Until only a few years ago, pathogenic fungi were a well-defined group, some of which were limited to geographical regions and were well known by clinicians. However, the situation has changed considerably, and new infectious agents are continually appearing, around 20 species yearly. These new opportunistic pathogens have increased the base of knowledge of medical mycology, and unexpected changes have been seen in the pattern of fungal infections in humans. It is also possible that most of the recently reported taxa have caused infections which previously passed unnoticed due to inadequate diagnostic expertise. This situation and the rapid appearance of such a wide range of new pathogens have created a growing interest in fungal systematics. Fungal taxonomy is a dynamic, progressive discipline that consequently requires changes in nomenclature; these changes are often difficult for clinicians and clinical microbiologists to understand. Another difficulty for microbiologists inexperienced in mycology is that fungi are mostly classified on the basis of their appearance rather than on the nutritional and biochemical differences that are of such importance in bacterial classification. This implies that different concepts have to be applied in fungal taxonomy. Generally, medical mycologists are familiar with only one aspect of pathogenic fungi, i.e., the stage that develops by asexual reproduction. Usually microbiologists ignore or have sparse information about the sexual stages of these organisms. However, the sexual stages are precisely the baseline of fungal taxonomy and nomenclature. It seems evident that in the near future, modern molecular techniques will allow most of the pathogenic and opportunistic fungi to be connected to their corresponding sexual stages and integrated into a more natural taxonomic scheme. The aim of this review is to update our present understanding of the systematics of pathogenic and opportunistic fungi, emphasizing their relationships with the currently accepted taxa of the phyla Ascomycota and Basidiomycota.

Different concepts have been used by mycologists to define the fungal species. The morphological (phenetic or phenotypic) concept is the classic approach used by mycologists; in this approach, units are defined on the basis of morphological characteristics and ideally by the differences among them. The polythetic concept is based on a combination of characters, although each strain does not have to have the same combination. The ecological concept, which is based on adaptation to particular habitats rather than on reproductive isolation, is often used for plant-pathogenic fungi. The biological concept, which was developed before the advent of modern phylogenetic analysis, emphasizes gene exchange (i.e., sexual and parasexual reproduction) within species and the presence of barriers that prevent the cross-breeding of species (111). A species is considered to be an actual or potential interbreeding population isolated by intrinsic reproductive barriers (13). However, application of the biological-species concept to fungi is complicated by the difficulties in mating and in assessing its outcome (302). Also, whether a cross is considered fertile or sterile depends on the frame of reference. In this sense, published accounts of crosses between different species are often difficult to interpret because authors have failed to specify the type of infertility and its severity (428). The biological-species concept cannot be applied to organisms that do not undergo meiosis (484). It is applied only to sexual fungi, whereas asexual ones need only possess similar characteristics to each other. However in asexual fungi, genetic exchange through somatic hybridization is a theoretical possibility, although it is limited by vegetative incompatibility (87). For asexual dermatophytes, the cohesion-species concept, based on a demographic exchangeability of phenotypes, has been used to explain the proliferation of disjunct phenotypes. The demographic exchangeability would be the ecological analogue of the genetic exchangeability of sexual species (523).

Two recent and important developments have greatly influenced and caused significant changes in the traditional concepts of systematics. These are the phylogenetic approaches and incorporation of molecular biological techniques, particularly the analysis of DNA nucleotide sequences, into modern systematics. Molecular techniques, which were previously used only in research laboratories, are now commonplace. These developments have provided new information that has caused the biological-species concept to come under criticism in favor of the phylogenetic-species concept. This new concept has been found particularly appropriate for fungal groups in which no sexual reproduction has been observed (deuteromycetes). Hence, new concepts, specifically formulated within the field of phylogenetics, are becoming familiar to mycologists. Population studies and molecular data are increasingly showing that many widely used morphospecies actually comprise several biological or phylogenetic species. One of the problems for morphologists involves deciding how many base differences are required for strains to be considered different species. This has been partly solved by the phylogenetic-species concept, especially when based on cladistic analysis of molecular characteristics, which offers consistency in the delineation of species. Cladogram topology indicates the existence of monophyletic groups, which may represent species or supra- or subspecific taxa (302, 484). Peterson and Kurtzman (430) correlated the biological-species concept with the phylogenetic-species concept by comparing the fertility of genetic crosses among heterothallic yeasts. They demonstrated that the D₂ region, a variable region of the 25S rDNA gene, is sufficiently variable to recognize biological species of yeasts and that conspecific species generally show less than 1% nucleotide substitution.

The phylogenetic relationships among higher fungal taxa remains uncertain, mainly because of a lack of sound fossil evidence, and remains a source of much controversy. The proposed phylogenetic relationships among the Animalia, Plantae, and Fungi kingdoms depend on the molecular regions and methods used by different investigators. Phylogenetic analysis has shown that the fungal kingdom is part of the terminal radiation of great eukaryotic groups (Fig. ​(Fig.1)1) which occurred one billion years ago (499, 540). Surprisingly, although mycology has been classically considered a branch of botany, there is also evidence that the kingdom Fungi is more closely related to Animalia than to Plantae (390). The analysis of amino acid sequences from numerous enzymes indicated that plants, animals, and fungi last had a common ancestor about a billion years ago and that plants diverged first (135). Another former hypothesis, i.e., that fungi are derived from algae, has been definitively abandoned (238).

Berbee and Taylor (37), following Hennig’s criteria (247), used geological time to calculate the appearance of nonsister taxa in an evolutionary tree. Just as sister lineages are equivalent units because they are equal in age, other lineages should receive equal rank because they diverged at about the same time. On this basis, it has been hypothesized that all the ranks from classes to families have successively appeared between the Cambrian and Tertiary periods.

The dual modality of fungal propagation, i.e., sexual and asexual, has meant that since the last century (463) there has been a dual nomenclature. The fungus, as a whole, comprises a teleomorph (sexual state) and one or more anamorphs (asexual states) (246). The term “holomorph” has been reserved for fungi with teleomorphic sporulation together with all their sporulating or vegetative anamorphs (180). The anamorph and teleomorph generally develop at different times and on different substrates, although in zygomycetes they often occur together. Since each phase has been described in total ignorance of the existence of the other in many cases, the ICBN maintains that it is legal to give them separate binomials. For a long time, the anamorphs that occurred alone have been grouped into anamorph genera because they share some morphological features. These anamorphs have been placed in a separate major high-level taxon called Deuteromycotina or Deuteromycetes. With the advent of molecular approaches in fungal taxonomy, some mycologists have advocated abandoning the dual system of naming because unified classification of all fungi may be possible on the basis of the rDNA sequences of the anamorphs (47, 71, 452). Other authors do not agree with this proposal and have considered it absolutely necessary to conserve deuteromycete taxon names, at least for identification purposes (180, 484). During the Holomorph Conference (453), it was agreed to maintain the term deuteromycetes with a lowercase “d” and not to formally recognize this group of organisms at a particular rank.

Another controversy resulted from the replacement of the terms “anamorph” and “teleomorph” with “mitosporic fungus” and “meiosporic fungus”, respectively, in the last edition of Ainsworth and Bisby’s Dictionary of the Fungi (238); this source is considered a fundamental framework for fungal terminology and taxonomy. These changes have not been accepted by numerous authors (179, 180, 286), who consider that the anamorph and teleomorph phases of a fungus are determined not simply by the type of cellular processes (meiosis or mitosis) that precede sporulation but also by morphological features. Additionally, it has been argued that the cytological events preceding sporulation have not been investigated in sufficient depth to correlate teleomorph morphology with sexual recombination (179).

Analysis of the SSU rDNA sequence shows that fungal organisms belong to four monophyletic groups: Acrasiomycota, Myxomycota, Oomycota, and Fungi (71). It also shows that the first two groups diverged separately prior to the terminal radiation of eukaryotes (231, 499, 540), which is consistent with morphology and function, because these two groups include slime molds, which are at present in the kingdom Protozoa. Similarly, phylogenetic analysis shows that Oomycota grouped with different types of algae (41, 167, 540), which is also consistent with their morphology and structure. At present, Oomycota are included in the kingdom Chromista (238). The rank “kingdom” has also been questioned, arguing that this term has no molecular definition (415). In addition, it has been argued that if animals, plants, and fungi are considered to be taxonomic kingdoms, we must recognize at least a dozen other eukaryotic groups as kingdoms. These groups have at least as much independent evolutionary history as that which separates the three traditional kingdoms (415). Above the rank of kingdom, the now-recognized three primary lines of evolutionary descent termed “urkingdoms” or “domains,” i.e., Eucarya (eukaryotes), Bacteria (initially called eubacteria), and Archaea (initially called archeobacteria), have been proposed (591, 592). In this context, the term “kingdom” indicates the main lines of radiation in the particular domain.

The kingdom Fungi is organized into phyla and then into classes and orders. However, some authors prefer to avoid particular categories above orders. Mycologists previously used the term “division” instead of “phylum” because it is more inherent to botany, but in the last 5 years the term “phylum,” used mainly by zoologists, has been used as an alternative and has practically replaced “division.” The four phyla presently accepted in Fungi are Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota (Table ​(Table1).1). However, the inclusion of Chytridiomycota in the Fungi has been controversial because these organisms possess flagella. On this basis, they have been included in the Protoctista (326), but comparison of cell wall polysaccharides (19) and lysine synthesis (562) linked them firmly with the other classical phyla of Fungi. Analysis of 18S rDNA sequences also showed that chytridiomycetes cluster with representatives of Ascomycota and Basidiomycota (61) in a separate clade from ciliate protists. Subsequent analysis of many fungal 18S rDNA sequences (70) showed that Chytridiomycota and Zygomycota are difficult to separate and are basal to the Ascomycota and Basidiomycota. Although Chytridiomycota form the basal branch in the kingdom Fungi, flagella may have been lost more than once during the evolution of the ancestors through to Zygomycota, Ascomycota, and Basidiomycota. It has been demonstrated that among the nonflagellated fungi, the Zygomycota diverged first, and the branch defining the Ascomycota and Basidiomycota as terminal sister groups is strongly supported (33, 70) (Fig. ​(Fig.11).

There are thought to be so many species of fungi that insects are the only group with more varieties. Currently, approximately 1.4 million living species of microorganisms, fungi, plants, and animals have been recorded (198, 478). Most of these species are insects (950,000) and plants (250,000). On the basis of the current rate of discovery, it has been estimated that the number of undiscovered and undescribed species ranges from 1 million to more than 10 million (478). Fungi by far outnumber bacteria and viruses. In 1995, approximately 70,000 fungal species were accepted (236) compared to only 3,100 known bacteria species and 5,000 viruses (478). However, the number of fungal species so far discovered is probably only a small proportion of those that actually exist, since few habitats and regions have been intensively studied. Many extreme environments are still unexplored or not adequately explored. It has been conservatively argued that the total number of fungal species in the world must be at least 1 to 1.5 million (234, 478), meaning that we have so far recognized only about 5 to 7% of the world’s mycobiota. Other authors indicate that less than 20% of the terrestrial and marine fungi have been discovered (283). Since all proposed new species are catalogued in the Index of Fungi (edited twice yearly by the International Mycological Institute, Egham, United Kingdom), we can calculate that 800 to 1,500 new species are described annually. It is worth mentioning that some of the recently described new species have been found only in humans; these include Dissitimurus exedrus, Calyptrozyma arxii, Hormographiella spp., Onychocola canadensis, Ramichloridium mackenziei, Polycytella hominis, Pyrenochaeta unguis-hominis, Phoma cruris-hominis, Phoma oculo-hominis, Botryomyces caespitosus, and some dermatophytes.

The order Mucorales is the most clinically important. Its members are widely distributed and are found in food, soil, and air. Several species are thermophilic. Eleven genera, containing 22 species of medical interest, have been described and illustrated by de Hoog and Guarro (118). The most frequent, significant mucoralean genera in the clinical laboratory are Rhizopus and Absidia. Mucor is abundant as a contaminant but is very rarely an etiologic agent. However, in recent years, some rare genera have been associated with human infections, e.g., Cokeromyces (273), Saksenaea (330), Apophysomyces (140), and Chlamydoabsidia (79). The clinical picture is rather similar throughout the whole group. Most rhinocerebral mycoses are found in patients with diabetes mellitus, although other types of infection (e.g., gastrointestinal, pulmonary, cutaneous and systemic) are also frequently reported. Disseminated and severe infections are encountered mainly in patients with immunological disorders (156, 304, 481).

Recognition of a clinical isolate which belongs to mucoralean fungus is easy and can be done by observing only the macroscopic features. Lax, woolly colonies which spread over the whole petri dish in a few days and which have small dots (sporangia) (Fig. ​(Fig.3,3, structures a and d) on the periphery are sufficient to identify them. This identification can be microscopically confirmed by the presence of nonseptate, wide, hyaline hyphae with the typical fertile structures of mucorales. Although serological tests have been developed (129, 267), the identification of the species is rather more complicated. The procedure is both time-consuming and labor-intensive and usually requires special media, some of which are not commercially available. Some species have considerable morphological variation, and in these cases it is important to culture the fungi under optimal conditions to determine the variability of characteristics (29, 480, 481, 578). The species is identified almost exclusively by careful microscopic observation and measurements of several morphological characteristics which are typical of asexual reproduction. This process takes place by means of sporangiospores (Fig. ​(Fig.3,3, structure h) produced in sporangia (multispored) (structure d), in sporangioles (with one or very few spores) (structure e), or in merosporangia (spores in rows) (structure f). A sporangium generally has a central columella (structure g), which may extend and be visible below the sporangium as a swelling known as the apophysis. Other structures such as zygospores, chlamydospores, or a combination of them are produced only in some organisms. The value of zygospore morphology is limited because the sexual spore has never been reported for many taxa (29). However, the production of zygospores was considered to be very useful in clinical zygomycete taxonomy, especially for the identification of rare, heterothallic zygomycetes (578). An important limitation to this technique is the need for tester strains to try to stimulate zygospore production (578). Several species creep over the agar surface with stolons (Fig. ​(Fig.3,3, structure j), and the substrate can be penetrated by means of rhizoids (structure k). These structures also have a certain diagnostic value. Fatty acid composition has been investigated in Mortierella (6). A variety of biochemical and physiological tests (carbon and nitrogen assimilation, fermentation, requirement for thiamine, maximum temperature of growth, etc.) are also used by different authors (481, 578). Both SEM and TEM are important aids for the detailed observation of numerous structures and allow the morphology of surface ornamentations to be discerned. They can also resolve aspects of the ontogeny of sporangiospores (29, 404).

Benny (29) suggested exploring some traditional characteristics by phylogenetic studies. He considered it useful to investigate possible differences in sporangiospore ontogeny and distribution of chemical compounds and to search for unknown zygospores. It seems logical to expect that molecular studies will provide more consistent data. Molecular studies have only very rarely been performed in the Mucorales. Radford (443) compared sequences of the orotidine 5′-monophosphate decarboxylase gene and showed that Mucorales was a sister group of basidiomycetes. As a result of a preliminary cladistic analysis based on morphology and SSU rDNA sequences (407), Benny (29) pointed out that many characteristics used to define mucoralean families probably do not indicate relationships but are still useful for identification. The lack of agreement between molecular data and morphological observations could indicate that many of the characteristics which are considered advanced in the Mucorales have arisen several times in the order (29).

The basic characteristic which differentiates ascomycetes from other fungi is the presence of asci (Fig. ​(Fig.4,4, structures e to g) inside the ascomata (structures c and d). However, even in the absence of these important diagnostic characteristics, the ascomycetes can be recognized by their bilayered hyphal walls with a thin electron-dense outer layer and a relatively electron-transparent inner layer (238). The arrangement of the asci has played a major role in supraordinal systematics, and for a long time the ascomycetes have been grouped into six classes, i.e., Hemiascomycetes, Plectomycetes, Pyrenomycetes, Discomycetes, Laboulbeniomycetes, and Loculoascomycetes (372). The Plectomycetes are characterized by the presence of closed, more or less spherical fruiting bodies (cleisthothecia) (Fig. ​(Fig.4,4, structure d), with an irregular distribution of the asci in the cavity, and the ascospores are released after the disintegration of the thin walls of the asci. The dimorphic pathogens (Histoplasma, Coccidioides, Emmonsia, etc.) are included in this group, as are the teleomorphs of the dermatophytes and of the frequent and cosmopolitan Penicillium and Aspergillus among others. The Pyrenomycetes have pyriform (flask-shaped) fruiting bodies (perithecia) (Fig. ​(Fig.4,4, structure c) with usually saccate or cylindrical asci. The ascospores are forcibly extruded from the ascus. The teleomorphs of several opportunistic fungi are also included in this class. The class Loculoascomycetes comprises species with bilayered asci, sometimes enclosed in stromatic ascomata. The sexual states of numerous pigmented (dematiaceous) pathogenic fungi are included in this latter class. The class Hemiascomycetes comprises the yeasts. In the remaining two classes there are no fungi of medical interest. An alternative, long-accepted classification scheme placed the ascomycetes into the classes Hymenoascomycetes and Loculoascomycetes, depending on whether the ascus wall was single (Fig. ​(Fig.4,4, structure f) or bilayered (structure g), respectively (17, 18, 317). Several other taxonomic schemes have been established over the years and have been accepted to greater or lesser extents (238).

The traditional systems of ascomycete classification have been much criticized due to their artificial nature. It has been repeatedly argued that the supposed similarities among these major groups may not reflect homology. Another much questioned aspect has been the confusing terminology. One example is the term “plectomycete,” which has been defined as a closed ascoma (162) and also as scattered asci within the ascomal cavity (317). Another problem inherent in traditional classifications is the convergence of fruiting bodies (77, 320). It has been demonstrated that species which normally produce flask-shaped fruiting bodies can be induced to form closed fruiting bodies under certain environmental conditions (563). Some species, such as the recently reported opportunistic fungi, Microascus spp., have both the fruiting-body type of the Pyrenomycetes and the ascus arrangement characteristic of the Plectomycetes. For these reasons, it has been considered that there are too few stable morphological features which are useful for inferring relationships among higher taxa. Therefore, many mycologists currently deemphasize supraordinal rankings and the relationships that they define (150) while others support the use of these supraordinal rankings as reflecting natural groupings.

Molecular data are adding a new dimension to the understanding of the relationships among the different groups of ascomycetes. One of the first phylogenetic trees to depict the evolutionary history of ascomycetes was published by Berbee and Taylor (35), who studied morphological convergence in true fungi. They recognized three main groups of ascomycetes: (i) the basal ascomycetes, which included the Schizosaccharomycetales (fission yeasts) and Pneumocystis; (ii) the true yeasts, i.e., filamentous or unicellular ascomycetes without fruiting bodies; and (iii) the filamentous ascomycetes with fruiting bodies. Numerous authors subsequently provided sequences of many other fungi which have been useful for filling some of the gaps in the evolutionary history of ascomycetes. Soon it may be possible to build a phylogenetic tree for all ascomycetes. Meanwhile, it is evident that some traditional classes such as the Pyrenomycetes (Hypocreales, Microascales, Diaporthales, and Sordariales) and the Plectomycetes (Eurotiales and Onygenales) are also represented by well-supported monophyletic clades. However, the monophyly of the classes Hymenoascomycetes and Loculoascomycetes was rejected (501, 505). There are examples of perithecial and cleistothecial ascomycetes that do not group with these well-supported clades. Despite this, we consider that some of these old class names are useful, at least until sequences of more ascomycetes become available and the boundaries within these groups are defined. Therefore, in this article, and for the sake of simplicity, the taxa are arranged into five morphological groups, i.e., basal ascomycetes, unitunicate Pyrenomycetes, bitunicate Pyrenomycetes, Plectomycetes, and budding yeasts. The relationships among these groups are inferred from the analysis of 18S rDNA and suggest an early radiation of Schizosaccharomycetales and Pneumocystis carinii, which represent a basal branch in the Ascomycota (basal ascomycetes). This was followed shortly by a bifurcation leading to budding yeasts on one branch and filamentous fungi with fruiting bodies on the other. Among the latter, there is another radiation comprising the unitunicate Pyrenomycetes followed by the Loculoascomycetes (bitunicate Pyrenomycetes) and Plectomycetes (Fig. ​(Fig.5).5). However, the delimitations between these two groups are not well defined.

Eriksson (152) recently also used these groups to demonstrate the value of the signature sequences in the taxonomy of ascomycetes. Signatures are short sequences in moderately conserved areas of DNA, RNA, or protein. They are characteristic of taxa of various ranks and give phylogenetic information that is not provided by other methods. Studying the terminal part of stem-loop E23-1 in the V4 region of 18S rRNA according to the terminology of Neefs et al. (381), Eriksson found that in most cases it consisted of a short helix of 3 or 4 bp and an end-loop of usually 6 bases. Above the helix, there is almost always a bulge of a single C, and below is a bulge of usually 3 bases. Supposed signatures, end-loops, and a larger bulge in this helix were discussed by Eriksson for different groups of ascomycetes and, for comparison, for some basidiomycetes. He found that when numerous taxa of the Plectomycetes and Pyrenomycetes were examined, they practically all had the loop CTCACC, which was not found in any other group of either ascomycetes or basidiomycetes, and they all had a helix of 3 bp. Other noteworthy findings were found in the signature sequences of the other groups examined such as the budding yeasts. For example, a higher A+T content was found in these sequences than in other ascomycetes and basidiomycetes. Surprisingly, a great variation was found in stem-loop E23-1 of the basidiomycetes compared with ascomycetes.

At present, 46 orders are accepted in Ascomycota (238) but only 9 of them include fungi of clinical interest (see Tables ​Tables22 to ​to88).

Supraspecific taxonomic ranks such as genus and family are classified according to the mode of vegetative reproduction, morphological characteristics found during sexual reproduction, and several physiological characteristics such as the ability to assimilate inositol. However, recent chemosystematic studies suggest that the taxonomic system based on these characteristics is not appropriate (379). The monosaccharide composition of the cells, especially the presence or absence of xylose (193), and the ubiquinone (coenzyme Q) systems are thought to be more reliable systematic markers than the mode of vegetative reproduction and morphological criteria found during sexual reproduction. However, coenzyme Q composition is often heterogeneous in many currently defined genera and will require additional study before its taxonomic significance is fully understood (379). The presence of carotenoids and ballistoconidia (forcibly ejected vegetative cells) (Fig. ​(Fig.6,6, structure m) in some taxa has been used as a criterion for genus assignment. However, both characteristics are found among many genera of the basidiomycetous yeasts, suggesting that these traits are ancestral but not always expressed. Thus, they are of little value for defining taxa (161, 380). Ultrastructural features correlate well with chemosystematic characteristics and are regarded as reliable systematic criteria in higher taxonomic ranks. However, at lower ranks the phenetic approaches seem to be less useful, e.g., rRNA sequence analysis shows that Rhodotorula, Sporobolomyces (see Table ​Table10)10) and Cryptococcus (see Table ​Table9)9) are polyphyletic, further confirming that commonly used phenotype characteristics are insufficient for defining anamorphic genera (379).

Guého et al. (215) presented an overview of the phylogeny of basidiomycetous yeasts from measurements of divergence among partial sequences of LSU and SSU rRNAs. Three major groups were resolved: teliospore formers with hyphae having simple septal pores, teliospore formers with hypha having dolipore septa, and non-teliospore formers with hyphae having dolipore septa. Fell and Kurtzman (160) and Fell et al. (161) compared sequences from the D2 region of the LSU rRNA corresponding to numerous species and genera of basidiomycetous yeasts and obtained two major clades corresponding to the orders Ustilaginales and Tremellales, respectively. In general, molecular analysis supported the concept that taxa assigned to the Tremellales were characterized by dolipore septa and cellular xylose whereas taxa in the Ustilaginales form teliospores have simple septal pores and, with a few exceptions, lack cellular xylose. Blanz and Unseld (48) reached the same conclusions by using 5S rRNA. The same approach (161) demonstrated that teleomorphs clustered with their respective anamorphs such as Sporidiobolus/Sporobolomyces or Rhodosporidium/Rhodotorula (see Table ​Table10)10) and also allowed the separation of species and recognition of synonyms, e.g., the opportunistic pathogen Rhodotorula mucilaginosa and Cryptococcus vishniacii and their respective synonyms. In general, molecular biological results agreed with morphological criteria (159). On the basis of 18S sequence comparisons, Suh and Sugiyama (518) placed the smut fungus Ustilago maydis, a teliospore former, near the clade comprising representative genera of basidiomycetous yeasts. In turn, these yeasts appear to be a sister group of the Agaricales (36).

The basidiomycetes of medical interest are placed in the classes Basidiomycetes (Table ​(Table9)9) and Ustomycetes (Table ​(Table10)10) and in the orders Agaricales, Poriales, Schyzophyllales, Stereales, Tremellales, and Ustilaginales.

Although numerous deuteromycetes have also been found in aquatic habitats, the vast majority of these organisms are soil borne. They are the main components of the atmospheric mycobiota. The majority are either saprobes or weak plant parasites, and a few are parasites of other fungi. Deuteromycetes were once classically subdivided into three artificial orders, the Moniliales, Sphaeropsidales and Melanconiales; however, these terms are not currently used. It seems more practical to distinguish between hyphomycetes, which are the fungi which form sterile mycelium or bearing spores directly or on special branches of specialized hyphae (conidiophores) (Fig. ​(Fig.22 and ​and4,4, structure n), and coelomycetes, which have more complex reproductive structures.

Most of the molds found in the laboratory are hyphomycetes, a large portion of which are cultural states of Ascomycota, with asexual, mitotic propagation only. For routine identification, their biological relationship does not need to be determined, but the mode of conidium formation must be examined. As mentioned above, the process of conidiogenesis is very important in the identification of these fungi. Numerous hyphomycetes, including Beauveria, Cephaliophora, Engyodonium, Corynespora, Dichotomophthora, Dichotomophthoropsis, Metarhizium, Mycocentrospora, Nigrospora, Oidiodendron, Papulaspora, Phaeotrichoconis, Polypaecilum, Pseudomicrodochium, Stenella, Tetraploa, Thermomyces, Trichocladium, Tritirachium, Veronaea, Volutella, and Wallemia, have been reported as occasionally occurring in humans. Generally these genera are represented by only a single opportunistic species. A synoptic key and the main diagnostic characteristics for the identification of these fungi have been reported by Hoog and Guarro (118).

Approximately 1,000 species, found in a wide variety of ecological niches, are placed in the coelomycetes. Most are saprobic or plant pathogens and are characterized as producing conidia in fruiting bodies (conidiomata). Fruiting bodies of coelomycetes are spherical (pycnidia), with conidiogenous cells lining the inner cavity wall (Fig. ​(Fig.2,2, structure m) or are cup shaped (acervuli), in which case the conidiogenous cells form a palisade on the conidiomatal surface. These two types of structure characterize the two artificial orders Sphaeropsidales and Melanconiales. When grown in culture, the pycnidia can be confused with fruiting bodies of ascomycetes. The distinction between a pycnidium and an ascoma should be verified by squashing the structure under a coverslip. In the case of ascomycetes, provided that the ascoma is suitably young, ascospores inside asci are visible, whereas in the case of pycnidia, numerous free conidia are present, usually in mucous masses (Fig. ​(Fig.2,2, structure p). They are produced exogenously on conidiogenous cells. Eleven genera with approximately 20 species of coelomycetes were described as being pathogenic to humans as of 1995 (118). These taxa were isolated from clinical sources only very occasionally, but in the last 2 years a considerable number of infections caused by rare coelomycetes have been reported (9, 88, 91, 351, 368, 416, 458, 601). Some of them have been found for the first time in human lesions; they include Pleurophomopsis lignicola (91, 416) and Microsphaeropsis subglobosa (206). Punithalingham (440) described the culture and microscopic characteristics of the pathogenic coelomycetes that had been isolated from humans, although over the last 20 years numerous other opportunistic coelomycetes have been reported. The most important manual for identifying coelomycetes is that of Sutton (524). This manual is not easy to use for nonexperts, because the identification of taxa is based primarily on the condiogenesis pattern, which is not always easily observed in these fungi. Other approaches, based mainly on physiological and biochemical studies, have been used in an attempt to clarify the systematics of some complex genera of coelomycetes such as Phoma (36, 362).