General

Depending on the clinical situation, blood cultures should always be taken before starting antibiotic therapy to identify the causative pathogens if a systemic infection is suspected. If possible, at least two blood culture pairs (consisting of an aerobic and anaerobic bottle) should always be taken. Blood should only be taken for a blood culture from recumbent venous catheters in exceptional cases.

The total volume of blood collected increases the sensitivity of pathogen detection. A volume of 40 to 60 ml, distributed over 2 or 3 blood culture pairs, is optimal. A single blood culture bottle is filled with (8-)10 ml of blood.

A clinical deterioration of the patient under existing antibiotic therapy can, among other things, be an indication of ineffective antibiotic therapy. Here, too, the collection of blood cultures is recommended, even though the sensitivity of pathogen detection is lower than without existing antibiotic therapy. A maximum of 6 blood culture pairs are taken within 48 hours. If possible, blood should be taken at the end of the antibiotic dosing interval.

Extraction technology

1. First and foremost, disinfect your own hands! Since the skin is colonized by numerous bacteria, sufficient skin disinfection of the patient's puncture site is also mandatory for valid blood culture diagnostics. Spray or wipe disinfection twice is recommended. The twice disinfection includes first the cleaning step and then the disinfection step. The alcohol-based disinfectant is sprayed generously onto the skin or applied with a sterile swab and must be allowed to act for at least 1 minute (follow manufacturer's instructions). The puncture site must not be palpated with a non-sterile finger afterwards!
2. Collect 8- 10 ml of blood per blood culture bottle.
3. After removing the cap of the blood culture bottle, the rubber stopper underneath is disinfected with alcohol-based disinfectant. Inoculate one aerobic and one anaerobic BK bottle per collection. Please observe the instructions on the BK bottles regarding the minimum and maximum filling quantity. Label BK bottles with patient data: Name, date of birth, sender. Label aerobic and anaerobic bottles.
4. Specify the patient data, the collection day and time in the request document or on the accompanying bill. Provide further clinical information such as the type of material and collection site, infectiological question and/or suspected diagnosis, underlying diseases of the patient and previous or planned antibiotic therapy.

General

Meningitis is one of the life-threatening infectious diseases and is therefore usually also processed in the laboratory as an emergency. Rapid initiation of effective antibiotic therapy and identification of the responsible pathogen is life-saving. After obtaining the necessary materials, an effective calculated antibiotic therapy should be started - if necessary without waiting for the cultural microbiological findings. Microscopy of the cerebrospinal fluid can provide valuable information for this purpose. For the microbiological examination, the puncture of CSF and, in addition, the collection of blood cultures (see below) is useful. For the examination of the CSF sample, the microbiological on-call service can be reached at any time.

Extraction technology

1. Lumbar puncture for CSF collection must be performed under strictly aseptic conditions: Thoroughly spray on alcoholic skin disinfectant or apply several times with a sterile swab. Allow to react for at least three minutes. Perform puncture with sterile gloves.
2. As soon as the CSF drips off, drain 5 to 10 ml of CSF into 2-3 sterile tubes with screw caps. Close the tubes tightly so that the sample cannot leak. For the microbiological examination, the second sample should be used or the one that contains the least amount of blood.
3. If very little CSF can be obtained, it should be used for microbiological examination.
4. If tuberculous meningitis is suspected, at least 10 ml of CSF is required for the cultural examinations because of the frequently extremely low pathogen density. A larger volume of about 10 ml is also necessary for the detection of fungi.
5. Label the tubes with the CSF with patient data and explicitly state the material type CSF (otherwise there is a risk of confusion with urine!). 
6. Indicate the patient's data, the day and time of collection on the accompanying form. Provide further clinical information such as the type of material and collection site, infectious problem and/or suspected diagnosis, underlying diseases of the patient and previous or planned antibiotic therapy. It may be important to indicate previous neurosurgical or maxillofacial surgery or the presence of a CSF shunt or ventricular drainage.

Transportation

If acute meningitis is suspected, the CSF must be brought to the Institute of Medical Microbiology (Kreuzbergring 57) immediately and, if necessary, at the same time as the blood cultures - regardless of the time of day (if necessary, the microbiological on-call service should be requested via cell phone). Until the examination, the CSF should be kept at 37°C. If a delay in transport is unavoidable, an additional 1-2 ml of the CSF can be inoculated into an aerobic blood culture bottle. This should be incubated at 37oC and brought to the laboratory as quickly as possible without cooling.

Report of findings

If bacterial meningitis is suspected, the microscopic findings and, if applicable, the result of the direct antigen detection (agglutination reaction) from the CSF are immediately communicated to the attending physician by telephone. If the cultural findings are positive, the preliminary pathogen differentiation and - if available - a preliminary antibiogram are also communicated by telephone. Cultural testing is usually completed 48 to 72 hours after sample receipt. A final written report of the findings is then prepared.

The cause of a throat infection can usually be easily diagnosed by a throat swab. Because of the contaminating oral pharyngeal flora, the swab should be taken specifically from the site of infection, e.g., the tonsils. In the case of plaques, it is important to note whether they can be wiped away (e.g., in the case of candidiasis) or are fixed (e.g., in the case of diphtheria). The indication of whether tonsillitis is unilateral or bilateral can be indicative for further microbiological diagnostics.

Sample collection

The examination of swabs has the disadvantage of possible contamination with germs that have migrated secondarily into the lesion. Specimens should therefore be taken selectively. In the case of sessile coatings (e.g. diphtheria), these should be lifted off with forceps after local spray anesthesia and the smear taken from the now exposed mucosa. Transport media are available for transporting the smear. Indicate the patient's data, the day and time of collection on the accompanying form. Provide further clinical information such as the type of material and collection site, infectious question and/or suspected diagnosis, underlying diseases of the patient and previous or planned antibiotic therapy.

Transportation

Throat swabs should be taken to the Institute of Medical Microbiology (Kreuzbergring 57) as soon as possible because of the risk of overgrowth by normal flora. Outside the laboratory's acceptance times, these samples can be placed at the entrance to the institute in the mail slot located there (merges into a refrigerator). This is also useful on weekends, as the samples can then already be processed and the collection of findings is accelerated.

Report of findings

24 h after sample receipt, primary culture of rapidly growing pathogens is usually positive. Pathogen identification and antibiogram is completed in most cases 48-72 h after sample receipt. A written report of the findings is then issued.

General

Pneumonia requires detection of the responsible pathogens by microbiological examination for optimized therapy. Germs can be detected from variously obtained secretions of the deep respiratory tract such as sputum, tracheal/bronchial secretions, bronchial lavage and bronchioalveolar lavage (BAL) as well as transtracheal aspiration, transthoracic lung puncture and lung biopsy. The collection of these materials is invasive to a varying degree and in some cases involves a not insignificant burden for the patient. Therefore, sputum is usually examined first. During material collection, there is a risk of contamination with the site flora of the nasopharynx. This contamination must be avoided as far as possible. In some patients there is a bacteremia with the responsible pathogens (especially in pneumococcal pneumonia). For this reason, blood cultures should always be taken in the case of pronounced pneumonia.
The presence of tuberculosis or atypical (interstitial) pneumonia must always be indicated, since the pathogens causing these infections require special microbiological diagnostics.

Tuberculosis:
- Mycobacteria

Atypical pneumonia:
- Pneumocystis jiorovecii
- Mycoplasma (including serology)
- Chlamydia (including serology)
- Viruses, e.g. CMV (including serology)
- Legionella (including antigen detection from urine)
-Fungi, e.g.Aspergillus (including serology)

Extraction technology

1. Saliva is NOT sputum!!! The first sputum sample obtained early in the morning is the most suitable for microbiological examination. Good sputum shows only low contamination with the flora of the nasopharynx, only a few squamous cells and as a sign of the existing infection - significant amounts of leukocytes.
2. The patient should cough deeply and place the sputum in a sterile sputum container. Before collecting the sputum, any dentures should be removed and the mouth thoroughly rinsed with water to reduce site flora.
3. The portion of sputum best suited for cultural examination is that which contains visible purulent deposits. In special situations, such portions of a sputum can be obtained with a swab specifically for examination.
4. Tightly seal the sputum container and label it with the patient data, the sender and the material designation (sputum).
5. Indicate the patient's data, the day and time of collection on the accompanying form. Provide further clinical information such as the type of material and collection site, infectiological question and/or suspected diagnosis, underlying diseases of the patient and previous or planned antibiotic therapy.

Transportation

Sputum should be taken quickly to the Institute of Medical Microbiology and Virology (Kreuzbergring 57).

If transport requires more than two hours, sputum specimens should be refrigerated. Outside the laboratory's acceptance times, sputum samples can be placed at the entrance to the institute in the mail slot located there (directs directly to a refrigerator). This is also useful on weekends, as the samples can then already be processed and the collection of findings is accelerated.

Report of findings

The majority of pathogens relevant for pneumonia (except mycobacteria and pathogens of atypical pneumonia) can usually be detected culturally after 24 - 48 hours; the cultural examination with antibiogram can thus usually be completed 48 hours after sample receipt. A written report of the findings is issued at the end of the examination; urgent or unusual findings are communicated in advance by telephone.

General

In the case of intestinal infections, fresh stool should reach the laboratory while still warm, if possible. The indication of a possible stay in the tropics (special pathogen spectrum) or a previous antibiotic or chemotherapy (pseudomembranous colitis) may be of great importance for the microbiological diagnosis.

Sample collection

A pea-sized stool sample in a stool tube is sufficient for the examination. In the case of macroscopically visible parasites (e.g. worms), these may be sent directly in a stool tube.

Transportation

The stool should be brought to the Institute of Medical Microbiology and Virology (Kreuzbergring 57) directly after delivery and if possible still warm. Outside the laboratory's acceptance times, these samples can exceptionally be placed at the entrance to the institute in the mail slot located there (directs the sample directly into a refrigerator).

Report of findings

In the case of a diarrheal disease caused by parasites, the microscopic preparation may already provide decisive information on the etiology of the corresponding process shortly after receipt of the samples in the laboratory. 24 h after sample receipt, the primary culture of rapidly growing pathogens is usually positive. Pathogen identification and antibiogram is completed in most cases 48-72 h after specimen receipt. A written report of the findings is then issued. If the constellation of findings is appropriate, the findings are communicated in advance by telephone.

General

Urinary tract infections are among the most common infections in both outpatient and inpatient settings. Microscopic and cultural examination of a urine sample that has been correctly obtained and immediately taken to the laboratory can very quickly provide a causative diagnosis of the pathogen. Many community-acquired septicemias are caused by infections of the urinary tract. If pyelonephritis and urosepsis are suspected, blood cultures should be taken in addition to the urine sample.

In most cases, a urine culture before the start of therapy is sufficient for symptomatic patients, which should be checked three days after the start of therapy and after the end of therapy. For bacteriological testing to detect bacteria and fungi, a volume of 5-10 ml of urine is sufficient. For the detection of mycobacteria, a larger amount of urine (preferably morning urine) of about 50-100 ml must be sent in a sterile, tightly closed container. If necessary, the examination should be carried out three times in order to be able to exclude urogenital tuberculosis with the necessary certainty.

Because of the possible contamination of midstream and catheter urine with site flora of the anterior urethra, urine cultures are examined quantitatively. In the case of midstream urine, a urinary tract infection can be assumed if the bacterial count is ≥ 105 CFU/ml. At 104 CFU/ml, the findings require control. If the bacterial count is lower, a manifest UTI is unlikely. In permanent catheter urine, bacterial counts of 103- 104 CFU/ml are already considered significant. In addition, the microscopic findings of the urine sediment also play an important role in the assessment of all types of urine (e.g. leukocytes?).

Collection technique

Medium stream urine (MSU)

1. If possible, collect urine 3 hours after the last micturition, preferably in the morning.

For females:
Clean external genitalia with soap and water.
Spread labia.
Drain and discard the first 20-25 ml of urine.
Collect the following volume of urine in a sterile container without interrupting the stream.

In man:
Strip back foreskin and glans penis with water.
Leave the first 20-25 ml of urine and discard.
Obtain the following volume of urine without interrupting the stream in a sterile container.

2. The urine is filled into a sterile, tightly sealable tube, which is labeled with the patient's data, the sender and the type of material. 

Because of the risk of breakage, glass tubes must not be used under any circumstances.

3. Indicate the patient's data, the day and time of collection on the accompanying form. Provide additional clinical information such as the type of material and collection site, infectious and/or suspected diagnosis, patient's underlying diseases, and previous or planned antibiotic therapy. Be sure to inform the laboratory that the urine is midstream urine (MSU) and indicate whether the patient has typical symptoms of a urinary tract infection.

Puncture urine

1. In difficult conditions and with inconclusive findings from MSU, the collection of bladder puncture urine is helpful. Bladder puncture urine is usually sterile in healthy individuals.
2. Puncture is performed under aseptic conditions with a filled bladder using a sterile syringe.
3. The urine is filled into a sterile, tightly sealable tube, which is labeled with the patient data, the sender and the material designation.
4. Request voucher / accompanying document see above: It is essential to inform the laboratory that this is puncture urine (PU) and to state whether the patient has typical symptoms of a urinary tract infection.

Catheter urine

1. Thoroughly disinfect the sampling site or the drain tube.
2. A cannula is used to puncture the specimen collection site and the urine specimen is collected into a sterile syringe.
3. Under no circumstances separate the catheter and urinary drainage system for urine collection. Never use urine from the urine bag for culture!
4. The urine is filled into a sterile, tightly sealable tube, which is labeled with the patient data, the sender and the material designation (K-urine). 
5. Accompanying bill see above: Be sure to inform the laboratory that the urine is catheter urine (KU) and indicate whether the patient has typical symptoms of a urinary tract infection.

Transportation

Since urine is an optimal culture medium for bacteria, urine samples must be brought to the Institute of Medical Microbiology (Kreuzbergring 57) as soon as possible. A urine sample that cannot be examined in the laboratory within 30 min should be stored at 4oC until examination. The urine sample should arrive at the laboratory within 24h at the latest. Outside the laboratory's acceptance hours, urine samples can be placed at the entrance of the institute (Kreuzbergring 57) in the mail slot located there, which leads directly into a refrigerator. This is also useful on weekends, as the samples can then already be processed and the collection of findings is accelerated.

Report of findings

In most cases, the cultural examination will be completed with germ differentiation and antibiogram on the day after sample receipt in the laboratory. A written report of the findings will be prepared. In the case of unusual constellations of findings or an urgent clinical situation, the findings will be communicated by telephone.
In addition to the material-dependent (MSU, PU, KU) bacterial count, the leukocyte findings and the clinical symptoms are particularly decisive for the question of a required therapy. Since bladder puncture urine is sterile in healthy individuals, any evidence of germs will generally provide indications for appropriate therapy.

General

Colonization of the vagina with pathogens potentially dangerous to the child at birth can usually be easily diagnosed by a vaginal swab. Because of the contaminating local flora (lactobacteria and fecal flora), it should be specifically stated by the clinician that this is a screening as part of maternity care.

Sample collection

Since the general colonization of the vagina is to be examined, the smear can be taken directly from the vagina. Indicate the patient's data, the day and time of collection on the accompanying form. Provide further clinical information such as the type of material and collection site, infectious problem (pregnancy monitoring!!!).

Transportation

Vaginal swabs should be taken to the Institute of Medical Microbiology (Kreuzbergring 57) as soon as possible because of the risk of overgrowth by normal flora. Outside the laboratory's acceptance times, these samples can be placed at the entrance to the institute in the mail slot located there (merges into a refrigerator). This is also useful on weekends, as the samples can then already be processed and the collection of findings is accelerated.

Report of findings

24 h after sample receipt, primary culture of rapidly growing pathogens is usually positive. Pathogen identification and antibiogram is completed in most cases 48-72 h after sample receipt. A written report of the findings is then issued.

General

For microbiological examinations of wound swabs, the exact anatomical localization must be specified. It should also be specified whether the wound infection is superficial or deep, or whether it is an open or closed process, as the respective typical pathogen spectrum may differ.

Sample collection

Examination of swabs has the disadvantage of possible contamination with germs that have migrated secondarily into the lesion or open abscess. Before taking the specimen, the contaminating superficial flora should therefore be removed as far as possible. To do this, remove exudate with sterile swabs. Then obtain a sample with a swab from the base and the edge of the lesion by scraping off chunks of tissue. For dry skin and mucosal ulcers, obtaining tissue biopsies from the wound bed or margin is preferable.

Transportation

Wound swabs should be brought to the Institute of Medical Microbiology (Kreuzbergring 57) as soon as possible. Outside the laboratory's acceptance times, these samples can be placed at the entrance to the institute in the mail slot located there (merges into a refrigerator). This is also useful on weekends, as the samples can then already be processed and the collection of findings is accelerated.

Report of findings

24 h after sample receipt, the primary culture of rapidly growing pathogens is usually positive. Pathogen identification and antibiogram is completed in most cases 48-72 h after sample receipt. A written report of findings is then issued. In the case of infectious processes such as abscesses, deep wound infections, etc., the involvement of anaerobes must also be regularly expected. The primary cultivation and differentiation as well as antibiogram preparation of these pathogens takes longer than that of aerobically growing pathogens (72 to 96 hours). A written follow-up report is then submitted for the findings report. Because of the regular involvement of anaerobes in such infection processes and the difficulty of diagnosis, these pathogens must always be taken into account in a calculated therapy.