When a urine test shows unexpected bacteria, it often causes concern about a potential infection. These organisms are frequently the body’s natural microbial communities, known as flora, appearing in the collected sample. The skin, genital area, and lower urinary tract host numerous types of bacteria that are harmless in their usual environments. During collection, these external microbes can be inadvertently transferred into the sample cup. Understanding the difference between these external bacteria and a true infection-causing pathogen is necessary for interpreting test results.
The Normal State of the Urinary Tract
The long-held belief that a healthy urinary tract is completely sterile has been corrected by modern scientific techniques. Advances in DNA sequencing have revealed a dynamic microbial community residing within the bladder and urethra, known as the urinary microbiome, or urobiome. This internal population of bacteria is normal and does not signify disease or contamination.
The urobiome contains a lower number of organisms compared to the gut, and includes many familiar types of bacteria. Common residents include certain species of Lactobacillus, Corynebacterium, and Streptococcus. These organisms are thought to play a role in maintaining the health of the urinary tract lining, potentially by preventing the colonization of more harmful bacteria. Establishing this baseline of resident bacteria is important for differentiating it from external skin flora introduced during collection.
Distinguishing Contamination from Infection
The presence of skin flora in a urine sample is defined as contamination, which is distinct from a true urinary tract infection (UTI). Contamination occurs when bacteria from the surrounding skin, perineal, or vaginal areas are introduced into the specimen during collection. This collection error can lead to a misleading result, suggesting an infection that is not present in the bladder.
Laboratories differentiate contamination from infection by analyzing the type of bacteria and the colony count. A true UTI is typically caused by a single uropathogen, such as Escherichia coli, growing in high numbers (\(\geq 10^5\) Colony Forming Units per milliliter). In contrast, a contaminated sample frequently shows “mixed flora,” meaning the growth of multiple different organisms, often at lower colony counts.
Common skin contaminants include Coagulase-negative Staphylococcus, Corynebacterium species, or various Enterococcus species. The report may also note the presence of squamous epithelial cells, which are skin cells shed from the external genital area. This finding suggests the sample passed over the skin without adequate cleansing, picking up these cells and associated bacteria. When a sample is flagged as contaminated, the result is unreliable for diagnosing a UTI, and a repeat collection is required.
Techniques for Minimizing Sample Contamination
To obtain a reliable urine culture, the “clean-catch” or “midstream” method must be followed to minimize contamination from skin flora. The process begins with thorough hand washing and opening the sterile collection cup without touching the inside or the inner lid surface. Cleansing the genital area is the next necessary step to reduce surface bacteria that could enter the sample.
For females, the labia should be separated, and the area wiped from front to back using a provided antiseptic towelette. Keep the labia separated until the sample has been collected. Males must retract the foreskin, if present, and wipe the head of the penis with the towelette.
The “midstream” technique is crucial for preventing contamination. The individual should begin urinating a small amount into the toilet first; this initial flow flushes out bacteria residing in the distal urethra. Without stopping the flow, the sterile cup is then moved into the stream to collect the middle portion of the urine.
Once the cup is approximately half-full, it should be removed, and the remaining urine can be passed into the toilet. The lid must then be secured tightly, again without touching the inside of the cup or lid, and the sample transported promptly. Following these precise steps ensures the sample accurately reflects the state of the urinary tract, preventing misdiagnosis from external skin flora contamination.