!e ultimate benchtool for diagnostics. Introduction Introduction of ATLAS Introduction CLINICAL FUNGI Introduction
The ultimate benchtool for diagnostics Introduction Introduction Introduction
Sample pages Introduction
G.S. de Hoog, J. Guarro, J. Gené, S. Ahmed, Introduction A.M.S. Al-Hatmi, M.J. Figueras and R.G. Vitale
1 ATLAS of CLINICAL FUNGI !e 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 Tax Kreger & Veenhuis (1971) Pore Tax Moore (1987) Karyology Tax Takeo & de Hoog (1991) Co-Q Tax Yamada et al. (1987) Carbohydrate pattern Tax Weijman & Golubev (1987) Classical physiology Tax Yarrow (1998) API 32C Diag Guého et al. (1994b) API-Zym Diag Fromentin et al. (1981) mole% G+C Tax Guého et al. (1992b) SSU seq Tax Gargas et al. (1995) SSU-RFLP Tax Machouart et al. (2006) LSU Diag Kurtzman & Robnett (1998) ITS seq/RFLP Diag Lieckfeldt & Seifert (2000) IGS Epid Diaz & Fell (2000) Tubulin Tax Keeling et al. (2000) Actin Tax Donnelly et al. (1999) Chitin synthase Tax Karuppayil et al. (1996) Elongation factor Diag Helgason et al. (2003) NASBA Tax Compton (1991) nDNA homology Epid Voigt et al. (1997) RCA Epid Barr et al. (1997) LAMP Tax Guého et al. (1997) MLPA Diag Sun et al. (2010) Isoenzymes (MLEE) Epid Pujol et al. (1997) Maldi-tof Diag Schrödl et al. (2012) Fish Diag Rigby et al. (2002) RLB Diag Bergmans et al. (2008) PCR-ELISA Diag Beifuss et al. (2011) Secondary metabolites Tax/Diag Frisvad & Samson (2004) SSR Epid Karaoglu et al. (2005) rep-PCR Epid MacDonald et al. (2000) rt-PCR Diag Bergmans et al. (2010) RAPD / UP-PCR Tax Doherty et al. (2003) M-13 Epid/Tax Weising et al. (1995) T3B Epid Gäser et al. (2000) Microsatellites Epid/Tax Cai et al. (2013) mtDNA RFLP Epid Ishizaki et al. (1996) AFLP Epid Savelkoul et al. (1999) Karyotyping Epid Franzot et al. (1998) MLST Epid Meyer et al. (2009)
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 agar commercial BHI agar 52 g CEA: Casamino acids erythritol agar casamino acids (Bacto) 3 g
MgSO4 0.1 g
KH2PO4 1.8 g meso-erythritol 10 g albumin 10 mL agar 15 g CDBT: Creatine dextrose bromothymol blue thymine agar Solution A:
2 ATLAS of CLINICAL FUNGI Clinical pathology fused with secondary skin infections caused by systemic in"ammation occurs. According to the appearance of the fungi treated below. causative agent as seen in native preparations, the follow- ing subdivision is made: Dermatophyte infections of the dermis Hyalohyphomycosis. #e fungal elements are colourless. Phaeohyphomycosis. #e fungal elements are melanised Dermatophytes are normally con!ned to cutis, hair and (special staining often necessary). nails, but occasionally the dermis is involved.
Chromoblastomycosis Introductions Majocchi’s granuloma. Perifollicular granulomatous in"ammation. #e dermatophyte may be present in the #e disease occurs mostly on the extremities and is char- cutis, but also deeper skin layers are involved. acterized by localized, slowly expanding lesions. Super!- cial, warty to cauli"ower-like tumours and deformations Kerion (pseudomycetoma). Subcutaneous, elevated, develop, due to hyperkeratosis and acanthosis. #e le- spongy lesion by dermatophytes with local necrosis and sions are greyish, crusted and dry in appearance. #e fun- with presence of hyphae or grain-like structures. gus occurs as dark, muriform cells in the tissue. Causative agents: Fonsecaea monophora, F. nubica, F. pedrosoi, Clado- Non-ulcerative infections by diverse fungi phialophora carrionii, Phialophora verrucosa, Rhinocladiella aquaspersa. #e following types can be distinguished, of #ese concern local, non-ulcerative infections caused by which several may occur in the same patient (adapted a variety of fungi. #e fungus is present in the form of from Queiroz Telles et al., 2009): septate hyphae or hyphal elements. In the case of hy- Nodular. Moderately elevated, fairly soft, dull to pink phomycotic cysts the a$ected area is surrounded by a violaceous growth. Surface smooth, verrucous or scaly. !brous, collagenous secretion of the host, and hence no With time lesions may gradually become tumorous.
Main types of histopathological response to subcutaneous and deep infection
Subcutaneous Special features
Purulence Granuloma Fibrosis Necrosis
- + - -,w Hyphae with melanin - + - -,w Hyphae without melanin + + + + Grains - + + - Muriform cells + + + + Asteroid bodies, rabbit ears - + - - Wide hyphal elements, oedema
Pulmonary
+ + - + Hyphae without melanin + + + - Yeast cells with wide base + + + - Spherules + + + + Pilot wheel/Mickey Mouse - + + - Intracellular yeast - + + - Adiaspores - + - - Intracellular arthroconidia
Rhinoorbital
+ - - + Wide hyphal elements, oedema - + + - Splendore-Hoeppli - + + - Hyphae
Systemic yeast infection
+ + - + Yeast cells, pseudohyphae - + - - Capsular yeast cells
Overview of histopathological features in subcutaneous, deep and disseminated infections in immunologically competent individuals: host responses and fungal tissue forms.
3 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Phylum Basidiomycota
#e life cycle of a prototypical basidiomycete is depicted. #e 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. #e septa are perforated by a single, central pore. #e 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. #is 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
4 ATLAS of CLINICAL FUNGI Basidio !lamentous Basidio
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.
5 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
A. longipes CBS 540.94 A. gossypina CBS 104.32 A. gaisen CBS 632.93 A. arborescens CBS 102605 A. alstroemeriae CBS 118809 A. burnsii CBS 107.38 A. tomato CBS 114.35 Section A. jacinthicola CBS 133751 Alternaria A. doliconidium KUMCC 17-0263 100 A. alternata CBS 916.96 A. betae-kenyensis CBS 118810 A. eichhorniae CBS 489.92 A. iridiaustralis CBS 118486 A. hordeicola CBS 121458 A. montsantina FMR 17060 A. graminicola CBS 119400 A. conjuncta CBS 196.86 A. caespitosa CBS 177.80 A. intercepta CBS 119406 A. cesenica MFLUCC 13-0450 A. novae-zelandiae CBS 119405 A. broccoli-italicae CBS 118485 A. dactylidicola MFLUCC 15-0466 A. fimeti FMR 17110 A. ventricosa CBS 121546 A. quercicola CBS 141466 A. triticina CBS 763.84 A. triticimaculans CBS 578.94 A. merytae CBS 119403 Section A. pseudoventricosa FMR 16900 Infectoriae A. lawrencei FMR 17004 A. alternarina CBS 119396 A. curvata FMR 16901 A. daucicaulis CBS 119398 A. ethzedia CBS 197.86 A. hordeiaustralica CBS 119402 A. infectoria CBS 210.86 A. slovaca CBS 567.66 x3 A. aconidiophora FMR 17111 99 A. metachromatica CBS 553.94 A. arbusti CBS 596.93 A. incomplexa CBS 121330 84 A. oregonensis CBS 542.94 A. pobletensis FMR 16448 97 A. cetera CBS 121340 A. obclavata CBS 124120 Section 99 A. malorum CBS 135.31 Chalastospora A. breviramosa CBS 121331 A. abundans CBS 534.83 94 A. armoraciae CBS 118702 80 A. chlamydospora CBS 491.72 A. phragmospora CBS 274.70 A. limaciformis CBS 481.81 Section A. molesta CBS 548.81 Phragmosporae A. mouchaccae CBS 119671 A. papavericola CBS 116606 A. penicillata CBS 116608 0.01
Maximum Likelihood (ML) tree of four sections of the genus Alternaria based on con!dently aligned rDNA ITS sequences using ClustalW. #e sub- stitution model is Kimura 2-parameter and gamma distributed (K2+G). #e tree was bootstrapped 1000 times and values above 80% are indicated near of the nodes and with thick branches. #e tree is rooted with Alternaria papavericola and A. penicillata. Note that the general barcoding marker ITS does not allow species distinction within species complexes.
6 ATLAS of CLINICAL FUNGI Asco !lamentous
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 characteristics m diam in face view, 5 m wide in lateral view, with a Colonies (OA) growing moderately rapidly, dull black- distinct equatorial germ slit. ish-brown, with dark grey patches of conidiation. Pathogenicity Microscopy RG-1, BSL-1. Cellulolytic saprophyte. A maxillary sinus- Conidiophores straight, sti$, profusely branched, up to itis was reported by Singh et al. (1996). 1 mm tall, 3.5-5.5 m wide, with pale, thin-walled vesi- cles at the bends. Conidiogenous cells terminal and lat- References eral, cylindrical, bearing clusters of conidia on denticles. Ames (1963), Hawksworth (1971). Conidia verrucose, yellowish-olivaceous, (sub)spherical, 5-7 × 3-6 m. Perithecia black, pear-shaped with apical Nomenclature opening, 130-230 m wide, discharching a black spore- Ascotricha chartarum Berkeley - Ann. Nat. Hist. 1: 257, 1838. cirrhus, bearing olivaceous-brown, erect, sti$ setae, ge- Dicyma ampullifera Boulanger - Revue Gén. Bot. 9: 25, 1897. niculate with pale, thin-walled vesicles at the bends. Asci Ascotrichum chartarum Berkeley var. orientalis Castellani & Jacono - J. cylindrical, 8-spored, 65 × 10 m. Ascospores one-celled, Trop. Med. Hyg. 37: 362, 1934. olivaceous-brown to black, smooth-walled, lenticular, 8 Asco
Ascotricha chartarum, CBS 657.95. a. Ascoma; b. ascus; c. oblate ascospore; d, e. anamorph with conidia.
7 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Antifungal susceptibility Antifungal GM Strains Reference AMB 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. Conidiophores and conidia.
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.
8 ATLAS of CLINICAL FUNGI Asco !lamentous
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.
References Guého et al. (1985), Cano & Guarro (1990).
Key to the treated species of Aphanoascus A. keratinophilus A. fulvescens
Aphanoascus fulvescens (Cooke) Apinis
Colony characteristics Colonies (OA) growing moderately rapidly, white to tan, "at.
Microscopy Fertile hyphae hyaline, not di$erentiated. Terminal and lateral conidia chrysosporium-like, sessile or on short, un- swollen protusions, solitary, hyaline, smooth- and moder- ately thick-walled, clavate, 15.0-17.5 × 3.7-6.0 µm, with conspicuous basal scars. Intercalary conidia frequent, cy- Asco lindrical, 11-15 × 4.0-5.5 µm. Ascomata spherical, non-os- tiolate, to light brown, 290-500 µm diam. Peridium pseudoparenchymatous. Asci subspherical to ellipsoidal, 8-spored, 9.5-11.0 × 7-9 µm. Ascospores light brown, yel- lowish to pale brown in mass, irregularly reticulate, lens- shaped, 3.5-4.7 × 2.5-3.5 µm.
Pathogenicity RG-1, BSL-2. Keratinolytic species. Several cases of skin infection in man (Guého et al., 1985; Marín & Campos, 1984) and in animals (Vanbreuseghem & de Vroey, 1979; Pal, 1995b) have been reported.
References Guého et al. (1985), Cano & Guarro (1990).
Nomenclature Badhamia fulvescens Cooke - Grevillea 4: 69, 1875 Aphanoascus fulves- cens (Cooke) Apinis - Mycopath. Mycol. Appl. 35: 99, 1968 Anixiop- sis fulvescens (Cooke) de Vries - Mykosen 12: 120, 1969. Eurotium stercorarium Hansen - Videnskab. Medd. Naturh. For. Kjöben- havn 1876: 310, 1876 Anixiopsis stercoraria (Hansen) Hansen - Bot. Aphanoascus fulvescens, FMR 3946. a. Ascoma; b. part of peridium; c. Ztg. 55: 127, 1897 Anixiopsis fulvescens (Cooke) de Vries var. sterco- asci; d. ascospores; e. fertile hyphae and conidia. raria (Hansen) de Vries - Mykosen 12: 121, 1969.
9 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Arthroderma eboreum (Brasch & Gräser) Gräser & de Hoog
Colony characteristics Differential diagnostics Colonies (SGA) expanding, powdery, with feathered mar- Di$ers from Trichophyton terrestre by the presence of gin, purely white; reverse white, without exuding pig- hard, white sclerotia. ments. Pathogenicity Microscopy RG-1, BSL-1. Zoophilic or geophilic species found in asso- Hyphae thin- and smooth-walled, hyaline. Macroconidia ciation with with European badgers and rabbits (Camp- abundant in fresh cultures, smooth- and thin-walled, 3-8- bell et al., 2006). Occasionally isolated from human skin septate, clavate to cylindrical, up to 6-30(-50) × 2-6 µm. (Brasch & Gräser, 2005), causing very mild infection Microconidia sessile alongside hyphae, hyaline, smooth- (Keller et al., 2013). walled, short- clavate, 2.8-5.0 × 1.3-2.5 µm, with "at basal scars. Spirally twisted hyphae present. Hyphae anasto- References mosing and producing dense complexes of rather thick- Campbell et al. (2006), Brasch & Gräser (2005). walled, curved, intertwined hyphal elements, leading to the formation of hard, white sclerotia, 100-200 µm diam. Nomenclature Chlamydospores absent. Heterothallic. Ascomata spher- Trichophyton eboreum Brasch & Gräser - J. Clin. Microbiol. 43: 5235, ical, white to pale yellow, 300-800 µm diam. Peridium 2005 Arthroderma eboreum (Brasch & Gräser) Gräser & de Hoog, 50-100 µm thick. Peridial hyphae septate, curved, occa- in de Hoog, Dukik, Monod, Packeu, Stubbe, Hendrickx, Kupsch, sionally branched, 5-7 µm wide, composed of constrict- Stielow, Freeke, Göker, Rezaei-Matehkolaei, Mirhendi & Gräser - My- ed, rough-walled, dumbbell-shaped cells 7-10 µm long. copathologia 182: 26, 2017. Some peridial hyphae terminate in smooth-walled, coiled Arthroderma olidum Campbell, Borman, Linton, Bridge & Johnson - Med. appendages. Asci subspherical, thin-walled, evanescent, Mycol. 44: 457, 2006. 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.
Growth characteristics Cycloheximide 0,1% + - Hair perforation + NaCl 2% + NaCl 5% + Trichophyton agar-1 + Trichophyton agar-2 + Trichophyton agar-3 + Trichophyton agar-4 + Trichophyton agar-5 + Trichophyton agar-6 + + 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.
10 ATLAS of CLINICAL FUNGI Asco !lamentous
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 di$erentiated conidiophores.
Arthrographis kalrae (Tewari & Macpherson) Sigler & Carmi- chael
Colony characteristics from onychomycosis, which is a main pathology (Sugiu- Colonies (PDA) with slow to moderate growth, cream-co- ra & Hironaga, 2010). Tewari & Macpherson (1968) ob- loured to tan. served neurotropism in arti!cial inoculation. Pichon et al. (2008) reported a cerebral case extending from the sinus Microscopy in an alcoholic patient, Chin-Hong et al. (2001) a menin- Conidiophores (sub)hyaline, narrow, branched, often in gitis secondary to sinusitis in an AIDS patient, and Denis bundles, occasionally forming whitish, 0.5 cm large, lin- et al. (2016) a fungemia in a CF patient. Cases of keratitis ear synnemata. Arthroconidia 1-celled, hyaline, smooth- were reported by Perlman & Binns (1997), #omas et al. walled, cylindrical, with truncate ends, 2.5-9.0 × 1-2 µm, (2011), Ramli et al. (2013), Chow et al. (2014) and Biser dry. Trichosporiella-like synanamorph forming solitary, et al. (2004), ophthalmitis by Xi et al. (2004), endocardi- (sub)spherical, thin- and smooth-walled, hyaline conidia, tis (de Diego Candela et al., 2010), a pulmonary infection 2-4 × 2-3 µm, formed laterally and sessile on undi$erenti- (Vos et al., 2012) and a mycetoma by Degrave et al. (1997). ated hyphae. Some isolates produce intercalary or termi- A traumatic infection was reported by Boan et al. (2012). nal chlamydospores with smooth or slightly rugose walls, Two infections in immunocompromised patients were usually hyaline to subhyaline but occasionally brown giv- presented by Delage et al. (1998). #e species is soilborne. ing a dark pigmentation to the colony. Very rarely imma- ture ascomata submerged in the agar are produced. References Tewari & Macpherson (1971), Sigler & Carmichael (1976, Asco
Pathogenicity 1983), Malloch & Sigler (1988), Gené et al. (1996b), Sugi- RG-1, BSL-2. Cochet (1939) already reported the fungus ura & Hironaga (2010), Giraldo et al. (2014).
Nomenclature Growth characteristics Arthrographis langeronii Cochet - Annls Parasit. Hum. Comp. 17: 97, Benomyl - 1939. Cycloheximide 0,1% + Oidiodendron kalrae Tewari & Macpherson - Mycologia 63: 603, 1971 + Arthrographis kalrae (Tewari & Macpherson) Sigler & Carmichael - Hair perforation + Mycotaxon 4: 360, 1976. Keratinase +
Antifungal susceptibility
Antifungal Range GM MIC50 MIC90 Strains Reference AMB 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 >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)
11 ATLAS of CLINICAL FUNGI !e 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 "agella; K. germinating spore. Scale bars = 10 µm.
12 ATLAS of CLINICAL FUNGI Mortierellomycotina, Mortierellales, Mortierellaceae. Genus: MORTIERELLA Lower fungi
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.
13 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Maximum Likelihood (ML) tree of the genera Cryptococcus and its relatives Cysto!lobasidium, Filobasidium, Naganishia, Papiliotrema and Vanrija based on con!dently aligned ITS sequences using ClustalW. #e substitution model is Tamura 3-parameter Gamma distributed (T92+G). #e tree was bootstrapped 1000 times and values above 80% are indicated near of the nodes and with thick branches.
14 ATLAS of CLINICAL FUNGI Basidio yeast
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 !brosis (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 characteristics house of a summer-type hypersensitivity pneumonitis Colonies (YM agar) yellowish wrinkled moist, with undu- patient in Japan (Sugita et al.,1995, 2004), is rare. It was late border. also isolated from a cat with chronic cystitis (Sakamoto et al., 2001). Microscopy Cells (YM broth) spherical or ovoidal, 3.7-4.8 × 5.2-12.8 References Basidio yeast µm; pseudo- and septate hyphae present, falling apart Sugita et al. (1995, 1999, 2004). into arthroconidia. Nomenclature Serology Trichosporon domesticum Sugita, Nishikawa & Shinoda – J. Gen. Appl. Among the Trichosporon species, Ikeda et al. (1996) typi- Microbiol. 41: 431, 1995 Apiotrichum domesticum (Sugita, Nishi- !ed the species as serotype III. kawa & Shinoda) Yurkov & Boekhout, in Liu, Wang, Göker, Groe- newald, Kachalkin, Lumbsch, Millanes, Wedin, Yurkov, Boekhout & Pathogenicity Bai - Stud. Mycol. 81: 141, 2015. RG-1, BSL-1. #e species, originally isolated from the
Fermentation
D-Glucose D-Galactose Maltose Sucrose a-a-Trehalose Lactose
------
Growth characteristics D-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 + - 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 +
15 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Cutaneotrichosporon mucoides (Guého & M.Th. Smith) X.Z. Liu et al.
Colony characteristics !cial locations, where it causes pubic white piedra Colonies (SGA) moderately expanding, moist and shiny, (Thérizol-Ferly et al., 1994) or is involved in onychomyco- elevated, with deep, narrow radial !ssures. sis. It may cause disseminated infections in patients with impaired innate immunity (Herbrecht et al., 1993; Nettles Microscopy et al., 2003). Budding cells present in primary cultures. Broadly clav- ate, terminal or lateral blastoconidia often present, at References maturity developing a thick cell wall. Arthroconidia bar- Herbrecht et al. (1993), Guého et al. (1994). rel-shaped. Nomenclature Differential diagnostics Trichosporon mucoides Guého & M.Th. Smith, in Guého, Smith, de Growth with melibiose and at 37°C; tolerant to 0.1 % cy- Hoog, Billon-Grand, Christen & Batenburg-van der Vegte - An- cloheximide. Liu et al. (2015) reclassi!ed the species as Cutaneotrichosporon mu- Cutaneotrichosporon mucoides in Trichosporonaceae. coides (Guého & M.Th. Smith) X.Z. Liu, F.Y. Bai, M. Groenewald & Boekhout, in Liu, Wang, Göker, Groenewald, Kachalkin, Lumbsch, Pathogenicity Millanes, Wedin, Yurkov, Boekhout & Bai - Stud. Mycol. 81: 140, RG-1, BSL-2. #e species is fairly common on super- 2015.
Fermentation
D-Glucose D-Galactose Maltose Sucrose a-a-Trehalose Lactose
------
Growth characteristics D-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 + + 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 susceptibility Antifungal GM MICs range Strains Reference AMB 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 0.5-128 16 Rodriguez-Tudela et al. (2005)
16 ATLAS of CLINICAL FUNGI Basidio yeast
Naganishia uzbekistanensis (Á. Fonseca et al.) X.Z. Liu et al.
Colony characteristics Pathogenicity Colonies (20°C, MYP) withe to pinkish, butyrous with a BSL-1. Powel et al. (2012) reported the species in a patient slightly glossy, smooth surface. with lymphoma.
Microscopy References Budding cells (YM broth) subspherical to broadly ellipsoi- Powel et al. (2012). dal, 6.1-7.0 × 4.2-5.5 µm, singly or with buds. Nomenclature Molecular diagnostics Cryptococcus uzbekistanenis Á. Fonseca, Scorzetti & Fell - Can. J. Micro- Liu et al. (2015) classi!ed the species as Naganishia uzbeki- biol. 46: 25, 2000 Naganishia uzbekistanensis (Á. Fonseca, Scor- stanensis as a member of the order Filobasidiales, family zetti & Fell) X.Z. Liu, F.Y. Bai, M. Groenewald & Boekhout, in Liu, Filobasidiaceae. Wang, Göker, Groenewald, Kachalkin, Lumbsch, Millanes, Wedin, Yurkov, Boekhout & Bai - Stud. Mycol. 81: 119, 2015
Fermentation
D-Glucose D-Galactose Maltose Sucrose Lactose
------
Growth characteristics Basidio yeast D-Glucose + Cellobiose + D-Mannitol + D-Galactose - Salicin + Galactitol - L-Sorbose + Melibiose - myo-Inositol + D-Ribose -,+ Lactose - D-Gluconate + D-Xylose + + 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.
17 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
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.
18 ATLAS of CLINICAL FUNGI Asco yeast
Antifungal susceptibility (Continued)
Antifungal MICs range MIC 90 Strains Reference MCF 0.03 Ostrosky-Zeichner et al. (2003) MCF 0.06 2,563 Lyon et al. (2010) MCF 4,283 Pfaller et al. (2010) PCZ 0.13 Ostrosky-Zeichner et al. (2003) PCZ 0.03 2,359 Pfaller et al. (2004) PCZ 0.13 Ostrosky-Zeichner et al. (2003) PCZ 0.06 Pfaller & Diekema (2010) PCZ 0.25 2,563 Lyon et al. (2010) PCZ 0.06-0.5 59 Lass-Flörl et al. (2008) VCZ 0.015 5,826 Pfaller & Diekema (2010) VCZ 0.06 Ostrosky-Zeichner et al. (2003) VCZ 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 0.015 2,359 Pfaller et al. (2004) VCZ 0.004-8 55 Heyn et al. (2005) Asco yeast
Candida albicans, strain Kerkm. a. Pseudomycelium emerging from cellular clumps; b. chlamydospores.
19 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Aspergillus montevidensis Talice & Mackinnon
Colony characteristics dermatomycosis (Janke, 1954), cerebral abscess (David Colonies (CzA) restricted, growing rapidly on media with et al., 1951), onychomycosis (Grigoriu & Grigoriu, 1975), 20% additional sucrose, yellow to dull yellow-grey. keratitis (Shukla et al., 1985) and pulmonary infections (Young et al., 1972). Microscopy Conidial heads radiate to loosely columnar, olive-green. References Conidiophores smooth-walled, 275-350 m long. Vesicles Raper & Fennell (1965), Blaser (1975). spherical, 18-25 m diam. Conidiogenous cells uniseriate, 5-8 × 3.4-5.0 m, covering at least the upper two-third Nomenclature of the vesicle. Conidia !nely roughened to densely spinu- Aspergillus montevidensis Talice & Mackinnon - Compt. Rend. Soc. Biol. lose, spherical to subspherical, 3-5 m diam. Ascomata Fr. 108: 1007, 1931 Eurotium montevidense (Talice & Mackinnon) clustered, forming a dense layer, spherical, bright yellow, Malloch & Cain - Can. J. Bot. 50: 64, 1972 Eurotium amstelodami 120-160 m diam. Asci 8-spored, spherical to subspheri- Mangin var. montevidense (Talice & Mackinnon) Kozakiewicz - My- cal, 10-12 m diam. Ascospores pale, rough-walled, with col. Pap. 161: 86. 1989. a V-shaped equatorial furrow, lenticular, 4.5-6.0 × 3.5-4.0 Eurotium amstelodami Mangin - Annls Sci. Nat., Bot., Sér. 9, 10: 360, m. 1909 Aspergillus amstelodami (Mangin) #om & Church - #e As- pergilli p. 113, 1926. Pathogenicity Aspergillus vitis Novobranova - Nov. Sist. Niszh. Rast. 9: 175, 1975. RG-1, BSL-1. #e species has been isolated from a wide Aspergillus hollandicus Samson & W. Gams, in Samson - Adv. Pen. Asp. range of human mycoses: otitis (Wadhwani & Srivastava, Syst. p. 33, 1985. 1984), mycetoma (Fonseca, 1930; Lacaz & Netto, 1954),
Aspergillus montevidensis, CBS 518.65. a. Ascomata; b. asci; c. ascospores; d. conidiophores; e. conidia.
20 ATLAS of CLINICAL FUNGI Asco !lamentous
Aspergillus brasiliensis Varga et al.
Colony characteristics Molecular diagnostics Colony diameters in 7 days: CYA and CYAS: 71-76 mm, #e species can be distinguished from other members of MEA 52-70 mm, YES: 75-80 mm, OA: 32-36 mm, CREA: Aspergillus section Nigri using mtDNA and rDNA RFLP 32-44 mm, poor growth, strong acid production. Colonies data (Varga et al., 1994), and sequence analysis of ITS, !rst white, then dark brown to black. Exudates absent; B-tubulin or calmodulin genes (Varga et al., 2007c; Sam- reverse cream coloured to light brown. son et al., 2007b).
Microscopy Pathogenicity Conidial heads spherical at !rst, later radiate, occasion- RG-1, BSL-1. Human keratitis (Kredics et al., 2008). ally developing into several conidial columns; stipes 700- 1700 x 8-13 µm, pale brown, thick- and smooth-walled. References Vesicles 30-45 µm wide, nearly spherical, biseriate; met- Varga et al. (2007c), Kredics et al. (2008). ulae covering virtually the entire surface of the vesicle, measuring 22-30 × 3-6 µm. Phialides "ask-shaped, 7–9 × Nomenclature 3-4 µm. Conidia subspherical, 3.5-4.8 µm diam, echinu- Aspergillus brasiliensis Varga, Frisvad & Samson – Int. J. Syst.. late. No sclerotia observed in the culture ex type. Evol. Microbiol. 57: 1929, 2007. Asco
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.
21 ATLAS of CLINICAL FUNGI !e ultimate benchtool for diagnostics
Aspergillus tubingensis Mosseray
Colony characteristics then pinkish bu$ and sometimes darkening to almost Colonies on CZA at 25°C attaining diameters of 4-5 cm in black in age, commonly 500-800 µm in diam. 10 days, velvety, somewhat zonate, consisting of a fairly compact white basal mycelium. Conidial heads in slightly Molecular diagnostics greyish black-brown shades, borne on long conidiophores; Aspergillus tubingensis can be distinguished from other reverse white; exudate and odor lacking. Colonies on MEA related members of Aspergillus section Nigri using mtD- at 25°C growing rapidly, reaching 6 cm in diam in 10 days, NA and rDNA RFLP data (Varga et al., 1993, 1994), and thin, plane, velvety, indistinctly zonate, heavily sporulat- by sequence analysis of beta-tubulin or calmodulin genes ing in very dark brown shades; reverse uncoloured. (Samson et al., 2007b).
Microscopy Pathogenicity Conidial heads spherical to radiate, mostly 200-300 µm. RG-1, BSL-1. Agent of invasive aspergillosis (Kano et al., Conidiophores smooth, long and coarse, commonly 15-20 2008a; Howard et al., 2008), of osteomyelitis (Bathoon µm diam, usually lightly coloured in brown shades, thin- et al., 2013) and of keratitis (Kredics et al., 2009). A cu- walled; vesicles spherical, rather variable in size, most taneous infection nwas reported by Frias-De-Leon et al. commonly 40-60 µm diam, fertile over their entire surface. (2018). #e species appears to be relatively commonly in- Conidia spherical with hyaline echinulations when !rst volved in pulmonary disorders (Gautier et al., 2016). formed, becoming progressively darker and rougher and !nally appearing longitudinally striate from conspicuous References bars of colouring material, mature conidia somewhat Raper & Fennell (1965), Horn et al. (2013). horizontally "attened, 3.0-3.5 µm in diam. Sclerotia produced in some strains, occasionally dominating the Nomenclature colony appearance, (sub)spherical, cream coloured at !rst Aspergillus tubingensis Mosseray - La Cellule 43: 245-247, 1934.
Antifungal susceptibility
Antifungal MICs range GM MIC50 MIC90 Strains Reference AMB 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 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)
22 ATLAS of CLINICAL FUNGI Asco !lamentous Asco
Aspergillus de"ectus, 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.
23 ATLAS of CLINICAL FUNGI