Pocket Guide to Mycological Diagnosis

Rossana de Aguiar Cordeiro

• Publisher: CRC Press
• Year: 2019
• ISBN:
  9781351677660
• Edition: 1
• Topic: Medicine
• Subtopic: Infectious Diseases

The Pocket Guide to Mycological Diagnosis provides useful and concise information for microbiologists and professionals diagnosing the most medically relevant fungal species. Cellular and molecular techniques, immunological methods, and more accurate microscopy equipment available in most mycology laboratories now make diagnosis more routine. Furthermore, information regarding medical mycology, including identification of specific fungal pathogens, is widely available. This book helps mycologists address the emerging challenges of diagnosis.

Key Features

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• Succinct summary of fungal disease diagnosis

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• Includes opportunistic fungal infections that can afflict immunocompromised patients

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• Permits the identification of common fungal pathogens

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• Reviews antifungal drugs

Related Titles

Ghannoum, M. A. & John R. Perfect, eds. Antifungal Therapy, 2nd ed. (ISBN 978-1-4987-6814-6)
Miyaji, M., ed. Animal Models in Medical Mycology (ISBN 978-1-3158-9059-3)
Razzaghi-Abyaneh, M., M. Shams-Ghahfarokhi and M. Rai, eds. Medical Mycology: Current Trends and Future Prospects (ISBN 978-1-4987-1421-1)

1

Mycological Diagnosis

General Principles

Rossana de Aguiar Cordeiro

Contents

1.1 Introduction

1.2 Collection of clinical specimens

1.3 Mycological processing (conventional tests)

1.3.1 Direct microscopic examination

1.3.2 Culture

1.4 Identification

1.4.1 Standard culture-based methods: Phenotypical analysis

1.4.2 Culture-independent methods

1.4.2.1 Molecular diagnosis

1.4.2.2 Immunological diagnosis

1.4.2.3 Matrix-assisted laser desorption ionization-time of flight mass spectrometry

1.5 Conclusions

Bibliography

1.1 Introduction

Mycological laboratories have an important role in the complex scenario of understanding the etiology of fungal infections. They provide information not only related to diagnosis, but also to the treatment, prevention, and control of mycosis. Through such technical data, it is also possible to gain insight into the epidemiology of fungal infections, which brings great responsibilities to the lab staff. Therefore, standardized and internationally validated protocols and routines must be followed.

In order to achieve these goals, mycological labs need to be equipped with biosafety items: individual and community barriers must be available (Table 1.1), and personnel must be engaged in continuous biosafety training. Labs pertaining only to dermatological routines need to be designed to reach level 2 biological safety criteria. On the other hand, labs with complex attendance routines, that is, oncological patients, post-transplant patients, and patients suspected of deep-seated infections, need risk 3 biological safety criteria. Additionally, mycologists need continued education to become familiar with new fungal species and modern diagnostic procedures. A general scheme of mycological diagnosis stages is shown in Figure 1.1.

Table 1.1 Minimum Biosafety Items Required for Clinical Mycological Laboratories
Primary Barriers		Secondary Barriers
Individual Protection Equipment	Structural Issues	Inside the Lab	Outside the Lab
Long-sleeved laboratory coats Gowns Gloves Masks and respiratory apparatus Eye protection/safety goggles Facial protection (face shields/splatter guard) Shoe covers	Restricted containment areas Class II biological safety cabinet Incinerators Bioaerosol-contention equipment Containers for disposal of sharp materials Mechanical pipetting device Washable floor Sturdy furniture	Sinks for hand washing Bench tops impervious to water and chemicals Autoclave Sealed windows or windows fitted with screens	Self-closing and lockable doors Eyewash station Safety shower Fire extinguisher/blanket

Figure 1.1 Stages of mycological diagnosis in clinical settings.

1.2 Collection of clinical specimens

After clinical examination of the patient by physicians, the first step of mycological diagnosis is to collect clinical specimens. Mycologists should be aware that: (a) specimens must always be collected from the representative site of infection, (b) collection should preferably be performed prior to the start of antifungal therapy, (c) the amount of material collected should be suitable for performing all the required tests, (d) specimens should be transported to the lab and processed as soon as possible, and (e) all clinical material can be infected with other hazardous microorganisms besides fungi. In addition, lab members are responsible for precise identification (patient’s full name, ID number...