General information

Cystic fibrosis (CF) is dominated by chronic bacterial infections of the upper and lower respiratory tract. The special milieu of the CF lung offers ideal conditions for colonisation, especially with bacteria that are ubiquitous in the environment, some of which are phylogenetically closely related to each other. Many of these pathogens are very rarely found as infectious agents in non-CF patients. In addition to the classic pathogens of respiratory tract infections in CF (“CF lead germs”), especially P. aeruginosa, S. aureus, Haemophilus influenzae and B. cepacia complex, numerous other pathogens are found more rarely. These often come from the group of non-fermenters (e.g. other Pseudomonas spp., Chryseobacterium spp., Pandoraea spp., Ralstonia spp., Inquilinus limosus and many others). In CF, therefore, there is always an indication for microbiological diagnostics, which must be oriented towards the special spectrum of pathogens in CF and is carried out primarily within the framework of regular control examinations and in the case of clinical deterioration (“exacerbation”).

Range of services

• Pathogen isolation and identification via semi-quantitative culture on special and selective media as well as molecular methods
• Subtyping based on phenotypic and/or genotypic characteristics
• Advice on antibiotic therapy

Background

Molecular biological detection methods have become established in many areas of medical microbiology. Specific DNA detection methods have made it possible to detect and identify bacteria without cultivation, to obtain information on resistance behaviour (e.g. vancomycin resistance in enterococci, methicillin resistance in S. aureus, clarithromycin resistance in H. pylori) or even to uncover infection chains in hospitals on a molecular level (e.g. spa typing of MRSA isolates, MLST for Legionella).

Molecular laboratory diagnostics of infectious diseases at the Max von Pettenkofer Institute

The molecular biological diagnostics of the Max von Pettenkofer Institute currently allow the direct PCR-based detection of approx. 35 human pathogens (including e.g. Borrelia, Mycoplasma). Using a so-called “universal” PCR, we are also able to detect DNA from more than 99% of human pathogens and identify them by subsequent sequencing.

This is particularly useful when pathogens are difficult or impossible to cultivate or when antibiotic therapy has already taken place before the sample was taken (e.g. apparently “sterile” meningitis, pleurisy or joint effusions). Another field of molecular diagnostics is the rapid detection of “atypical” pneumonia pathogens, such as Mycoplasma pneumoniae, Chlamydophila pneumoniae or Legionella. The rapid detection of MRSA and VRE is also part of molecular diagnostics.

Most PCR examinations are carried out daily, in many cases a result is obtained on the same day. Molecular diagnostics at the Max von Pettenkofer Institute is of course carried out according to the highest quality standards and has been subject to strict internal and external controls for years. The laboratory division “Molecular Diagnostics” is accredited by the Central Office of the Federal States for Health Protection with regard to Medicinal Products and Medical Devices (ZLG).

You can find further information in our list of services.

Range of services

Microscopic examination of biopsies, punctates, secretions for protozoa and helminths.
Echinococcus granulosus serology.

For parasitological stool examination we recommend sending 3 stool samples from different days. The stool samples for parasitological examinations should be filled into special sample containers with stabiliser (MIF Fixativ) (stool: at least the size of a hazelnut; duodenal juice: at least 1 ml of sediment; 24-h collection urine). Sample containers with stabiliser can be ordered from the Max von Pettenkofer Institute (089/2180-72811).

Attention: MIF solution has a disinfecting effect. For this reason, the prepared sample material is no longer suitable for cultures (e.g. bacteriology).

You can find further information in our List of Services.

Notes on material collection:

Swabs: For both molecular and cultural diagnostics, please use flocked swabs in liquid medium (e-swab or similar). If possible, obtain swabs before starting anti-infective therapy.

Abscesses: A punctate provides much more conclusive findings than swabs. If smears are sent in, as much material as possible should be obtained from the depth and marginal areas of the inflammatory focus. Contamination with neighbouring skin or mucous membrane areas should be avoided; this applies in particular to wounds with high contamination (e.g. skin ulcerations, diabetic foot, etc.).

Eye swab: Local anaesthetics may contain antibacterial additives. The material should therefore be obtained before anaesthesia. For conjunctival samples, be sure to moisten the swab with sterile saline and swipe vigorously 2-3 times over the lower conjunctiva. False negative results are often caused by insufficient amounts of material. Take swabs (separately) from both eyes, using swabs for this purpose. In ulcers, always take material from the edge of the ulcer.

BAL: 20-30ml in a sterile screw-top vial.

Blood cultures: Blood sampling should be done before starting antibiotic therapy or at the end of the dosing interval, if possible. Each collection should include one aerobic and one anaerobic bottle. The filling quantity is 8-10ml of blood; PEDS bottles can be used for children. These are filled with 0.5 – 5ml of blood. If sepsis is suspected: obtain 2 – 3 samples at short intervals (5-30 min), if endocarditis is suspected: obtain 3 – 6 samples at 4 – 6 hour intervals. To exclude persistent Staphylococcus aureus bacteraemia: Send follow-up blood cultures within 2 days after starting therapy. Ensure sufficient skin disinfection (contact time min. 1 minute). In general: Do not take blood samples from a lying catheter because of the risk of contamination (exception: if catheter infection is suspected, take samples from catheter and peripheral vein); arterial blood cultures are not advantageous. Transport to the laboratory should be done as soon as possible. It is possible to send the bottles by pneumatic tube. Incubation prior to transport should not be done as it interferes with pathogen detection.

Endotracheal aspiration (ENTA), tracheal secretion, bronchoscopy Secretion: 2-5ml in sterile screw-top vial

Ear canal swab: Avoid touching inconspicuous areas of skin. For dry inflammatory forms, moisten swab with sterile saline solution. If otomycosis is suspected, remove skin flakes with sterile spatula and send in sterile tube.

Tissue: Tissue should be sent in a sterile screw-top tube. To protect the sample from drying out, please add a small amount of NaCl solution.

Catheter tip, heart valve, implant: Part of the implant (not longer than 5 cm !!) sterile screw-top tube.

Bone marrow puncta: If there is a question of mycobacteria, please send in citrate tubes, otherwise in blood culture bottles.

CSF: 1-2ml in sterile screw-top tube

Gastric fasting secretion/ gastric lavage water: usually sent for mycobacteria detection. Please use transport tubes with trisodium phosphate.

The “Varia” section examines various patient samples, such as blood cultures, urine, materials from the respiratory tract, smears and tissue samples of all kinds from all body regions, as well as stool samples.
The examination programme includes all major aerobic and anaerobic bacteria as well as yeasts and moulds.

In the diagnostic area “Varia”, all conventional methods of bacteriological diagnostics are offered. These include microscopy, also as rapid diagnostics, cultural cultivation under aerobic and anaerobic conditions, identification of pathogens and sensitivity testing of relevant bacteria against all antibiotics listed in the KUM drug list. On special request, other antibiotics can of course also be included in the testing.

In addition, antigen detection is offered as rapid tests for legionella, pneumococci and meningococci as well as C. difficile toxin detection.

The Varia department also carries out the entire mycological diagnostics. Here, too, microscopy, culture, identification of yeasts and moulds and sensitivity testing of yeasts and, on special request, of moulds against the essential antimycotics are offered.

You can find the detailed information in our List of Services.

Of course, the medical staff of this unit are always available for consultation on diagnostic and therapeutic issues.

In addition to comprehensive analysis, we offer advice on the rational and effective use of microbiological diagnostics (diagnostic stewardship) as well as assistance in interpreting findings and in anti-infective therapy. We support the Antibiotic Stewardship (ABS) initiative and work in an interdisciplinary team consisting of infectiologists, pharmacists and ABS certified microbiologists. Our goal is to achieve optimal clinical treatment outcomes for patients, avoid unnecessary toxicities and have a favourable impact on the development of resistance and costs through evidence-based therapy recommendations. Our guideline-based therapy recommendations take into account the local germ frequency and resistance statistics collected by the Max von Pettenkofer Institute at the University Hospital of Munich (KUM). Consultation takes place within the framework of regular or occasion-related microbiological / ABS rounds and by telephone on weekdays from 8:00 a.m. to 5:00 p.m. as well as outside office hours via the microbiological service telephone. Case discussions take place in cooperation with the clinical infectious diseases department in the infection colloquium on Mondays from 13:00 to 14:00. Written recommendations for the therapy of defined infectious disease patterns are drawn up by the infectious diseases colloquium at the KUM (iKUM) in a clinic-wide consensus and are continuously updated.

Links
ABS Initiative Deutschland
Antiinfektiva Surveillance
Die Bayerische Antibiotikaresistenz-Datenbank BARDa

interne Links
Stabstelle ABS (derzeit nur aus dem Intranet abrufbar)
Apotheke KUM
Stabstelle klinische Mikrobiologie und Hygiene
Sektion Infektiologie Med IV

Background

Serological tests are of great importance in the differential diagnosis of many infectious diseases. The prerequisite is an intact immune system that is capable of producing antibodies when confronted with a pathogen. Since this usually takes a few days, serology is not suitable for acute diagnosis. In general, IgM detection correlates with a recent infection, while IgG antibodies are indicative of a chronic or past infection. A seroconversion or a significant rise in titer of more than 2 levels also speaks for an acute disease event. Therefore, a second examination of the serum is usually indicated.

Serological examinations can be disturbed by cross-reactions (antigen communities of different pathogens) or by polyclonal immune stimulation (e.g. in EBV infection). Autoantibodies such as rheumatoid factors can lead to false positive IgM detections. Therefore, serological findings should always be evaluated in conjunction with the clinical picture and other microbiological examinations and are usually not suitable as the sole basis for a diagnosis.

Serological examinations require approx. 5-10 ml of blood (serum tube) or 1 ml of cerebrospinal fluid (sterile tube). For the determination of the CSF/serum index, CSF and serum should be sent from the same day of collection.

If you have any questions, please contact us at the following telephone number:

Serology Main Laboratory: +49 89 2180-72840

Background

Mycobacteria are slow-growing bacteria whose cultural cultivation requires special conditions. Mycobacteria include the tuberculosis pathogens (M. tuberculosis, M. bovis, M. caprae, M. africanum, M. microti, M. canetii, M. pinnipedii), which are grouped together as the Mycobacterium tuberculosis complex, as well as more than 100 other mycobacterial species that are widely distributed in the environment. The tuberculosis laboratory at the Max von Pettenkofer Institute offers tests for the detection of the Mycobacterium tuberculosis complex as well as atypical mycobacteria. The pathogen is usually detected from sputum, bronchial secretion or tracheal secretion, but is also possible from gastric juice, urine, pleural exudate, cerebrospinal fluid and other puncture samples or biopsy samples.

For rapid clarification of infectivity, a microscopic examination for acid-fast rods (Ziehl-Neelsen stain) should always be carried out in cases of suspected pulmonary tuberculosis. About 10^4 germs/ml must be present to obtain a positive result, and a reliable differentiation between tuberculosis bacteria and environmental mycobacteria is not possible. Therefore, it is always necessary to do a culture as well. For the rapid diagnosis of Mycobacterium tuberculosis complex from patient samples, a molecular rapid detection by PCR is available (result is available within 1-2 working days). If the result is negative, however, infection with mycobacteria cannot be ruled out. After successful treatment of tuberculosis, DNA can sometimes still be detected after a year. At the Max von Pettenkofer Institute, a combination of liquid and solid media is used after decontamination of the test material. By using a liquid medium with indicators for bacterial growth, the detection time is reduced to 1 – 2 weeks. However, the cultures are incubated for up to 6 weeks (liquid media) to exclude delayed growth.

Non-tuberculous mycobacteria can also be detected culturally in our laboratory. As these are increasingly isolated, especially in immunocompromised or cystic fibrosis patients, reliable and rapid detection is also an important part of our diagnostics. Resistance tests for non-tuberculous mycobacteria are not part of our range of services. In this case, please contact the National Reference Centre for Mycobacteria in Borstel (Prof. Dr. med. Florian Maurer; Nat. Reference Centre Tel: 04537 – 188 – 2110). Reference is made to the ATS – Guidelines for the Treatment of Non-Tuberculous Mycobacterial Infections of the American Thoracic Society and the recommendations of the DZK – Central Committee for the Control of Tuberculosis.

If you have any other questions, you can reach us at the following telephone number: Tuberculosis Laboratory: +49 89 2180-72844

Range of services

• Microscopic detection of acid-fast rods
• Culture cultivation of mycobacteria with liquid and solid culture media
• Detection of Mycobacterium tuberculosis complex with nucleic acid amplification methods
• Differentiation of mycobacteria with conventional methods and molecular biological techniques
• Susceptibility testing of Mycobacterium tuberculosis complex in liquid culture media

Useful information on diagnostics (briefly summarised)

A test of 3 sputums taken on consecutive days can exclude overt tuberculosis with a very high probability in the case of culturally negative findings.
If pulmonary tuberculosis is suspected: BAL, sputum (if overt TB) or gastric juice.
If extrapulmonary tuberculosis is suspected: Biopsy, punctate or cerebrospinal fluid.

Open tuberculosis is said to exist if there is at least one cultural detection of MTB complex from a material that is excreted by the body (e.g. urine or sputum).

Emergency preparation

A so-called native preparation without pre-enrichment for rapid diagnosis is not recommended, because the diagnostic sensitivity decreases significantly due to loss of patient material. If no acid-fast rods are detected in it, this by no means excludes a tuberculosis infection.

You can find more information in our List of Services.

For the highly sensitive, molecular detection of SARS-CoV-2, we perform PCR-based, quantitative detection of the pathogen from respiratory swab material seven days a week. Both rapid diagnostics (result approx. 1-2 hours after sample receipt) and stand tests (result approx. 4-6 hours after sample receipt) are available.

Furthermore, we routinely perform quantitative determinations of antibodies against the spike antigen (vaccination success) and the nucleocapsid antigen (serological detection of infection) of SARS-CoV-2.

In research projects, we continue to perform neutralization activity assay against replication-competent variants of SARS-CoV-2 (EU1, as well as variants-of-concern (VoCs) alpha, beta, gamma, delta, and omicron-BA.1, BA.4, BA.5) and other current VoCs or variants-of-interest (VoIs). We also quantify the avidity of anti-spike IgGs to better assess not only the quantity but also the quality of these important antibodies for protection against infection and disease.

The hygiene laboratory is approved as a drinking water testing centre according to §15 TrinkwV and carries out hygienic-microbiological examinations of water samples for both hospitals and private senders. In addition, we offer a wide range of hygienic-microbiological examinations for quality assurance in medical facilities (especially in clinics and medical or dental practices).