Introduction ATLAS

The ultimate benchtool for diagnostics.

1 A T L A S ofCLINICAL FUNGI

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G.S. de Hoog, J. Guarro, J. Gené, S. Ahmed, G.S. de Hoog, J. Guarro, J. Gené, S. Ahmed, A.M.S. Al-Hatmi, M.J. Figueras and R.G. VitaleA.M.S. Al-Hatmi, M.J. Figueras and R.G. Vitale

A T L A S ofCLINICAL FUNGI

The ultimate benchtool for diagnosticsThe ultimate benchtool for diagnostics

Sample pages

Sample pages

The ultimate benchtool for diagnostics


Overview of approximate effective application of comparative techniques in mycology

Use Strain Variety Species Genus Family Order Class Keyref

Cell wall PoreKaryologyCo-QCarbohydrate patternClassical physiologyAPI 32CAPI-Zymmole% G+CSSU seqSSU-RFLPLSUITS seq/RFLPIGSTubulinActinChitin synthaseElongation factorNASBAnDNA homologyRCALAMPMLPAIsoenzymes (MLEE)Maldi-tofFishRLBPCR-ELISASecondary metabolitesSSRrep-PCR rt-PCRRAPD / UP-PCRM-13T3BMicrosatellitesmtDNA RFLPAFLPKaryotypingMLST

TaxTaxTaxTaxTaxTaxDiagDiagTaxTaxTaxDiagDiagEpidTaxTaxTaxDiagTaxEpidEpidTaxDiagEpidDiagDiagDiagDiagTax/DiagEpidEpidDiagTaxEpid/TaxEpidEpid/TaxEpidEpidEpidEpid

Kreger & Veenhuis (1971)Moore (1987)Takeo & de Hoog (1991)Yamada et al. (1987)Weijman & Golubev (1987)Yarrow (1998)Guého et al. (1994b)Fromentin et al. (1981)Guého et al. (1992b)Gargas et al. (1995)Machouart et al. (2006)Kurtzman & Robnett (1998)Lieckfeldt & Seifert (2000)Diaz & Fell (2000)Keeling et al. (2000)Donnelly et al. (1999)Karuppayil et al. (1996) Helgason et al. (2003)Compton (1991)Voigt et al. (1997)Barr et al. (1997)Guého et al. (1997)Sun et al. (2010)Pujol et al. (1997)Schrödl et al. (2012)Rigby et al. (2002)Bergmans et al. (2008)Beifuss et al. (2011)Frisvad & Samson (2004)Karaoglu et al. (2005)MacDonald et al. (2000)Bergmans et al. (2010)Doherty et al. (2003)Weising et al. (1995)Gäser et al. (2000)Cai et al. (2013)Ishizaki et al. (1996)Savelkoul et al. (1999)Franzot et al. (1998)Meyer et al. (2009)

AFLP = Amplifi ed Fragment Length Polymorphism; Co-Q = Coenzyme Q; IGS = InterGeneric Spacer; ITS = Internal Transcribed Spacer; LAMP = Loop-medicated Isothermed Amplifi cation; LSU = Large SubUnitMaldi-tof= Matrix-assisted Laser-Desorption/Ionisation time-of-fl ight; MLEE = MultiLocus Enzyme Electrophoresis; MLPA = Multiplex Ligation - Dependent Probe Amplifi cation; MLST = Multi-locus Sequence Typing; NASBA = Nucleic Acid Sequence-Based Amplifi cation; RAPD = Random Amplifi ed Polymorphic DNA; RCA = Rolling Circle Amplifi cation; RFLP = Restric-tion Fragment Length Polymorphism; SSU = Small SubUnit rDNA; UP-PCR = Universally Primed PCR.Diag = Diagnostics; Epid = Epidemiology; Tax = Taxonomy.

Recipes of recommended media (all recipes based on 1 litre medium)BCPCG: Bromocresol purple casein glucose agar

skimmed milk 80 g

bromocresol purple 1% in ethanol 2 mL

glucose 40 g

agar 30 g

pH 6.8

BHI: Brain-heart infusion agarcommercial BHI agar 52 g

final pH 7.4

CEA: Casamino acids erythritol agarcasamino acids (Bacto) 3 g

MgSO4 0.1 g

KH2PO4 1.8 g

meso-erythritol 10 g

albumin 10 mL

agar 15 g

final pH 6.8

CDBT: Creatine dextrose bromothymol blue thymine agarSolution A:

Clinical pathology

3A T L A S ofCLINICAL FUNGI

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fused with secondary skin infections caused by systemic fungi treated below.

Dermatophyte infections of the dermis

Dermatophytes are normally confined to cutis, hair and nails, but occasionally the dermis is involved.

Majocchi’s granuloma. Perifollicular granulomatous inflammation. The dermatophyte may be present in the cutis, but also deeper skin layers are involved.

Kerion (pseudomycetoma). Subcutaneous, elevated, spongy lesion by dermatophytes with local necrosis and with presence of hyphae or grain-like structures.

Non-ulcerative infections by diverse fungi

These concern local, non-ulcerative infections caused by a variety of fungi. The fungus is present in the form of septate hyphae or hyphal elements. In the case of hy-phomycotic cysts the affected area is surrounded by a fibrous, collagenous secretion of the host, and hence no

Subcutaneous Special features

Hyphae with melaninHyphae without melaninGrainsMuriform cellsAsteroid bodies, rabbit earsWide hyphal elements, oedema

Pulmonary

Rhinoorbital

Systemic yeast infection

Hyphae without melanin Yeast cells with wide baseSpherulesPilot wheel/Mickey MouseIntracellular yeastAdiasporesIntracellular arthroconidia

Wide hyphal elements, oedemaSplendore-HoeppliHyphae

Yeast cells, pseudohyphaeCapsular yeast cells

Purulence Granuloma Fibrosis Necrosis

Main types of histopathological response to subcutaneous and deep infection

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inflammation occurs. According to the appearance of the causative agent as seen in native preparations, the follow-ing subdivision is made:Hyalohyphomycosis. The fungal elements are colourless.Phaeohyphomycosis. The fungal elements are melanised (special staining often necessary).

Chromoblastomycosis

The disease occurs mostly on the extremities and is char-acterized by localized, slowly expanding lesions. Superfi-cial, warty to cauliflower-like tumours and deformations develop, due to hyperkeratosis and acanthosis. The le-sions are greyish, crusted and dry in appearance. The fun-gus occurs as dark, muriform cells in the tissue. Causative agents: Fonsecaea monophora, F. nubica, F. pedrosoi, Clado-phialophora carrionii, Phialophora verrucosa, Rhinocladiella aquaspersa. The following types can be distinguished, of which several may occur in the same patient (adapted from Queiroz Telles et al., 2009):Nodular. Moderately elevated, fairly soft, dull to pink violaceous growth. Surface smooth, verrucous or scaly. With time lesions may gradually become tumorous.

Overview of histopathological features in subcutaneous, deep and disseminated infections in immunologically competent individuals: host responses and fungal tissue forms.



Phylum Basidiomycota

The life cycle of a prototypical basidiomycete is depicted. The thallus consists of a septate, dikaryotic mycelium, often provided with clamp connections; these are bridges between adjacent cells to provide each of them with a nucleus derived from one of the parent strains. The septa are perforated by a single, central pore. The wall of the pore canal is often characteristically swollen; such a structure is called a dolipore. Spores each produce a short-lived, haploid myce-lium. Cells of suitable mating type show plasmogamy, but karyogamy is postponed. Consequently a heterokaryon with clamp connections is formed. This condition is maintained during the major part of the life cycle, including fruitbody production. Karyogamy, immediately followed by meiosis, takes place in the basidium, which produces meiospores (basidiospores) exogenously, the spores often being forcibly discharged.

Prototypical life cycle Basidiomycota

Basidio filamentous


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Bjerkandera adusta, CBS 230.93. A. Fruitbody in natural habitat on rotten wood, left carpophores, right backside with pores; B. colony (MEA, 1 wk, 24°C, blue light), obverse; C. colony (OA, 4 wk, 24°C, blue light), obverse, with fruiting structures formed near colony edge; D-F. details of fruiting structures; G. section of fruiting structure; H-K. basidia with basidiospores; L. arthroconidia; M. clamp connection. Scale bars = 10 µm.



A. longipes CBS 540.94A. gossypina CBS 104.32A. gaisen CBS 632.93A. arborescens CBS 102605A. alstroemeriae CBS 118809

A. burnsii CBS 107.38A. tomato CBS 114.35A. jacinthicola CBS 133751A. doliconidium KUMCC 17-0263A. alternata CBS 916.96

A. betae-kenyensis CBS 118810A. eichhorniae CBS 489.92

A. iridiaustralis CBS 118486A. hordeicola CBS 121458A. montsantina FMR 17060A. graminicola CBS 119400A. conjuncta CBS 196.86A. caespitosa CBS 177.80

A. intercepta CBS 119406A. cesenica MFLUCC 13-0450

A. novae-zelandiae CBS 119405A. broccoli-italicae CBS 118485

A. dactylidicola MFLUCC 15-0466A. fimeti FMR 17110A. ventricosa CBS 121546A. quercicola CBS 141466A. triticina CBS 763.84A. triticimaculans CBS 578.94A. merytae CBS 119403A. pseudoventricosa FMR 16900A. lawrencei FMR 17004A. alternarina CBS 119396A. curvata FMR 16901A. daucicaulis CBS 119398A. ethzedia CBS 197.86A. hordeiaustralica CBS 119402A. infectoria CBS 210.86A. slovaca CBS 567.66

A. aconidiophora FMR 17111A. metachromatica CBS 553.94

A. arbusti CBS 596.93A. incomplexa CBS 121330A. oregonensis CBS 542.94

A. pobletensis FMR 16448A. cetera CBS 121340

A. obclavata CBS 124120A. malorum CBS 135.31

A. breviramosa CBS 121331A. abundans CBS 534.83

A. armoraciae CBS 118702A. chlamydospora CBS 491.72

A. phragmospora CBS 274.70A. limaciformis CBS 481.81

A. molesta CBS 548.81A. mouchaccae CBS 119671

A. papavericola CBS 116606A. penicillata CBS 116608

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Section Alternaria

Section Infectoriae

Section Chalastospora

Section Phragmosporae

Maximum Likelihood (ML) tree of four sections of the genus Alternaria based on confidently aligned rDNA ITS sequences using ClustalW. The sub-stitution model is Kimura 2-parameter and gamma distributed (K2+G). The tree was bootstrapped 1000 times and values above 80% are indicated near of the nodes and with thick branches. The tree is rooted with Alternaria papavericola and A. penicillata. Note that the general barcoding marker ITS does not allow species distinction within species complexes.

Asco filamentous


Asc

ofilam

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Ascomycota, Pezizomycotina, Sordariales, Chaetomiaceae.Genus: ASCOTRICHA

Recommended barcoding gene: rDNA ITS. Saprobic genus with several dozens of species. Ascomata are often produced, and the conidial are sympodial and have conidiophores with often very characteristic setae.

Ascotricha chartarum Berk.

Colony characteristicsColonies (OA) growing moderately rapidly, dull black-ish-brown, with dark grey patches of conidiation.

MicroscopyConidiophores straight, stiff, profusely branched, up to 1 mm tall, 3.5-5.5 μm wide, with pale, thin-walled vesi-cles at the bends. Conidiogenous cells terminal and lat-eral, cylindrical, bearing clusters of conidia on denticles. Conidia verrucose, yellowish-olivaceous, (sub)spherical, 5-7 × 3-6 μm. Perithecia black, pear-shaped with apical opening, 130-230 μm wide, discharching a black spore-cirrhus, bearing olivaceous-brown, erect, stiff setae, ge-niculate with pale, thin-walled vesicles at the bends. Asci cylindrical, 8-spored, 65 × 10 μm. Ascospores one-celled, olivaceous-brown to black, smooth-walled, lenticular, 8

μm diam in face view, 5 μm wide in lateral view, with a distinct equatorial germ slit.

PathogenicityRG-1, BSL-1. Cellulolytic saprophyte. A maxillary sinus-itis was reported by Singh et al. (1996).

ReferencesAmes (1963), Hawksworth (1971).

NomenclatureAscotricha chartarum Berkeley - Ann. Nat. Hist. 1: 257, 1838.

Dicyma ampullifera Boulanger - Revue Gén. Bot. 9: 25, 1897.

Ascotrichum chartarum Berkeley var. orientalis Castellani & Jacono - J.

Trop. Med. Hyg. 37: 362, 1934.

Ascotricha chartarum, CBS 657.95. a. Ascoma; b. ascus; c. oblate ascospore; d, e. anamorph with conidia.



Alternaria botrytis, CBS 197.67. Conidiophores and conidia.

Antifungal susceptibilityAntifungal GM Strains ReferenceAMB 2 3 Pujol et al. (2000)

5FC 256 3 Pujol et al. (2000)

FCZ 40.3 3 Pujol et al. (2000)

ITZ 0.99 3 Pujol et al. (2000)

KTZ 2 3 Pujol et al. (2000)

MCZ 4 3 Pujol et al. (2000)

Alternaria botrytis, CBS 197.67. A-C. Colonies (1 wk, 25°C, on MEA, OA, PDA, respectively), obverse; D-K conidiophores with single or sympodial, non-catenate conidia; L. liberated conidia. Scale bars = 10 µm.

Asco filamentous


Asc

ofilam

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Ascomycota, Pezizomycotina, Onygenales, Onygenaceae. Genus: APHANOASCUS

Colonies cottony, dry, white to pale pigmented. Cleistothecia pseudoparenchymatous, with subspherical asci; asco-spores 1- celled, ornamented.Recommended barcoding gene: rDNA ITS. A small genus of which species, in the absence of sexual fruitbodies, often were referred to under the name conidial name Chrysosporium.

ReferencesGuého et al. (1985), Cano & Guarro (1990).

Aphanoascus fulvescens (Cooke) Apinis

Colony characteristicsColonies (OA) growing moderately rapidly, white to tan, flat.

MicroscopyFertile hyphae hyaline, not differentiated. Terminal and lateral conidia chrysosporium-like, sessile or on short, un-swollen protusions, solitary, hyaline, smooth- and moder-ately thick-walled, clavate, 15.0-17.5 × 3.7-6.0 µm, with conspicuous basal scars. Intercalary conidia frequent, cy-lindrical, 11-15 × 4.0-5.5 µm. Ascomata spherical, non-os-tiolate, buff to light brown, 290-500 µm diam. Peridium pseudoparenchymatous. Asci subspherical to ellipsoidal, 8-spored, 9.5-11.0 × 7-9 µm. Ascospores light brown, yel-lowish to pale brown in mass, irregularly reticulate, lens-shaped, 3.5-4.7 × 2.5-3.5 µm.

PathogenicityRG-1, BSL-2. Keratinolytic species. Several cases of skin infection in man (Guého et al., 1985; Marín & Campos, 1984) and in animals (Vanbreuseghem & de Vroey, 1979; Pal, 1995b) have been reported.

ReferencesGuého et al. (1985), Cano & Guarro (1990).

NomenclatureBadhamia fulvescens Cooke - Grevillea 4: 69, 1875 ≡ Aphanoascus fulves-

cens (Cooke) Apinis - Mycopath. Mycol. Appl. 35: 99, 1968 ≡ Anixiop-

sis fulvescens (Cooke) de Vries - Mykosen 12: 120, 1969.

Eurotium stercorarium Hansen - Videnskab. Medd. Naturh. For. Kjöben-

havn 1876: 310, 1876 ≡ Anixiopsis stercoraria (Hansen) Hansen - Bot.

Ztg. 55: 127, 1897 ≡ Anixiopsis fulvescens (Cooke) de Vries var. sterco-

raria (Hansen) de Vries - Mykosen 12: 121, 1969.

Key to the treated species of Aphanoascus1a. Ascospores 6.5-8.5 × 4.5-6.0 μm; conidia 8.5-13.0 × 5.5-9.0 μm A. keratinophilus

1b. Ascospores 3.5-4.7 × 2.5-3.5 μm; conidia 11-15 × 4.0-5.5 μm A. fulvescens

Aphanoascus fulvescens, FMR 3946. a. Ascoma; b. part of peridium; c. asci; d. ascospores; e. fertile hyphae and conidia.



Arthroderma eboreum (Brasch & Gräser) Gräser & de Hoog

Colony characteristicsColonies (SGA) expanding, powdery, with feathered mar-gin, purely white; reverse white, without exuding pig-ments.

MicroscopyHyphae thin- and smooth-walled, hyaline. Macroconidia abundant in fresh cultures, smooth- and thin-walled, 3-8- septate, clavate to cylindrical, up to 6-30(-50) × 2-6 µm. Microconidia sessile alongside hyphae, hyaline, smooth-walled, short- clavate, 2.8-5.0 × 1.3-2.5 µm, with flat basal scars. Spirally twisted hyphae present. Hyphae anasto-mosing and producing dense complexes of rather thick-walled, curved, intertwined hyphal elements, leading to the formation of hard, white sclerotia, 100-200 µm diam. Chlamydospores absent. Heterothallic. Ascomata spher-ical, white to pale yellow, 300-800 µm diam. Peridium 50-100 µm thick. Peridial hyphae septate, curved, occa-sionally branched, 5-7 µm wide, composed of constrict-ed, rough-walled, dumbbell-shaped cells 7-10 µm long. Some peridial hyphae terminate in smooth-walled, coiled appendages. Asci subspherical, thin-walled, evanescent, 6.3-7.3 µm diam, 8-spored. Ascospores hyaline, yellow in mass, smooth-walled, oblate, 2.8-3.8 µm × 1.8-2.3 µm.

Differential diagnosticsDiffers from Trichophyton terrestre by the presence of hard, white sclerotia.

PathogenicityRG-1, BSL-1. Zoophilic or geophilic species found in asso-ciation with with European badgers and rabbits (Camp-bell et al., 2006). Occasionally isolated from human skin (Brasch & Gräser, 2005), causing very mild infection (Keller et al., 2013).

ReferencesCampbell et al. (2006), Brasch & Gräser (2005).

NomenclatureTrichophyton eboreum Brasch & Gräser - J. Clin. Microbiol. 43: 5235,

2005 ≡ Arthroderma eboreum (Brasch & Gräser) Gräser & de Hoog,

in de Hoog, Dukik, Monod, Packeu, Stubbe, Hendrickx, Kupsch,

Stielow, Freeke, Göker, Rezaei-Matehkolaei, Mirhendi & Gräser - My-

copathologia 182: 26, 2017.

Arthroderma olidum Campbell, Borman, Linton, Bridge & Johnson - Med.

Mycol. 44: 457, 2006.

Growth characteristicsCycloheximide 0,1% +

Growth at 37°C -

Hair perforation +

NaCl 2% +

NaCl 5% +

Trichophyton agar-1 +







Urease w

Arthroderma eboreum, CBS 117155. A. Colony (SGA, 3 wk, 27°C), obverse and reverse; B-D. complexes of intertwined hyphal elements with sclerotium formation; E-G. details of early intertwined hyphal elements; H, I. microconidia; J. chlamydospore-like cell. Scale bars = 10 µm.

Asco filamentous


Asc

ofilam

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Ascomycota, Pezizomycotina, Eurotiales, Eremomycetaceae. Genus: ARTHROGRAPHIS

Recommended barcoding gene: rDNA ITS. Small genus of species that are mostly associated with keratin-rich sub-strates. Arthroconidia are formed in dense arrangement on clustered, somewhat differentiated conidiophores.

Arthrographis kalrae (Tewari & Macpherson) Sigler & Carmi-chael

Colony characteristicsColonies (PDA) with slow to moderate growth, cream-co-loured to tan.

MicroscopyConidiophores (sub)hyaline, narrow, branched, often in bundles, occasionally forming whitish, 0.5 cm large, lin-ear synnemata. Arthroconidia 1-celled, hyaline, smooth-walled, cylindrical, with truncate ends, 2.5-9.0 × 1-2 µm, dry. Trichosporiella-like synanamorph forming solitary, (sub)spherical, thin- and smooth-walled, hyaline conidia, 2-4 × 2-3 µm, formed laterally and sessile on undifferenti-ated hyphae. Some isolates produce intercalary or termi-nal chlamydospores with smooth or slightly rugose walls, usually hyaline to subhyaline but occasionally brown giv-ing a dark pigmentation to the colony. Very rarely imma-ture ascomata submerged in the agar are produced.

PathogenicityRG-1, BSL-2. Cochet (1939) already reported the fungus

from onychomycosis, which is a main pathology (Sugiu-ra & Hironaga, 2010). Tewari & Macpherson (1968) ob-served neurotropism in artificial inoculation. Pichon et al. (2008) reported a cerebral case extending from the sinus in an alcoholic patient, Chin-Hong et al. (2001) a menin-gitis secondary to sinusitis in an AIDS patient, and Denis et al. (2016) a fungemia in a CF patient. Cases of keratitis were reported by Perlman & Binns (1997), Thomas et al. (2011), Ramli et al. (2013), Chow et al. (2014) and Biser et al. (2004), ophthalmitis by Xi et al. (2004), endocardi-tis (de Diego Candela et al., 2010), a pulmonary infection (Vos et al., 2012) and a mycetoma by Degrave et al. (1997). A traumatic infection was reported by Boan et al. (2012). Two infections in immunocompromised patients were presented by Delage et al. (1998). The species is soilborne.

ReferencesTewari & Macpherson (1971), Sigler & Carmichael (1976, 1983), Malloch & Sigler (1988), Gené et al. (1996b), Sugi-ura & Hironaga (2010), Giraldo et al. (2014).

NomenclatureArthrographis langeronii Cochet - Annls Parasit. Hum. Comp. 17: 97,

1939.

Oidiodendron kalrae Tewari & Macpherson - Mycologia 63: 603, 1971 ≡

Arthrographis kalrae (Tewari & Macpherson) Sigler & Carmichael -

Mycotaxon 4: 360, 1976.

Growth characteristicsBenomyl -

Cycloheximide 0,1% +

Growth at 37°C +

Hair perforation +

Keratinase +

Antifungal susceptibilityAntifungal Range GM MIC50 MIC90 Strains ReferenceAMB 1-4 2.64 2 4 22 Sandoval-Denis et al. (2014)

AND <0.015->8 14.54 >8 >8 22 Sandoval-Denis et al. (2014)

CAS 0.05->8 1.29 >8 >8 22 Sandoval-Denis et al. (2014)

ITZ <0.03-2 0.55 0.5 1 22 Sandoval-Denis et al. (2014)

MCF <0.015->8 15.27 >8 >8 22 Sandoval-Denis et al. (2014)

PCZ <0.03-5 0.28 0.25 0.5 22 Sandoval-Denis et al. (2014)

TBF <0.004-0.06 0.04 0.03 0.06 22 Sandoval-Denis et al. (2014)

VCZ 0.06-1 0.55 0.5 1 22 Sandoval-Denis et al. (2014)


The ultimate benchtool for diagnostics.

Pythium insidiosum, CBS 673.85. A-C. Colonies (8 d, 25°C, on MEA, OA, PDA, respectively; D. on water agar with infected grass, 24 h, 37°C; E-H. de-veloping sporangia liberating sporangiospores; J. liberated zoospore with unique flagella; K. germinating spore. Scale bars = 10 µm.


Low

er fu

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Mortierella polycephala, CBS 327.72. A-C. Colonies (5 d, 21°C, on MEA, OA, PDA, respectively), obverse; D. stereo microscopy of sporangiophores; E-L branched sporangiophores Scale bars = 10 µm.

Mortierellomycotina, Mortierellales, Mortierellaceae. Genus: MORTIERELLA



Maximum Likelihood (ML) tree of the genera Cryptococcus and its relatives Cystofilobasidium, Filobasidium, Naganishia, Papiliotrema and Vanrija based on confidently aligned ITS sequences using ClustalW. The substitution model is Tamura 3-parameter Gamma distributed (T92+G). The tree was bootstrapped 1000 times and values above 80% are indicated near of the nodes and with thick branches.

Basidio yeast


Basid

io y

east

Basidiomycota, Agaricomycotina, Trichosporonales, Trichosporonaceae. Genus: APIOTRICHUM

Recommended barcoding gene: rDNA ITS. For phylogenetic reasons, several species of Trichosporon were transferred to Apiotrichum (Liu et al., 2015); see also the phylogenetic tree of Trichosporon, where also a key to Trichosporon species and relatives is provided. Trichosporon mycotoxinovorans has been reported from lungs of patients with cystic fibrosis (Hickley et al., 2009; Hirschi et al., 2012; Shah et al., 2014), but pathology has not been proven.

Apiotrichum domesticum (Sugita et al.) Yurkov & Boekhout

Colony characteristicsColonies (YM agar) yellowish wrinkled moist, with undu-late border.

MicroscopyCells (YM broth) spherical or ovoidal, 3.7-4.8 × 5.2-12.8 µm; pseudo- and septate hyphae present, falling apart into arthroconidia.

SerologyAmong the Trichosporon species, Ikeda et al. (1996) typi-fied the species as serotype III.

PathogenicityRG-1, BSL-1. The species, originally isolated from the

house of a summer-type hypersensitivity pneumonitis patient in Japan (Sugita et al.,1995, 2004), is rare. It was also isolated from a cat with chronic cystitis (Sakamoto et al., 2001).

References Sugita et al. (1995, 1999, 2004).

NomenclatureTrichosporon domesticum Sugita, Nishikawa & Shinoda – J. Gen. Appl.

Microbiol. 41: 431, 1995 ≡ Apiotrichum domesticum (Sugita, Nishi-

kawa & Shinoda) Yurkov & Boekhout, in Liu, Wang, Göker, Groe-

newald, Kachalkin, Lumbsch, Millanes, Wedin, Yurkov, Boekhout &

Bai - Stud. Mycol. 81: 141, 2015.

Growth characteristicsD-Glucose + Me a-D-Glucoside + Ribitol -,+ Propane 1,2 diol +

D-Galactose + Cellobiose + Xylitol -,+ Butane 2,3 diol -

L-Sorbose -,+ Salicin -,+ Arabinitol - Nitrate -

D-Glucosamine + Arbutin + D-Glucitol -,+ Nitrite -

D-Ribose + Melibiose - D-Mannitol + Ethylamine +

D-Xylose + Lactose + Galactitol - L-Lysine +

L-Arabinose + Raffinose - myo-Inositol + Cadaverine +

D-Arabinose - Melezitose + 2-Keto-D-Gluconate + Creatinine -

L-Rhamnose - Inulin - D-Gluconate - Glucosamine +

Sucrose + Starch + DL-Lactate + Cycloheximide 0,01% +

Maltose + Glycerol + Succinate + Cycloheximide 0,1% +

a,a-Trehalose + Erythritol - Citrate +

Fermentation

D-Glucose D-Galactose Maltose Sucrose a-a-Trehalose Lactose Raffinose- - - - - - -



Colony characteristicsColonies (SGA) moderately expanding, moist and shiny, elevated, with deep, narrow radial fissures.

MicroscopyBudding cells present in primary cultures. Broadly clav-ate, terminal or lateral blastoconidia often present, at maturity developing a thick cell wall. Arthroconidia bar-rel-shaped.

Differential diagnosticsGrowth with melibiose and at 37°C; tolerant to 0.1 % cy-cloheximide. Liu et al. (2015) reclassified the species as Cutaneotrichosporon mucoides in Trichosporonaceae.

PathogenicityRG-1, BSL-2. The species is fairly common on super-

Cutaneotrichosporon mucoides (Guého & M.Th. Smith) X.Z. Liu et al.

ficial locations, where it causes pubic white piedra (Thérizol-Ferly et al., 1994) or is involved in onychomyco-sis. It may cause disseminated infections in patients with impaired innate immunity (Herbrecht et al., 1993; Nettles et al., 2003).

ReferencesHerbrecht et al. (1993), Guého et al. (1994).

NomenclatureTrichosporon mucoides Guého & M.Th. Smith, in Guého, Smith, de

Hoog, Billon-Grand, Christen & Batenburg-van der Vegte - An-tonie van Leeuwenhoek 61: 312, 1992 ≡ Cutaneotrichosporon mu-coides (Guého & M.Th. Smith) X.Z. Liu, F.Y. Bai, M. Groenewald & Boekhout, in Liu, Wang, Göker, Groenewald, Kachalkin, Lumbsch, Millanes, Wedin, Yurkov, Boekhout & Bai - Stud. Mycol. 81: 140, 2015.

Fermentation

D-Glucose D-Galactose Maltose Sucrose a-a-Trehalose Lactose Raffinose- - - - - - -

Growth characteristicsD-Glucose + Me a-D-Glucoside + Ribitol + Propane 1,2 diol +

D-Galactose + Cellobiose + Xylitol + Butane 2,3 diol -,+

L-Sorbose + Salicin + Arabinitol + Nitrate -

D-Glucosamine + Arbutin + D-Glucitol + Nitrite +

D-Ribose + Melibiose + D-Mannitol + Ethylamine +

D-Xylose + Lactose + Galactitol + L-Lysine +

L-Arabinose + Raffinose + myo-Inositol + Cadaverine +

D-Arabinose + Melezitose + 2-Keto-D-Gluconate + Creatinine -

L-Rhamnose + Inulin - D-Gluconate + Glucosamine +

Sucrose + Starch + DL-Lactate + Cycloheximide 0,01% +

Maltose + Glycerol + Succinate + Cycloheximide 0,1% +

a,a-Trehalose + Erythritol + Citrate +

Antifungal susceptibilityAntifungal GM MICs range Strains ReferenceAMB 0.02 4 Guého et al. (1994)

AMB 0.69 0.015-16 16 Rodriguez-Tudela et al. (2005)

5FC 50 4 Guého et al. (1994)

5FC 30.6 4-128 16 Rodriguez-Tudela et al. (2005)

FCZ 10.5 4 Guého et al. (1994)

FCZ 7 0.5-128 16 Rodriguez-Tudela et al. (2005)

Basidio yeast


Basid

io y

east

Naganishia uzbekistanensis (Á. Fonseca et al.) X.Z. Liu et al.

Colony characteristicsColonies (20°C, MYP) withe to pinkish, butyrous with a slightly glossy, smooth surface.

MicroscopyBudding cells (YM broth) subspherical to broadly ellipsoi-dal, 6.1-7.0 × 4.2-5.5 µm, singly or with buds.

Molecular diagnosticsLiu et al. (2015) classified the species as Naganishia uzbeki-stanensis as a member of the order Filobasidiales, family Filobasidiaceae.

PathogenicityBSL-1. Powel et al. (2012) reported the species in a patient with lymphoma.

ReferencesPowel et al. (2012).

NomenclatureCryptococcus uzbekistanenis Á. Fonseca, Scorzetti & Fell - Can. J. Micro-

biol. 46: 25, 2000 ≡ Naganishia uzbekistanensis (Á. Fonseca, Scor-

zetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenewald & Boekhout, in Liu,

Wang, Göker, Groenewald, Kachalkin, Lumbsch, Millanes, Wedin,

Yurkov, Boekhout & Bai - Stud. Mycol. 81: 119, 2015

Fermentation

D-Glucose D-Galactose Maltose Sucrose Lactose Raffinose- - - - - -

Growth characteristicsD-Glucose + Cellobiose + D-Mannitol +

D-Galactose - Salicin + Galactitol -

L-Sorbose + Melibiose - myo-Inositol +

D-Ribose -,+ Lactose - D-Gluconate +

D-Xylose + Raffinose + DL-Lactate -,+

L-Arabinose + Melezitose + Succinate +

D-Arabinose -,+ Inulin - Citrate +

L-Rhamnose + Starch -,+ Nitrate +

Sucrose + Glycerol - Ethylamine -,+

Maltose + Erythritol - L-Lysine -,+

a,a-Trehalose + Ribitol - Cadaverine +

Me a-D-Glucoside + D-Glucitol + w/o vitamins _

Naganishia uzbekistanensis, CBS 8683. A, B. Colonies (YPGA, 2 d, 24°C), obverse and reverse; C, D. budding cells. Scale bars = 10 µm.



Candida albicans, CBS 5736. A. Colony (SGA, 24 h, 24°C), obverse and reverse; B. colony (CandiSelect-4 medium, 24 h, 24°C), obverse and reverse; C. colony (Chromagar, 24 h, 24°C), obverse and reverse; D. budding cells; E-H. chlamydospores. Scale bars = 10 µm.

Asco yeast


Asc

o ye

ast

Antifungal susceptibility (Continued) Antifungal MICs range MIC 90 Strains ReferenceMCF 0.03 733 Ostrosky-Zeichner et

al. (2003)

MCF ≤0.008-≥16 0.06 2,563 Lyon et al. (2010)

MCF 0.007-0.5 4,283 Pfaller et al. (2010)

PCZ 0.13 733 Ostrosky-Zeichner et al. (2003)

PCZ 0.007->8 0.03 2,359 Pfaller et al. (2004)

PCZ 0.13 733 Ostrosky-Zeichner et al. (2003)

PCZ 0.007-2 0.06 5,827 Pfaller & Diekema (2010)

PCZ ≤0.03-≥64 0.25 2,563 Lyon et al. (2010)

PCZ 0.06-0.5 59 Lass-Flörl et al. (2008)

VCZ 0.007-4 0.015 5,826 Pfaller & Diekema (2010)

VCZ 0.06 733 Ostrosky-Zeichner et al. (2003)

VCZ ≤0.008-≥16 0.06 2,563 Lyon et al. (2010)

VCZ <0.03-1 0.125 84 Bourgeois et al. (2010)

VCZ 0.06-0.25 59 Lass-Flörl et al. (2008)

VCZ 0.007->8 0.015 2,359 Pfaller et al. (2004)

VCZ 0.004-8 55 Heyn et al. (2005)

Candida albicans, strain Kerkm. a. Pseudomycelium emerging from cellular clumps; b. chlamydospores.



Aspergillus montevidensis Talice & Mackinnon

Colony characteristicsColonies (CzA) restricted, growing rapidly on media with 20% additional sucrose, yellow to dull yellow-grey.

MicroscopyConidial heads radiate to loosely columnar, olive-green. Conidiophores smooth-walled, 275-350 μm long. Vesicles spherical, 18-25 μm diam. Conidiogenous cells uniseriate, 5-8 × 3.4-5.0 μm, covering at least the upper two-third of the vesicle. Conidia finely roughened to densely spinu-lose, spherical to subspherical, 3-5 μm diam. Ascomata clustered, forming a dense layer, spherical, bright yellow, 120-160 μm diam. Asci 8-spored, spherical to subspheri-cal, 10-12 μm diam. Ascospores pale, rough-walled, with a V-shaped equatorial furrow, lenticular, 4.5-6.0 × 3.5-4.0 μm.

PathogenicityRG-1, BSL-1. The species has been isolated from a wide range of human mycoses: otitis (Wadhwani & Srivastava, 1984), mycetoma (Fonseca, 1930; Lacaz & Netto, 1954),

dermatomycosis (Janke, 1954), cerebral abscess (David et al., 1951), onychomycosis (Grigoriu & Grigoriu, 1975), keratitis (Shukla et al., 1985) and pulmonary infections (Young et al., 1972).

ReferencesRaper & Fennell (1965), Blaser (1975).

NomenclatureAspergillus montevidensis Talice & Mackinnon - Compt. Rend. Soc. Biol.

Fr. 108: 1007, 1931 ≡ Eurotium montevidense (Talice & Mackinnon)

Malloch & Cain - Can. J. Bot. 50: 64, 1972 ≡ Eurotium amstelodami

Mangin var. montevidense (Talice & Mackinnon) Kozakiewicz - My-

col. Pap. 161: 86. 1989.

Eurotium amstelodami Mangin - Annls Sci. Nat., Bot., Sér. 9, 10: 360,

1909 ≡ Aspergillus amstelodami (Mangin) Thom & Church - The As-

pergilli p. 113, 1926.

Aspergillus vitis Novobranova - Nov. Sist. Niszh. Rast. 9: 175, 1975.

Aspergillus hollandicus Samson & W. Gams, in Samson - Adv. Pen. Asp.

Syst. p. 33, 1985.

Aspergillus montevidensis, CBS 518.65. a. Ascomata; b. asci; c. ascospores; d. conidiophores; e. conidia.

Asco filamentous


Asc

ofilam

entous

Aspergillus brasiliensis Varga et al.

Colony characteristicsColony diameters in 7 days: CYA and CYAS: 71-76 mm, MEA 52-70 mm, YES: 75-80 mm, OA: 32-36 mm, CREA: 32-44 mm, poor growth, strong acid production. Colonies first white, then dark brown to black. Exudates absent; reverse cream coloured to light brown.

MicroscopyConidial heads spherical at first, later radiate, occasion-ally developing into several conidial columns; stipes 700- 1700 x 8-13 µm, pale brown, thick- and smooth-walled. Vesicles 30-45 µm wide, nearly spherical, biseriate; met-ulae covering virtually the entire surface of the vesicle, measuring 22-30 × 3-6 µm. Phialides flask-shaped, 7–9 × 3-4 µm. Conidia subspherical, 3.5-4.8 µm diam, echinu-late. No sclerotia observed in the culture ex type.

Molecular diagnosticsThe species can be distinguished from other members of Aspergillus section Nigri using mtDNA and rDNA RFLP data (Varga et al., 1994), and sequence analysis of ITS, B-tubulin or calmodulin genes (Varga et al., 2007c; Sam-son et al., 2007b).

PathogenicityRG-1, BSL-1. Human keratitis (Kredics et al., 2008).

ReferencesVarga et al. (2007c), Kredics et al. (2008).

NomenclatureAspergillus brasiliensis Varga, Frisvad & Samson – Int. J. Syst..

Evol. Microbiol. 57: 1929, 2007.

Aspergillus brasiliensis, CBS 101740. A-C. Colonies (10 d, 25°C, on MEA, CYA, DG18 respectively), obverse; D-G. conid-iophores with sporulating vesicles; H-I. conidial chains. Scale bars = 10 µm.



Aspergillus tubingensis Mosseray

Colony characteristicsColonies on CZA at 25°C attaining diameters of 4-5 cm in 10 days, velvety, somewhat zonate, consisting of a fairly compact white basal mycelium. Conidial heads in slightly greyish black-brown shades, borne on long conidiophores; reverse white; exudate and odor lacking. Colonies on MEA at 25°C growing rapidly, reaching 6 cm in diam in 10 days, thin, plane, velvety, indistinctly zonate, heavily sporulat-ing in very dark brown shades; reverse uncoloured.

MicroscopyConidial heads spherical to radiate, mostly 200-300 µm. Conidiophores smooth, long and coarse, commonly 15-20µm diam, usually lightly coloured in brown shades, thin-walled; vesicles spherical, rather variable in size, most commonly 40-60 µm diam, fertile over their entire surface. Conidia spherical with hyaline echinulations when first formed, becoming progressively darker and rougher and finally appearing longitudinally striate from conspicuous bars of colouring material, mature conidia somewhat horizontally flattened, 3.0-3.5 µm in diam. Sclerotia produced in some strains, occasionally dominating the colony appearance, (sub)spherical, cream coloured at first

then pinkish buff and sometimes darkening to almost black in age, commonly 500-800 µm in diam.

Molecular diagnosticsAspergillus tubingensis can be distinguished from other related members of Aspergillus section Nigri using mtD-NA and rDNA RFLP data (Varga et al., 1993, 1994), and by sequence analysis of beta-tubulin or calmodulin genes (Samson et al., 2007b).

PathogenicityRG-1, BSL-1. Agent of invasive aspergillosis (Kano et al., 2008a; Howard et al., 2008), of osteomyelitis (Bathoon et al., 2013) and of keratitis (Kredics et al., 2009). A cu-taneous infection nwas reported by Frias-De-Leon et al. (2018). The species appears to be relatively commonly in-volved in pulmonary disorders (Gautier et al., 2016).

ReferencesRaper & Fennell (1965), Horn et al. (2013).

NomenclatureAspergillus tubingensis Mosseray - La Cellule 43: 245-247, 1934.

Antifungal susceptibilityAntifungal MICs range GM MIC50 MIC90 Strains ReferenceAMB 0.032-0.25 2 Kredics et al. (2009)

AMB 0.06-2 0.1 0.12 29 Alastruey-Izquierdo et al. (2014)

AND 0.03-0.06 0.03 0.03 29 Alastruey-Izquierdo et al. (2014)

AMB 0.25 0.25 8 Hagiwara et al. (2019)

CAS 0.06-1 0.28 1 29 Alastruey-Izquierdo et al. (2014)

CFG 0.06-0.25 2 Kredics et al. (2009)

EFCZ 0.25-0.5 0.39 8 Hagiwara et al. (2019)

5FC 4-16 6.73 8 Hagiwara et al. (2019)

FCZ >256 2 Kredics et al. (2009)

FCZ >64 8 Hagiwara et al. (2019)

ISA 1-8 4 8 66 Pfaller et al. (2018)

ITZ 1-2 2 Kredics et al. (2009)

ITZ 0.12-32 0.63 2 29 Alastruey-Izquierdo et al. (2014)

ITZ 1-4 2 4 48 Pfaller et al. (2018)

ITZ 0.5-2 1 8 Hagiwara et al. (2019)

LACZ 0.004-0.008 0.011 8 Hagiwara et al. (2019)

LLCZ 0.004-0.008 0.005 8 Hagiwara et al. (2019)

MCF 0.03-0.25 0.04 0.12 29 Alastruey-Izquierdo et al. (2014)

MCF <0.015 0.015 8 Hagiwara et al. (2019)

MCZ 4-8 5.66 8 Hagiwara et al. (2019)

PCZ 0.03-0.5 0.12 0.25 29 Alastruey-Izquierdo et al. (2014)

Asco filamentous


Asc

ofilam

entous

Aspergillus deflectus, CBS 536.65. A-C. Colonies (1 wk, 25°C, on MEA, CYA, DG18, respectively), obverse; D-G. conidiophores and phialides; H. conid-ia. Scale bars = 10 µm; G = SEM ×1600.

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Introduction ATLAS