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Institute for Hygiene and Microbiology

Diagnostic Microbiology

The diagnosis of infectious diseases is an essential part of modern medicine. Nowadays most infections are treatable - given that they are detected correctly and quickly enough. In close cooperation with the treating colleagues, we aim to find the causes of infectious diseases, identify pathogens and define a promising therapy regimen. Accordingly, the Institute for Hygiene and Microbiology is also accredited as a medical laboratory by the German Accreditation Body (DAkkS) in accordance with DIN EN ISO 15189-2014: Accreditation certificate & attachment

Division Management Microbiological Diagnostics:
Prof. Dr. rer. nat. Dr. med. Christoph Schoen
phone: +49 931-31-46162

Deputy Division Management Microbiological Diagnostics:
PD Dr. med. Thiên-Trí Lâm
phone: +49 931-31-46737

Division Management Infection Serology:
Prof. Dr. med. Alexandra Schubert-Unkmeir
phone +49 931-31-46721

In addition to laboratory work, counselling - by telephone or directly at the patient's bedside - is an essential part of the "Microbiological Diagnostics" service. Therefore, a medical consultation service is available around the clock for IHM senders.

As a research-active university institute, it is also our task to implement new techniques and microbiological findings in diagnostic methods and to evaluate them. This is done both within the framework of the National Reference Centres NRZMyk for Invasive Fungal Infections (main location: Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena), NRZMHi for meningococci and Haemophilus influenzae and in the consiliary laboratory for echinococcosis, which are located at the Institute, and in the daily work of the wokring group "Diagnostics Research". For this reason, the annex to the accreditation certificate does not always reflect the current status of the procedures used in the accredited area. Therefore, a list of the currently used examination procedures is available for download.

Regular Service Hours:

Monday – Friday: 8:00 AM –   5:00 PM (deadline for acceptance   4:30 PM)
Saturday: 8:00 AM – 12:00 AM (deadline for acceptance 11:30 AM)
Sunday and Holidays: 9:00 AM – 12:00 AM (deadline for acceptance 11:30 AM)


Special opening hours apply for certain holidays (e.g. Easter, Whitsun) and the turn of the year. These are announced in advance on the homepage of the Institute for Hygiene and Microbiology.

The diagnostic laboratories are staffed at the times indicated and can be reached for information by telephone via the central results information line (Tel. 31-46939). All examination materials are accepted.

Please note:

  • Please register materials that will not be dispatched until after 4 pm by calling 31-46939..
  • In order to ensure rapid and preferential processing and interim findings, we ask that urgent emergency examinations be notified in advance by telephone and that an appropriate note (e.g. "urgent" or "cito!") be made on the requisition slip."
  • In the case of urgent examinations, materials may also be processed outside regular service hours (see below). In these cases, the doctor on duty can be reached through the 201-13 switchboard via an emergency number.
  • On weekends, we offer limited routine diagnostics. This includes microscopic and cultural detection of bacterial pathogens in all clinical samples as well as MRSA screening (PCR rapid test). The infection serology and molecular biology laboratories are not staffed at weekends.

Transport and storage conditions for materials for examination at the Institute of Hygiene and Microbiology

Outside the regular gate opening hours, we ask that material be placed in the refrigerator or 25°C cabinet in the entrance area of the Institute. The following applies:

25°C - cupboard (room temperature):

  •         Blood cultures (no pre-incubation please!)
  •         Punctates (pleura, ascites, joint punctate)
  •         Swabs (nasal, throat, wound, abscess swabs)
  •         CSF for bacterial examinations (native or in blood culture bottles)
  •         Uricults (urine native in refrigerator)


  •         Catheter tips
  •         Respiratory materials (sputum, tracheal secretions, bronchial secretions)
  •         Urine native
  •         Stool
  •         Serum
  •         CSF for serological tests
  •         Samples for hospital and environmental hygiene


Materials stored differently must be packaged and labelled separately.

For telephone counselling, please contact us during regular office hours at the central information desk:

For enquiries about findings/information during regular office hours, please dial the following number
central information desk: 31-46939.

Current findings are medically validated during regular office hours and are usually available from 1:30 PM. They can be accessed directly via LAURIS. Medically validated preliminary findings can also be retrieved directly via LAURIS at any time in the form of PDF documents.

The microbiological telephone consultation in emergency and weekend service includes:

- Information on material submission and pre-analytical requirements
- Questions on the selection of further microbiological examinations in the case of a suspected infectious disease
- Pathogen-specific hospital hygiene information
- Information on antibiotic therapy appropriate to the pathogen

The microbiological therapy recommendation is always pathogen- or infection-related on the basis of germ identification and antibiogram. Side effects, drug interactions and the patient's general clinical situation cannot be taken into account here.

Further microbiological-infectiological case discussions usually require a separate infectiological consultation by an infectiologist or clinical microbiologist. They are therefore not possible within the framework of the microbiological emergency and weekend service.

The following people are available for infectious diseases counselling:  
Doctor on duty:
For enquiries regarding microbiological diagnostics, please contact:  
Prof. Dr. Dr. C. Schoen 31-46162
Dr. T.-T. Lâm


For questions on serological pathogen diagnostics, please contact:  
Prof. Dr. A. Schubert-Unkmeir 31-46721
Dr. T.-T. Lâm 31-46737

Please direct hospital hygiene enquiries to the Hospital Hygiene Unit (Head Prof. Dr. U. Vogel) at

For administrative or billing enquiries, please dial

- Billing office:  31-46735/-46935
- Secretariat: 31-46161

In addition, national reference centres and consultant laboratories are located at the Institute of Hygiene and Microbiology. 

Microbiological on-call service and emergency diagnostics

Microbiological emergency diagnostics is available to the University Hospital of Würzburg, departments of the Mission Medical Clinic, the Juliusspital and the König-Ludwig-Haus. It is available to doctors at these facilities 24 hours a day via the switchboard 201-13 outside regular office hours and can be requested in the case of vital indications, or if specific therapeutic measures (i.e. measures that go beyond the calculated therapy) or further indispensable diagnostic or outbreak-preventing measures can be derived from immediate findings.

Indications for examinations within the framework of the microbiological on-call service must be discussed with the microbiologist on duty under the following aspects:

  •     Severity of the clinical picture
  •     Therapeutic consequences of the diagnosis
  •     Detection of sensitive pathogens
  •     Possibility of rapid diagnostics

Acute clinical pictures that usually require emergency microbiological diagnostics primarily include:

  • Suspected bacterial or fungal or parasitic meningitis/encephalitis.
  • Suspected septic arthritis
  • Suspected bacterial, fungal or parasitic endophthalmitis
  • CT-/MRI-supported or surgically removed samples from primarily sterile body cavities/organs with justified suspicion of bacterial or fungal or parasitic infections (e.g. brain abscess etc.)

All information on correct sample collection, sample transport and sample storage as well as on the range of microscopic, cultural, molecular biological and serological examinations offered can be found in the

Service catalogue of the Institute for Hygiene and Microbiology  (as of October 15, 2021)

A variety of bacteria can cause human infections. Detection of the pathogens and sensitivity testing to various antibiotics are in many cases crucial prerequisites for efficient therapy of these infections. In some cases, a rapid microbiological assessment can significantly influence a decision on therapeutic measures. For this reason, the IHM offers an on-call service for infectious disease emergencies for its senders around the clock, 365 days a year.

In recent years, multi-resistant bacteria have increasingly become a problem. Among the Gram-positive pathogens, methicillin-resistant S. aureus strains (MRSA) and vancomycin-resistant enterococci play an important role as infectious agents. Multi-resistant Gram-negative bacteria - including broad-spectrum beta-lactamase (ESBL)-forming Enterobactericeae and metallobetalactamase (MBL)-forming P. aeruginosa strains - also often pose difficult problems for the attending physician. Efficient and rapid detection of these pathogens is a prerequisite for effective therapy and the prevention of transmission. Hence, there is close cooperation between bacteriology and the field of molecular biology.

With a wide range of routine procedures as well as through the constant evaluation and integration of new procedures, we see it as our task to offer clinically active colleagues rapid and reliable diagnostics as well as comprehensive advice on infectiological issues.

The basis of most molecular biological methods for the diagnosis of infectious diseases are nucleic acid amplification techniques such as PCR (polymerase chain reaction). Through exponential amplification of target structures from the genome of microorganisms, a high sensitivity can be achieved in relatively short time. At the same time, these methods are independent of the vitality of the pathogens. Thus, even if - for example - antibiotics have been administered, or if cultivation is no longer successful, pathogens can still be detected. Molecular biology can also be a valuable component of diagnostics for pathogens that are difficult or impossible to cultivate.

Molecular methods are also the basis of modern typing procedures, which are indispensable in hygienic and epidemiological questions. Especially in the field of typing multi-resistant hospital germs (MRSA/VRE) and in typing of N. meningitidis in cooperation with the National Reference Centre for Meningococci, these techniques are used and further developed in our laboratory.

These advantages are offset by high demands on quality management and the verification of specificity as well as high technical expenditure. Therefore, molecular biological diagnostics should be used after specific indication within the framework of step-by-step diagnostics.

The following applies to all microbiological examinations, including molecular biology: the higher the quality of the examination material, the more meaningful the result. It is often advisable to consult us before sending in diagnostic samples. Therefore: Ask us! We will be happy to talk to you and try to develop optimal strategies for your problem.

The diagnosis of infections by mycobacteria forms a separate area at the IHM. These pathogens differ significantly from other bacteria in their staining behaviour and their cultivation requirements. The diagnosis of infections by Mycobacterium tuberculosis is at the centre of this area. Cultural cultivation is still the most sensitive diagnostic method. DNA detection from diagnostic materials is carried out in cooperation with the Molecular Biology Division. Resistance testing of M. tuberculosis is also carried out in our laboratory. The correct collection of the sample material is decisive for the significance of the test - you are welcome to contact us before the material is collected.

For the diagnosis of a latent M. tuberculosis infection, we offer a modern method for the detection of tuberculosis-specific T cells in the serology department. In addition to tuberculosis, atypical mycobacteria are also detected in our laboratory. The microscopic and cultural detection of MOTTs (Mycobacteria other than tuberculosis) plays an important role especially in skin infections, lymphatic infections and immunosuppressed patients.

With a continuously increasing number of immunocompromised patients and patients receiving maximum care in intensive care, the importance of invasive fungal infections has steadily increased in recent years. In addition to the detection of common pathogens such as Candida albicans and Aspergillus fumigatus, also rare fungi, which were previously not or only rarely associated with human infections are emerging as pathogens of invasive infections. The rapid and reliable identification of such pathogens is one of the major challenges in medical mycology. In addition to microscopic and cultural detection, serological and molecular biological examinations are also part of a complete mycological diagnosis. Therapeutic counselling plays a central role, which is carried out by telephone or within the framework of infectiological consults. In cooperation with the mycology research group (Prof. Oliver Kurzai), experimental procedures for identifying fungi, for example in fixed tissues, are also offered if required. An established methodology for resistance testing of fungi is also available. Especially in difficult cases, it is often advisable to contact our laboratory before sending in material.

A broad spectrum of parasites can infect humans. Worldwide, malaria and other infections by protozoa as well as infections by helminths are the cause of high morbidity and mortality. Such infections are also diagnosed in Germany as an unpleasant holiday souvenir. But indigenous parasites and worms are also infectiologically significant. One of the most threatening indigenous helminths is the fox tapeworm Echinococcus multilocularis. The interaction between this pathogen and the human host is a research focus at the IHM. In addition, the RKI has set up the consiliary laboratory for echinococcosis at our institute. There is a close link between the field of parasitology and the field of serology, as serological methods are used primarily or in addition for the diagnosis of many parasitoses. The most important example of this is toxoplasmosis, which can be particularly threatening for pregnant women.

In some bacterial infectious diseases, such as syphilis/lues or Lyme disease, the pathogens can only be detected for a short time after the onset of clinical symptoms, or direct pathogen detection is technically difficult.
Infections of the gastrointestinal tract by yersinia, salmonella, shigella and of the genitourinary tract by chlamydia and gonococci can be triggers of post-infectious reactive arthritis. Clinical symptoms are therefore present at a time when aetiological clarification by direct pathogen detection is usually no longer possible.
In these cases, the diagnosis should be confirmed by antibody detection.

In the infectious serology department at the IHM, more than 80 parameters of more than 30 different infectious agents are determined. The spectrum of methods used for antibody detection includes:

    Agglutinations (haemagglutination/particle agglutination),
    complement fixation reactions
    quantitative and qualitative ELISAs
    indirect immunofluorescence
    Immunoblots (Borrelia burgdorferi, Campylobacter, Yersinia, Helicobacter pylori, Treponema pallidum)

For the care and monitoring of immunocompromised patients and intensive care patients, we offer the determination of fungal antigens (Candida mannan antigen, Aspergillus galactomannan and Cryptococcus capsule antigen).

For the detection of latent M. tuberculosis infections, we have expanded our diagnostics by introducing the TB EliSpot assay. This involves the detection of γ-interferon secretion (T-cell interferon γ release assays - TIGRAs) by M. tuberculosis-specific T lymphocytes after contact with the antigens ESAT-6 or CFP-10.