Genomics of Plants and Fungi

Rolf A. Prade, Hans J. Bohnert, Rolf A. Prade, Hans J. Bohnert

• Publisher: CRC Press
• Year: 2003
• eBook ISBN: 9781135541323
• Topic: Biological Sciences
• Subtopic: Biology
• Index: Biological Sciences

This volume provides technical insight on how genomics-oriented studies may be used to bring new understanding to established models of fungal development. The book helps to assess and solve problems associated with multiple copies of genes and proteins with seemingly identical functions and depicts various industrial applications. To bridge the information gap resulting from this field's explosive growth, Genomics of Plants and Fungi addresses the implementation of workflow applications with the METEOR Workflow Management System, and discusses clinical manifestations of Aspergillus infection, stunted and medusa genes, hyphal mating and fertilization, and vegetative incompatibility.

1
Aspergillus

Michael J. Anderson and Jayne L. Brookman

University of Manchester, Manchester, England

David W. Denning

University of Manchester and Wythenshawe Hospital, Manchester, England

I. INTRODUCTION

Aspergillosis, the name given to all diseases caused in animals by fungi in the genus Aspergillus, includes allergic, superficial, saprophytic, and invasive disease. More than 180 species of Aspergillus are recognized (1), but only a few cause disease with any regularity: A. fumigatus, A. flavus, A. terreus, and A. niger group species. Aspergilli are common saprophytes in the environment, especially in composting facilities. The pathogenic Aspergilli are found the world over, but soil isolation rates do increase towards the equator. Most aerobiology studies have been done in Europe and some have shown a seasonal variation in airborne Aspergillus counts. Aspergillus species comprise from 1% to 6% of the total air flora outside and, if speciated, A. fumigatus comprises from 4% to 41% of the Aspergillus total (2). The usual concentration of Aspergillus conidia in outside air is 1 to 30 conidia/m³, but can rise to as high as 7 × 10⁷/m³ inside a barn, after hay or straw disturbance. In hospitals, conidia concentrations in air also vary typically from 0 to 1 × 10²/m³ with much variation in the same site (3–5). Inside human dwellings, Aspergillus species may be found in high concentrations in potted plants (50 conidia/g soil) (6), damp cellars, dusty crawl spaces, and condiments, especially pepper (10⁶ conidia/g) (2) and ground spices.

Human disease has been increasing over the 5 decades since invasive aspergillosis was first described in the immunocompromised patient (7). Invasive aspergillosis (IA) is the most common life-threatening invasive mold infection worldwide. It usually complicates treatments and diseases associated with immunosuppression, including allogeneic bone marrow transplantation, lung and liver transplantation, the treatment of acute leukemia, late-stage acquired immunodeficiency syndrome (AIDS) and a variety of other diseases treated with corticosteroids (8). Invasive aspergillosis rarely affects nonimmunocompromised patients. The incidence of invasive aspergillosis was calculated to have risen 14-fold in the 15-year period up to the end of 1992, as seen in autopsy data from one major teaching hospital in Frankfurt, Germany, with 5% of autopsied patients having invasive aspergillosis in the last year of this survey (9). In a national autopsy survey in Japan from 1969 to 1994, invasive aspergillosis increased from 0.4% to 1.3% in all autopsies (10). Another autopsy series in a European teaching hospital demonstrated a 4% rate of invasive aspergillosis in unselected autopsies (11). A culture-based population study in the San Francisco area (requiring cases to have, for example, two culture-positive bronchoscopy specimens or a sterile site positive by culture, which probably underrepresents invasive aspergillosis by perhaps 90%) showed increasing rates of disease over the last 25 years (12). Comparable figures from previous surveys had put the figure at 1.9 cases per million population in 1970, linearly rising to 12.4 per million in 1992/1993.

II. CLINICAL MANIFESTATIONS OF ASPERGILLUS INFECTION

A. Allergy

Wheezing in patients exposed to Aspergillus was recognized in the late 1800s, but was poorly understood. Allergic bronchopulmonary aspergillosis (ABPA), an extreme form of continuing local allergy to Aspergillus, was first reported in 1952 in 3 patients from the London Chest Hospital (13). Allergic bronchopulmonary aspergillosis complicates asthma and cystic fibrosis (CF), and patients develop exacerbations of the asthma, CF, or both. They are commonly “difficult-to-control” patients, in the pulmonary sense. Characteristic presentations include new pulmonary shadows, which resolve with steroids, and coughing up plugs of material. The diagnosis is made by a combination of criteria of which episodic wheezing (asthma), transient pulmonary shadows, elevated serum total immunoglobulin E (IgE) and Aspergillus-specific IgE, positive Aspergillus precipitins (IgG), and central bronchiectasis are the most important. Central bronchiectasis is not a useful diagnostic criterion in CF, as it is universally present. Some patients, especially those with long-standing disease, have barely detectable Aspergillus antibodies (14). Other criteria that have been used include peripheral eosinophilia and a positive immediate skin test to Aspergillus. Eventually, patients with untreated ABPA develop pulmonary fibrosis. Acute exacerbations are best treated with systemic corticosteroid therapy. Itraconazole (one of only two licensed oral antifungal agents available for aspergillosis) has shown benefit in several open studies (15, 16) and in a recent controlled trial (17).

Mold allergy is common among asthmatics, and this may represent a milder form of ABPA, although multiple other fungi are implicated. It is estimated that there are 275 million asthmatics worldwide (18). Of these, 5% have severe asthma, and there are around 100,000 deaths per year. Recent prevalence data in a population of asthmatics attending hospital regularly (19) compared the rates of fungal allergy in those admitted to the hospital at least twice annually with those not admitted. Skin testing to Aspergillus, Alternaria, Cladosporium, Penicillium, and Candida showed the frequency in the former to be 76%, but only 16% in the latter group. Rates of allergy to house-dust mite antigen were equivalent. Of interest, sensitization to Aspergillus is also common in patients with chronic granulomatous disease and hyper-IgE syndrome, both diseases usually being associated with invasive aspergillosis (20).

Allergic sinus disease caused by Aspergillus and other molds has been recognized in the last 15 or so years (21). The frequency of allergic fungal sinusitis or “eosinphilic fungal rhinosinusitis” is not known, and agreed-upon criteria for diagnosis are currently being evolved. Probably many cases of chronic sinusitis are related in part to fungal allergy, but this is hard to prove, as markers of allergy in blood are present in fewer than 30% of cases (21).

B. Saprophytic or Chronic Invasive/Necrotizing Aspergillus Disease

“Aspergilloma” is the term given to the colonization of an intrathoracic cavity by Aspergillus. A fungus ball is formed when spores are deposited in the cavity and germinate on the wall, where mycelia and debris attach to create an amorphous mass. An aspergilloma may form in any pre-existing lung cavity. There are many causes of pulmonary cavities including tuberculosis, sarcoidosis, pneumoconiosis, histoplasmosis, and bullae. Some idea of the prevalence of aspergilloma can be gained from a review of 60,000 chest radiographs: aspergillomata were identified in 0.01% (22). During an 11-year period, 15 patients with aspergilloma were admitted to a Veteran’s Administration Hospital, representing 0.02% of admissions (23). The frequency is much higher in patients with cavities of 2 cm or more in diameter. For example, in tuberculosis cavities of this size, 15% to 20% of British patients developed an aspergilloma (24). In a series of patients with pulmonary sarcoidosis, 10 of 19 (53%) patients with cystic parenchymal damage had aspergillomas, compared with none of 81 patients with noncystic pulmonary sarcoidosis (25). Many patients with aspergillomas have slowly progressive cavitary damage to the lung, which is termed “chronic necrotizing pulmonary aspergillosis (CPNA).” In AIDS, for example, progression of aspergillomas over time is seen with considerable morbidity and some mortality. This progression probably reflects invasion of cavity walls by Aspergillus and is, therefore, not strictly saprophytic Aspergillus disease.

The symptomatology of aspergilloma and CPNA is similar and variable in individual patients over time. Most patients are asymptomatic when an aspergilloma first forms. The most common presentation of aspergilloma is coughing up blood, which is because of new vessel formation in the vicinity of the aspergilloma. About 40% of patients are sensitized to Aspergillus and develop wheezing, weight loss, and malaise with or without fever. The patient is typically in the fourth to sixth decade of life and, as with all forms of aspergillosis, more men than women are affected. Chronic necrotizing pulmonary aspergillosis has similar clinical features, although weight loss is more profound.

Plain radiography of the chest in cases of aspergilloma shows a number of typical features, including a round solid mass that may be mobile within a cavity, separated from the wall by a rim of air. In classic aspergillomas, pleural thickening is also present and varies from several millimeters to 2 cm. All patients with CPNA have radiological evidence of a small or large cavitary lesion in the lung, usually in one or both upper lobes. Initially, infiltrates are ill-defined areas of consolidation or small cavities that progress to form well-defined multiple cavities with thickened walls—the cavities often contain an aspergilloma, debris, or fluid. Invasion of the pleura may follow.

Aspergillus precipitins are detectable in more than 95% of aspergilloma patients. The precipitin test may, however, be positive in some patients with cavities who do not have an overt aspergilloma, and these patients probably have CNPA. Two-thirds of patients have elevated levels of total IgE and Aspergillus-specific IgE. Most patients with aspergillomas have positive respiratory cultures of Aspergillus, usually A. fumigatus, and multiple variants and genotypes may be recovered. In a retrospective series, 25% of patients with pulmonary aspergillomas, 100% with a sinus aspergilloma, and 8% with disseminated aspergillosis had calcium oxalate crystals present in their tissue and, occasionally, renal oxalosis was observed (26). Aspergillus niger may be a more prolific producer of oxalate than A. fumigatus (27). Evidence of inflammation, such as the presence of C-reactive protein, is common in CPNA. We have recently observed mannose-binding protein deficiency as a probable association with CNPA (28). Pathologically, aspergillomas have multiple hyphae in cavities without invasion of cavity walls. In CPNA, hyphae may also be found in abnormal cavities without invading tissue. Distinguishing between aspergilloma and CNPA is clinically difficult and depends on progression over time.

Spontaneous resolution of aspergillomas occurs in 10% of cases within 3 years. However, the consequences of this type of Aspergillus infection can be dramatic. One report focused on the long-term outcome of 23 patients with aspergilloma and found that 5 died directly from complications of this infection (respiratory failure or hemoptysis) (29). Many patients with aspergillomas are elderly and have significant underlying disease, including severe respiratory compromise in addition to the aspergilloma. Thus, many patients die with an aspergilloma rather than of it. Treatment is problematic. Responses have been reported to intracavitary amphotericin B and older drugs, oral itraconazole, surgical resection, and corticosteroids. Bleeding is managed by resection or embolectomy. Like...

Table of contents

• Cover Page
• Title Page
• Copyright Page
• MYCOLOGY SERIES
• Preface
• Contributors
• 1: Aspergillus
• 2: Developmental Processes in Filamentous Fungi
• 3: Multiple GATA Transcription Factors Control Distinct Regulatory Circuits and Cellular Activities in Neurospora
• 4: Molecular Genetics of Metabolite Production by Industrial Filamentous Fungi
• 5: Acquiring a New Viewpoint: Tools for Functional Genomics in the Filamentous Fungi
• 6: Functional and Comparative Genomics of Cyanobacteria
• 7: Genomic Analysis of Arabidopsis Gene Expression in Response to a Systemic Fungicide
• 8: Identification of T-DNA Insertions in Arabidopsis Genes
• 9: Genomic Approaches for Studying Gene Families in Plants
• 10: Industrialization of Plant Gene Function Discovery
• 11: Functional Genomics of Plant Abiotic Stress Tolerance
• 12: Using Workflow to Build an Information Management System for a Geographically Distributed Genome Sequencing Initiative