This specimen will not reflex to a urine culture meaning

Interpreting culture results and laboratory tests has long been the bread and butter of clinical practice. Basic Chemistries are relatively straight forward, and modern lab result sheets come with a handy reference that shows the upper and lower limits of ‘normal’ values.

However, interpreting culture results is a bit more tricky. In this series, we will discuss the nuances of urine cultures, blood and body fluid cultures, and other cultures such as wound and respiratory cultures. First, let’s talk about urine cultures.

In today’s clinical practice, especially in the hospital or ER setting, automated or reflex urine cultures are quite common. Most hospital-based laboratories have parameters set that, if met, will trigger an automatic culture of a urine sample that appears to possibly be infected. For patients who are symptomatic of UTI, this is very helpful for us as clinicians to ensure that patients are being treated with appropriate antibiotics. However, what if the patient does not have symptoms to suggest UTI? How can we determine if this patient requires antibiotic therapy or not?

Specimen Collection

In order to discuss urine cultures, we first have to talk about specimen collection and the potential for contamination. The only way to completely eliminate the potential for contamination of the urine sample is a sterile, suprapubic percutaneous bladder tap. However, this is not a practical option in clinical practice, so let’s move on.

Next in order of aseptic collection would be urethral catheterization for a sample of urine directly from the bladder. This is easily achieved in clinical practice, and reasonably tolerated, however it still requires staff trained in the sterile technique and procedure.

The most common method for sample collection is the ‘clean catch’ midstream specimen. This is achieved by having the patient clean the urethral meatus with an antiseptic solution, void 10-20ml of urine to eliminate the risk of urethral contaminants, and then collect urine for testing. To avoid contamination of the specimen with cells from the genital mucosa or skin, uncircumcised men need to be sure to retract the foreskin and women need to separate the labia away from the urethral opening.

Urinalysis Assessments

Now that we have a good specimen, let’s discuss urinalysis interpretation. The majority of urinalysis’ are performed using the dipstick method in which a test strip is dipped into the urine sample for a specified amount of time, and then it is either ‘read’ by a colorimetric machine or compared to a standardized chart that is supplied with the kit. This will give information such as the urine pH, specific gravity, protein content, WBC count, and presence of Leukocyte Estrace and Nitrite.

UA’s performed not using the dipstick method may also report the presence/absence of bacteria and squamous epithelial cells. All of this information can help the astute clinician decide if the patient likely has a urinary tract infection, and whether or not a culture of the urine is warranted.

When assessing a urinalysis for potential infection, the two most common results looked at are the presence of Nitrite and leukocyte esterase in the urine.

Leukocyte esterase is a byproduct having WBC’s in the urine (pyuria), but does not always indicate active urinary tract infection. In women, the presence of leukocyte esterase in a urine sample, especially with large volumes of epithelial cells present, can represent improper cleaning prior to the collection of the specimen and contamination with vaginal secretions.

The presence of Nitrite in the urine is much more indicative of UTI, in both men and women. Nitrite is produced when bacteria in the urine convert dietary nitrate into nitrite. Not all urinary pathogens do this, however, so a negative nitrite test does not exclude UTI. Also, low bacteria concentrations and acidic urine (such as when a patient drinks Cranberry juice to treat UTI) will not allow the production of nitrite.

Conversely, substances that can add a red tint to the urine, such as AZO, Pyridium, and beets, can give a falsely positive nitrite test. The ideal UA result to indicate an active UTI in a symptomatic patient is one that shows the presence of nitrite, leukocyte esterase, and WBC’s without signs of contamination with epithelial cells.

Before we get into the culture results interpretation, we need to discuss some potential pitfalls. First, the presence of bacteria in the urine does not necessarily indicate active infection, especially in the asymptomatic patient.

Secondly, in women the presence of WBC’s in the urine without significant bacteria usually represents either an asymptomatic STI (usually Chlamydia), of some other inflammatory response within or adjacent to the urinary system such as pyelonephritis, chronic interstitial cystitis, or even diverticulitis/colitis. We won’t go into these topics here, but I want to make sure that they are in your differential.

To culture or not to culture?

So, now that we have a UA from a symptomatic patient that indicates infection, do we need to culture? If the patient has classic UTI symptoms without evidence of pyelonephritis on physical exam, and they do not have frequently recurrent UTI, then they probably do not warrant culture.

However, if they have a history of recurrent UTI, or ones that are difficult to treat requiring multiple courses of antibiotics, then a culture is a good idea. By obtaining a urine culture and sensitivity in these patients, you will be better able to treat your patient effectively without increasing the risk of developing antibiotic resistant infections.

Interpreting Culture Results

Once the C&S returns, how do we interpret it? Well, if you have selected your patient population for culture carefully, then the results should be straight forward. You should have an identified bacterial pathogen with >100,000 CFU/ml and a list of common antibiotic treatments and the ability of those medications to kill the pathogen, the sensitivity.

If you have prescribed your patient an antibiotic that displays resistance, then notifying your patient and changing medications should be all that is required. The tricky part comes in when you have results that are less clear cut.

Typically, if a patient has classic UTI symptoms, any culture that grows greater that 10,000 CFU/ml of a pathogenic bacteria is sufficient. If the result is between 10,000 CFU/ml and 100,000 CFU/ml of typically non-pathogenic bacteria or mixed urethral flora, then either the sample is contaminated or the patient may have a urethral irritation causing symptoms, but not necessarily an infection. Also, consider the fact that the patient may have an underlying STI causing the urethritis, so obtaining a careful history is crucial.

Beyond the Automatic Reflex

Now, remember that part earlier about automatic reflex to culture from hospital laboratories? What if you obtain a UA as part of a generalized “abdominal pain” work up, even though the patient has no specific urinary symptoms or complaints, and it shows 2+ WBC, is positive for leukocyte esterase, and has 3+ squamous epithelial cells? This is the kind of sample that is frequently reflexed for automatic culture.

However, because you have been thorough in your history taking and examination, as well as interpreting the UA, you have determined that the patient does not have a UTI and that this is a contaminated sample. But the culture comes back with 10,000 CFU/ml of E. coli, how do you handle this?

If your work up for the abdominal pain did not reveal a cause, and you chose not to treat this contaminated urine sample, the best course of action would be to contact the patient and see how they are feeling. If they continue to not have urinary symptoms, are afebrile, and otherwise stable, this can be considered a contaminant and the patient can be advised to follow up for a repeat UA. However, if they have begun to develop UTI symptoms, then a course of antibiotics is obviously recommended.

Know the Nuances

Laboratory result interpretation, especially urinalysis results, can seem straight forward. However, there is an art to it. It is important to know the nuances of the tests and their results in order to appropriately treat your patient, and to be a good antibiotic steward. The ‘shotgun’ approach to ordering laboratory tests does not promote good patient care or manage costs effectively, especially when asymptomatic patients are treated. Hopefully this can helped clear up some questions about urinalysis and urine cultures. In future articles, we will discuss blood cultures and wound cultures and their appropriate uses and interpretations.

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