount of bacteria is quantified using Colony-Forming Units per milliliter (CFU/mL).
Bacterial Count (CFU/mL)
A high number of a single type of organism, typically greater than 100,000 CFU/mL in a clean-catch sample, is considered a positive result indicative of a UTI. Low counts, such as less than 10,000 CFU/mL, often suggest the bacteria are contaminants collected during voiding. Lower counts may still be significant if the patient is symptomatic or the sample was collected using a catheter.
Type of Organism
The type of organism is a significant differentiating factor. Finding a high count of E. coli, which causes about 70% of UTIs, points toward infection. Conversely, if the growth is primarily skin organisms, such as Lactobacillus or Staphylococcus epidermidis, the result is often classified as contaminated, especially if the count is low. The microbiologist also considers the presence of white blood cells (pyuria), as a true infection involves an inflammatory response.
Diversity of Organisms
The third criterion is polymicrobial growth, defined as the presence of three or more different types of bacteria. A true UTI is overwhelmingly caused by a single dominant organism. If the report states “mixed flora” or shows multiple distinct organisms with no single type predominating, this suggests the sample was contaminated by external sources. In these cases, the lab may not perform susceptibility testing, recognizing the result as clinically irrelevant. The final interpretation requires correlating all lab findings with the patient’s clinical symptoms.
When a Repeat Test is Necessary
A healthcare provider requests a repeat urine culture when initial results are inconclusive or compromised but the patient’s symptoms persist. A common reason is when the lab report indicates contamination, such as “mixed flora” or a low CFU count, yet the patient still shows signs of a UTI (e.g., painful urination or frequency). The decision to re-test is based on clinical suspicion outweighing the ambiguous laboratory finding.
If the initial clean-catch sample yielded many different bacterial species, a doctor might opt for a more sterile collection method, such as a catheterized sample. This technique bypasses the external genitalia and urethra, virtually eliminating contamination by resident flora. A repeat culture is also necessary if symptoms do not improve after starting antibiotic treatment, suggesting possible treatment failure or organism resistance.