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In addition to the commonly known laboratory tests of blood and urine, there are also microbiological tests. Unfortunately, they are very often underestimated by doctors who prefer to prescribe an antibiotic “blind” and thus treat a disease caused by a pathogenic microorganism.
Routine blood and urine tests and microbiological tests
Most of us patients have been repeatedly referred to various types of laboratory tests. In order to diagnose or check general health, the doctor ordered blood or urine tests. Basic blood parameters such as blood count, blood glucose (blood glucose level), lipid profile (HDL cholesterol, LDL cholesterol and triglyceride levels), ESR (Biernacki’s test – a marker of inflammation in the body) are routinely measured. In the case of urine, the so-called general examination including the description of its color, pH level, specific gravity, glucose level, presence of ketones, protein level, bilirubin level, number of red and white blood cells, presence of oxalate or calcium crystals and others. The mentioned parameters are the most basic factors determined in patients. Everyone has had such tests at least once, and it should be remembered that they should be performed once a year as part of prophylaxis. As a rule, we know how to prepare for such analyzes and we can roughly interpret the test results. It can be said that blood and urine tests have, in a way, become routine, although perhaps they should be ordered a little more frequently.
In addition to the commonly known laboratory tests of blood and urine, there are also microbiological tests. Unfortunately, they are very often underestimated by doctors who prefer to prescribe an antibiotic “blind” and thus treat a disease caused by a pathogenic microorganism. Such a procedure often contributes to the unnecessary treatment of the patient with successive ineffective antibiotics, which leads to a prolonged period of illness and the formation of antibiotic-resistant bacteria. This unpopularity of microbiological research also results in patients knowing little or nothing about them. In this article, I will try to briefly explain the basics of such research, how to prepare for the collection of material and interpretation of the results. The information provided here may prove crucial for the proper performance of a microbiological test and thus for success in the treatment of ailments caused by pathogenic microorganisms.
General principles in microbiological research
The diagnostic value of a microbiological test depends on the quality of the material to be tested. Errors made at the stage of collecting the material usually make it impossible to determine the pathogenic factor of the infection, which can no longer be compensated by even the best quality laboratory diagnostics.
The second important factor for the correctness of microbiological diagnostics is the transport of materials to the microbiological laboratory. The effectiveness of the diagnostic process in the laboratory depends to a large extent on its organization and time.
An important problem in microbiological diagnostics is also distinguishing the commensal flora (physiological, i.e. the one that naturally occurs in certain regions of our organisms) from the microorganisms that cause the infection. It is important especially in the case of collecting material for examination, e.g. from the gastrointestinal tract, genital tract, skin, or the oral cavity. Usually, such a distinction is made by a microbiological laboratory and lists only pathogenic microorganisms as a result. The referring physician should also be prepared to correctly interpret the results from the laboratory.
Downloading materials for microbiological testing
The material for testing can theoretically be collected from almost any place in the body. The most common locations are: nasopharyngeal cavity with paranasal sinuses, ears, skin (wounds, skin lesions, abscesses, nails), venous blood, eyes, genital tract in women, urethra (along with prostate secretions) in men, urine, lower respiratory tract (bronchi, lungs), anus, cerebrospinal fluid from the spinal canal of the spine, body cavities such as the abdominal cavity, pleural cavity. The very location of some of the above-mentioned places in the body shows that the collection of material for examination requires the personal involvement of an experienced physician. I will not describe the individual procedures here, because it is not important knowledge for patients. Instead, I will try to present the correct procedure when collecting material for examination in a doctor’s office or in an outpatient clinic. In addition, I will describe how a patient can take a urine or stool sample at home for microbiological testing.
Rules of conduct:
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The materials should be collected before administering antimicrobial drugs (antibiotics), or at least 3 days after the end of treatment (follow-up examination)
If the patient has already received the drug, the referral should state what the drug is and for how long it was (was) administered.
Preparation of the patient
If the material is collected from body cavities or it is blood or cerebrospinal fluid, the skin should be decontaminated with iodine or alcohol (70%) preparation.
Material from the skin, nose, anus, genital tract, urethra, mouth, eye – it is enough to clean the place of collection with a sterile cotton swab moistened with saline solution. The use of disinfectants in these places is obviously not recommended !!!
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The material should be collected by trained persons (medical personnel)
The person collecting the material should wear disposable protective gloves.
The patient may collect the material on his own only if he has been instructed in the procedure (urine, faeces).
Material transport
Transport time as short as possible, and materials should be transported in special transport media that will keep the microorganisms in the sample alive.
Blood and cerebrospinal fluid should be transported at human body temperature.
Treat all samples as potentially infected with HBV (hepatitis B virus), HCV (hepatitis C virus), HIV.
Reference for testing – must be attached to the sample for testing.
It should contain all necessary information for the correct microbiological assessment of the material sent (diagnosis or suspicion of the disease, treatment (what), time of collection (when), other important circumstances accompanying the collection of the material, data enabling the identification of the patient, the doctor and the referring unit).
Regardless of the referral, on the sample containing the material for testing, write the name and surname of the patient as well as the date and time of collecting the material.
Self-collection of material by the patient:
Urine:
Physiologically urine should be sterile. Collecting urine for microbiological testing is of great importance for the correct interpretation of the test result. It is easy to contaminate the sample with the bacterial flora around the mouth of the urethra, foreskin, vagina or vulva. Morning urine (the highest number of microorganisms) is best suited for testing. Never collect potty urine or a duck for testing!
Wash your hands with soap and water and dry with a disposable towel.
In men, remove the foreskin and wash the glans penis with soap and water, then rinse.
In women, thoroughly wash the perineum from front to back, preferably four times with soapy water and then rinse. Pat dry with a disposable towel.
Drain about half of the contents of the bladder, and then, without stopping the stream, collect about 5 ml of urine into a sterile container. It is the collection of urine from the so-called middle stream. A sterile urine container can be purchased from any pharmacy.
Close the vessel immediately without touching its rim or the inside of the cap.
Until it is sent to the laboratory, keep the vessel in the refrigerator, but not longer than 3 hours.
In young children, special adhesive urine bags can be used, but this method carries a high risk of contamination of the sample.
Feces:
The patient should completely empty the bladder to avoid urinating when pushing to stool.
The patient should pass the faeces into a clean vessel (duck, potty) or into a toilet bowl, lined with a special insert preventing the contact of the sample with water.
Take a hazelnut-sized stool sample (preferably with mucus, blood, or pus if present) from the shipping container. If the stool is liquid, 1-2 ml is sufficient.
It is best to take 2-3 samples, which increases the chance of detecting the pathogen.
Send the samples to the laboratory within 2-3 hours.
If the sample is a swab, place the swab in a special transport medium that prevents the access of air (available at pharmacies) and send it to the laboratory.
It is relatively common to refer women to microbiological examinations of the genital tract. The gynecologist sometimes wants to find out if the inflammation in these areas is caused by a bacterial or fungal infection. The collection of the material should be performed on a gynecological chair, because this is the only way to properly obtain a sample from the affected areas. It also avoids touching the swab to the skin, which can falsify the test result. At this point, I would like to emphasize that before the examination, the patient should wash herself as much as possible. Sometimes there are women who say that the gynecologist recommended not to wash for several days before collecting the material for microbiological examination. This is obviously inadvisable, not only for hygienic reasons, but in fact, it will cause the appearance of microorganisms that multiplied precisely because the patient did not follow the hygiene rules. Before collecting the material for testing, wash yourself, but do not irrigate.
As for men, a similar test (although rarely performed) is collecting secretions from the prostate gland (prostate). Unfortunately, the gland itself is beyond the reach of a normal swab, so in order for the collection to be possible, the secretion of the gland must reach the opening of the urethra. For this purpose, the doctor or nurse initially performs a massage of the prostate area (the section between the scrotum and the anus or the finger through the anterior wall of the anus). The massage stimulates the prostate to produce a secretion that moves towards the opening of the urethra where it can be collected with a thin swab. Again, it is advisable to thoroughly wash the perineum and glans area before collecting the material to avoid contamination of the sample.
The interpretation of the results of laboratory tests is basically the responsibility of the doctor and the person performing the analysis, i.e. the laboratory diagnostician. The result of the microbiological test should include the following information:
Place or type of collected material, e.g. blood, abscess, etc.
Microorganism (with its full Latin name) cultured or detected by other tests, or absent.
If the result was positive, there must be information about the sensitivity of bacteria or fungi to selected antibiotics and antifungal drugs. This will allow the use of an effective drug.
In the case of urine, information is also provided whether the result was negative, doubtful (too few bacteria in the sample, which may indicate that everything is fine, but the urine sample was contaminated during its collection and it is advisable to repeat the test) or positive (a lot of bacteria). bacteria in urine).
Quantitative results are also often given for virological tests, where it is called viremia, i.e. the number of individual viruses per unit of blood volume. This is the case, for example, in the case of HIV. This procedure allows you to monitor the effectiveness of the treatment.
If the sample was taken from a site naturally inhabited by microorganisms, the result should indicate whether or not such microorganisms were detected. It is important to distinguish between pathogens and those that should be present.
Correct preparation for collecting the material, its correct collection, transport to the laboratory, carrying out the laboratory analysis itself and finally the correct interpretation of the test result are the key to success in the diagnosis and treatment of diseases caused by pathogenic microorganisms. In Poland, it is necessary to increase the number of ordered microbiological tests.
Text: Tomasz Gosiewski, MD, PhD
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