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Eukaryotic Microbio > Mycology > Flashcards

Mycology Flashcards

1
Q

What are fungi?

A

They are eukaryotic organisms

They arose around 1 billion years ago

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2
Q

What are the attributes that make a fungus a fungus?

A
  1. Main feeding body either comprised of microscopic filamentous tubes (hyphae) or individual yeast cells
  2. Do not move due to rigid cell walls
  3. Obtain energy from digestion of organic matter (heterotrophs)
    - Saprophytes – dead remains
    - Parasites – living organisms, harming them
    - Mutualists (symbionts) mutualistically beneficial
  4. Produce a huge range of spores
    - Sexual or asexual reproduction
    - Dispersal
    - Survival
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3
Q

How many species of fungi are there?

A

1.5 to 3 million species

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4
Q

How many copies of tandem repeats do fungi contain?

A

Fungal genomes can contain more than 200 copies in repeating sequences called tandem repeats

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5
Q

What are individual copies separated by?

A

By a sequence called the intergenic spacer region (IGS)

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6
Q

Name three useful genes that encode proteins?

A
  • Translation factor 1a
  • B-tubulin, actin
  • RNA pol II (RPB1 and RPB2)
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7
Q

Which subunit is used to study distantly related organisms?

A

18S subunit (small subunit)

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8
Q

Which subunit is used to study yeast ID?

A

28S subunit (large subunit)

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9
Q

What is used as a DNA barcode for fungal identification?

A

ITS1 and ITS2

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10
Q

What is found in all major lineages in the fungi tree of life?

A

Fungi that infect vertabrates

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11
Q

What are the sexual and asexual forms of fungi called?

A

Sexual = telomorph

Asexual = anamorph

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12
Q

What is the 2011 ‘Amsterdam Declaration’?

A

From 2013 onwards, fungi must retain a single name

  • Pre-existing convention teleomorph name should take precedence
  • Confusion in medical mycology – anamorph state isolated in lab
  • New instruction ‘follow the principle of priority of publication when selecting the generic name to adopt’
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13
Q

What are the characteristics of Phylum Basidiomycota?

A
  • 30,000 described species
  • Includes mushroom forming fungi, jelly fungi, yeasts, rusts, and smuts
  • Sexual spores = basidospores
  • Formation of basidospores on surface of haploid yeast cells following mitosis
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14
Q

What is the lifecycle of a Coprinus comatus?

A
  • Fruit body
  • Young basidia
  • Mature basidum
  • Basdiospores
  • Homokaryotic hyphae
  • Heterokaryotic hyphae
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15
Q

What is the lifecycle of a typical Basidiomycota?

A
  • Single basidiospore germinates → branching filamentous hyphae
  • Mycelium by mitosis = homokaryon
    • all nuclei are genetically identical clones
  • Homokaryotic mycelia expand through soil, wood etc.
  • Some produce fruit bodies without mating
  • Most - pair of sexually compatible homokaryons merge → heterokaryotic mycelia
  • Formation of fruit bodies (mature reproductive organ)
  • Basidia = heterokaryotic (nuclei from parent homokaryotic colonies)
  • Fuse then undergo meiosis → four basidiospores (usually, number can vary)
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16
Q

What is phylum ascomycota?

A

Largest phylum with more than 33,000 named species

Includes - yeasts, and filamentous fungi

Many species only asexual (anamorph) form known

Anamorph produces asexual spores on stalks called conidiophores

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17
Q

Where are sexual forms on phylum ascomycota found?

A

They are identified in most ascomycetes

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18
Q

What do the sexual organs contain?

A

Asci

These are characteristic spore producing cells

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19
Q

What is the lifecycle of a typical Ascomycota?

A
  • Used genetic research
    – Entire genome (7 chromosomes) sequenced
  • Perithecial (flask-shaped)
  • Ascospores = haploid
  • Heterothallic species with two mating types (MAT A and MAT a)
  • Airborne microconidia (a.k.a. spermatia) fuse with hyphae called trichogynes of opposite mating type → ascogenous hyphae
  • Ascogenous hyphae form hook-shaped tips – croziers
    Pair of nuclei – mitosis → four nuclei. Two (one each type) isolated in crook → ascus
  • Fuse – meiosis → four haploid nuclei
  • Each divide (mitosis) → Eight nuclei in separate ascospores
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20
Q

What is dikaryon?

A

A feature where compatible cell types can fuse cytoplasms. This can be maintained for all cells of the hyphae by synchronously dividing so that pairs are passed to newer cells

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21
Q

What contains 1% of described species?

A

Zygomyectes

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22
Q

What is the lifecycle of a zygomycete?

A
  1. Zygophores of compatible hyphae meet → gametangia
  2. Gametangia – plasmogamy
    (cytoplasm fusion without nuclei fusion)
  3. Zygote formed (heterokaryotic)
  4. Zygote → zygospore
    (thick walled – survive harsh environments)
  5. Karyogamy (nuclei fuse)
  6. Favourable conditions → meiosis → sporangiophore bearing sporangium
  7. Spores released
  8. Germinate → mating type + and mating type – mycelium
  9. Asexual reproduction – sporangiophores with sporangia formed directly from mycelium – all spores = genetically identical
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23
Q

What is a dimorphic fungi?

A

They have both yeast and filamentous forms

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24
Q

What is thermal dimorphism?

A

Temperature dependent phenotypic duality of forms of a fungus

Dimorphism – temperature regulated
– Ambient - filamentous moulds
– Infectious propagule – spore produced by filamentous form
37°C - yeast

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25
Q

Do saccharomyces cerevisae exist as haploid or diploid?

A

Both

They are capable of asexual reproduction by budding

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26
Q

What do haploid cells do?

A

Bud next to scar from preceding daughter cell

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27
Q

What do diploid cells do?

A

Buds form at opposite poles, alternating from one end to the other from division to division

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28
Q

What method of reproduction is rarer than budding?

A

Fission

Fission relies of a model organism with 3 chromosomes

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29
Q

Which fungal pathogens reproduce via budding?

A
  • Candida
  • Cryptococcus
  • Histoplasma
  • Blastomyces
  • Paracoccidioides
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30
Q

What fungal pathogen reproduce via fission?

A
  • Talaromyces marneffei
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31
Q

What is a microconidia?

A

Simple single celled

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32
Q

What is a macroconidia?

A

Larger and multi-celled

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33
Q

Which fungi produce both microconidia and macroconidia?

A

Fusarium

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34
Q

What are the characteristics of eukaryotic organisms?

A
  • DNA organised into chromosomes within nucleus
  • Distinct cytoplasmic organelles
    • endoplasmic reticulum
    • Golgi apparatus
    • mitochondria
    • storage vacuoles
  • Similar biosynthetic pathways to mammalian cells
    • DNA replication
    • Protein synthesis
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35
Q

What does the fungal cell structure contain?

A
  • Cell membrane
  • Cell wall
    • Rigid layer of chitin, layers of polypeptides with complex polysaccharides

– Variations in cell wall aid in hiding from the immune system

  • DNA and protein sythesis
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36
Q

What temperature do fungi grow at?

A
  • Body temperature (37.5C)
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37
Q

What are the factors of fungi metabolism?

A
  • grow at body temperature
  • often at rather low oxygen tensions
  • must obtain nutrients from human host
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38
Q

What is the most preferred carbon source for most fungi?

A

Glucose

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39
Q

What are some non-glucose based carbon sources?

A
  • Gained by active hydrolysis of host proteins or phospholipids
  • Many pathogens produce proteases, lipases and phospholipases
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40
Q

What is present at very low concentrations in fungi?

A
  • Micronutrients

Pathogenic fungi have evolved efficient micronutrient scavenging systems

  • Iron and Zinc

These are essential for the growth and survival of fungi

These two limit rate of growth in vivo

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41
Q

How does metabolism affect pathogenicity?

A

It influences pathogenicity at multiple levels

Contributes directly by supporting fungal growth

Affects antifungal drug susceptibility

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42
Q

How does metabolism contribute indirectly to pathogenicity?

A
  • cell wall remodelling
  • enhancing stress resistance
  • modulating expression of key virulence factors
  • affecting efficacy of immune surveillance by innate immune cells
43
Q

What is pathogenesis?

A

The ability of an organism to cause diseases

44
Q

What is virulence?

A

The relative ability of an organism to cause disease

45
Q

What is virulence factors?

A

Components that permit it to cause disease

46
Q

What is virulence attributes?

A

Components that have arisen through evolution in natural environment

47
Q

What are the 6 mechanisms of tissue damage in fungal infection?

A
  1. Direct invasion – leads to distortion and tissue destruction
  2. Obstruction – leads to 2° bacterial infection
  3. Blood vessel wall invasion – leads to thrombosis
  4. Embolism to distal vessels
  5. Intracellular persistence & even multiplication in macrophages & neutrophils
  6. Capsule formation – protects fungus and may damage tissue
48
Q

What are the 4 types of human fungal infection?

A
  1. Superficial - limited to outermost layers of skin and hair
  2. Cutaneous - extend deeper into epidermis, and include invasive hair and nail diseases
  3. Subcutaneous - involve dermis, subcutaneous tissues, muscle, and fascia
  4. Systemic - originate primarily in lungs and may spread to many organ systems
49
Q

What is the emerging importance of fungal diseases?

A

~ 3 million people acquire a life-threatening invasive fungal infection each year, and almost half will die
– more than tuberculosis or malaria

Biggest change – emergence of opportunistic mycoses as major causes of life-threatening infection in immunocompromised individuals

50
Q

What are the contributing factors to this?

A
  • Medical progress and changes in healthcare practices

Led to an expanding population of susceptible hosts

  • Changes in the environment

Climate change and extreme weather events

  • Increased international travel and commerce

Histoplasmosis and coccidioidomycosis increased in indiviuals who reside distant from endemic regions

  • Development of antifungal resistance

In general, less common than antibacterial resistance, but incidences rising

51
Q

What are the burdens of fungal diseases?

A
  • Our understanding of magnitude of burden and their socioeconomic impact largely incomplete
  • Developing burden estimates requires epidemiological surveillance data
  • Most public health agencies do not conduct surveillance for fungal diseases
52
Q

How many people die every hour from fungal infection according to GAFFI?

A

150 people

53
Q

What is the molecular epidemiology for fungi?

A
  • DNA fingerprinting

Random amplified polymorphic DNA and amplified fragment length polymorphism

Multi-locus sequence typing (MLST) and microsatellite typing (VNTR)

Whole genome sequencing (WGS)

54
Q

What are the characteristics of Candida?

A
  • Most well known fungal pathogen

- More than 150 disparately related species

55
Q

What are some candida species commonly implicated in human infections?

A
  • C. albincans
  • C. alabrata
  • C. parapsilosis
  • C. tropicalis
56
Q

Where do candida organisms primarily reside?

A
  • in gastrointestinal tract
  • vagina
  • urethra
  • on skin and under fingernails
57
Q

What is Candida auris?

A

First report of it appeared in 2009 (isolated from ear canal)

It its a deadly multi drug-resistant Candida yeast infection that spread in the US

No hyphal or pseudophyhal forms were noted

Single cases of detection - 9 countries

Multiple cases - 14 countries

58
Q

What is the most similar species to candida auris?

A

Candida lustaniae @ 82%

59
Q

What adaptations do candida make to human microflora?

A
  • Adhere to mucosal surfaces
  • Ability to withstand normal and fever-induced body temperature (37-39C)
  • Innate ability to rapidly adapt to changing microenviroments
  • Biofilm formation
60
Q

What is the morbidity and mortality rate for candidosis and what is the source of infection?

A

30 to 60%

The source of infection is often the patient

61
Q

What are the risk factors of Haematogenous candidosis?

A
  1. Increased colonisation
    - Endogenous: prolonged antibiotic therapies suppress endogenous microflora and enhance growth of endogenous Candida spp.
    - Exogenous: prolonged hospital stay increases risk of strains from healthcare workers
  2. Damage to integrity of gut mucosa
  3. Immunosuppression
62
Q

How are candida infections diagnosed?

A

Through a combination of clinical and laboratory

Lab

  1. Microbiology
  2. Histopathology
  3. Immunology

Direct microscopy

  • Wet mounts
  • Budding yeast cells and hyphae
  • Cytologic, histologic and Candida-specific immunofluorescent stains
63
Q

What biochemical tests are done to determine culture of candida?

A
  • API-20C strip
  • ID 32C, API Candida kit
  • AuxaColor 2
64
Q

What is the germ tube test?

A

The formation of unconstricted filaments in response to serum

65
Q

What is cryptococcus?

A

More than 70 species

Round or oval yeast like cells, cultures generally mucoid on solid media

66
Q

How do cryptococcus reproduce?

A

By multilateral budding

67
Q

What is the pathogenesis and epidemiology of Cryptococcus?

A
  • Infection acquired following inhalation of infectious propagule from environment
  • Most cases – no symptoms
  • Infections – localised or disseminate
  • Disease severity
    • fungal virulence factors
    • host’s immune response
  • Immunosupressed - systemic and life-threatening infection
    • Important cause of disease in HIV-infected individuals
  • Cryptococcosis – humans and animals
    • Animal-to-human and human-to-human rarely documented
  • Cryptococcus neoformans – two varieties var. grubii and var. neoformans
    • Species complex
    • Some consider them to be two species
68
Q

What is cryptococcus neoformans virulence factor?

A
  • High temperature (37-39C)
  • Extracellular polysaccharide capsule
  • Melanin
69
Q

What are the 6 steps of infections inside macrophages?

A
  1. phagocytic uptake
  2. phagolysosomal fusion
  3. dissolve the phagosomal compartment
  4. intracellular replication ensues
  5. Cn-derived polysaccharide builds up
  6. Ultimately, the host cell ruptures
70
Q

Where does primary cryptococcal disease primarily occur?

A

In the lungs

71
Q

Where is the foci (central site) of infection in cryptococcus?

A
  • CNS
  • Eyes
  • Lymph nodes
  • Skin
72
Q

What is cryptococcus morphology?

A
  • Anamorphic form (asexual)

- Grow in 48-72 hours on routine fungal culture media

73
Q

How are cryptococcus characterised?

A
  • From biochemical traits
    • Ability to assimilate inositol as sole carbon source
    • Produce urease
    • React with diazonium blue B (yellow Asco, red Basidio)
74
Q

How do we distinguish C. gattii and C. neoformans?

A

By using CGB media

C. gattii turns into a deep blue colour

75
Q

What is aspergillus?

A
  • Diverse genus
  • Spoil food
  • Mycotoxin producers
  • Commercially important (citric acid, soy sauce, sake, miso, lovastatin)
76
Q

What is the ecology of aspergillus?

A
  • Majority are saprophytic (commonly isolated from soil and plant litter decomposition process of Aspergillus spp. helps drive carbon cycle)
  • Commonly found indoors
  • Associated with outbreaks in hospitals
77
Q

What did the international commission of Penicillium and Aspergillus decide to do in 2012?

A

Option 3. keep the name Aspergillus and treat other (teleomorph) names to indicate structures with biological significance. Move species to Aspergillus based on DNA

e. g. Aspergillus glaucus with eurotium-type ascomata
e. g. Aspergillus fischeri with neosartorya-type fruiting bodies

Aspergillus now contains more than 339

78
Q

What are cryptic species?

A
  • Morphologically similar but genetically distinct

- Some of these cryptic species are more resistant to antifungal drugs than corresponding type species

79
Q

What is complex?

A

Cultured and no molecular identification

80
Q

What is section?

A

Taxonomically correct terminology if molecular identification has occurred

81
Q

What are some adaptations that facilitate becoming opportunistic pathogens?

A
  • Thermotolerant growth (37C)
  • Siderophores to chelate iron to maintain iron homeostatis
  • Small spores size to evade mucociliary clearence
  • Production of proteolytic enzymes
  • Giliotoxin as it blocks phagocytosis through immunosuppressive properties
  • Biofilm production
82
Q

What are the 3 consequences of exposure to airborne Aspergillus to the nasal cavity?

A
  1. Allergies
  2. Chronic aspergillosis (More than 3 months)
  3. Invasive aspergillosis
83
Q

What is allergic bronchopulmonary aspergillosis (ABPA)?

A
  • An allergic reaction to colonising Aspergillus
  • A. fumigatus colonises the sputum plugs in the bronchi of patients with asthma (and cystic fibrosis), with little or no tissue invasion by the organism
  • Burden of the disease
    • Asthma 1-5%
    • cystic fibrosis 2-15%
84
Q

What is invasive aspergillosis (IA)?

A
  • Portals of entry for Aspergillus include respiratory tract, damaged skin or other operative wounds, the cornea, and ear
  • The majority of patients (80% – 90%) pulmonary disease (IPA)
    other manifestations, including Aspergillus rhino-sinusitis
  • Mortality rate nearly 100% if not treated
85
Q

What is invasive pulmonary aspergillosis (IPA)?

A

Acute IPA

  • 25%–33% of patients initially have no symptoms
  • As disease progresses, symptoms appear
    cough (usually dry) and fever
  • Appearances of IPA on chest radiographs are extremely variable

Chronic IPA

  • Less common than acute disease
  • Chronic, productive cough is usual, often with mild or moderate haemoptysis (coughing of blood)
  • Fever is occasionally present but usually low grade
    Malaise and weight loss are usual
86
Q

How does invasive aspergillosis progress into the body?

A
  1. Airborne conidia
  2. adhere to pulmonary epithelial cells
  3. readily phagocytosed
  4. within epithelial cells conidia germinate → hyphae
  5. apical extension of hyphae, escape epithelial cells
  6. emergent hyphae penetrate abluminal surface of endothelial cells
  7. Induce endothelial damage
  8. Hyphal fragments disseminate haematogenously
  9. adhere to the luminal endothelial cell surface
  10. invade these cells
  11. luminal invasion → endothelial cell damage
  12. extracellular invasion of deep organs
87
Q

What are some non-culture based diagnosis?

A
  • Biomarkers and molecular techniques (cut time to diagnose)
  • Galactmannan antigen (component of cell wall)
  • PCR
88
Q

What is Zygomycosis?

A
  • Reproduce sexually by fusion of gametangia to form zygospores
    asexually by sporangiospores
  • Zygomycosis infections by members of Mucorales and Entomophthorales
89
Q

What are the differences between Mucorales and Entomiphthorales?

A
  • Mucorales

– Worldwide

– Asexual reproduction: Numerous asexual spores within sporangium

– Sexual reproduction: zygospores between suspensors from hyphae of 2 sexually compatible strains

– Thermotolerant (37C)

  • Entomophthorales

– Tropical and subtropical

– Asexual reproduction: single conidium (no sporangium) on each conidiophore
forcibly ejected upon maturation

– Sexual reproduction: zygospores produced by fusion of 2 adjacent hyphal cells

90
Q

How are mucoraceous mould infections diagnosed?

A
  • Direct microscopy / tissue stained with Calcofluor
  • Histology
  • Diagnostic PCR assays
  • Isolation and subsequent identification of pathogen for full diagnosis
91
Q

What are the 6 endemic regions where Ascomycota arises the most?

A
  1. Southwestern US (Coccidiomycosis)
  2. Eastern US (mostly contained histoplasmosis)
  3. South America
  4. Latin America (Coccidiomycosis)
  5. Tropical Africa
  6. Southeast Asia (Talaromycosis)
92
Q

How is histoplasmosis diagnosed?

A
  • Through growth of fungus from body fluids or tissues
  • Immunodiagnosis
    • Immunodiffusion
    • Complement fixation
    • Antigen tests - including EIA
93
Q

How does Coccidiodomycosis affect the body?

A

Endospores transported to the bloodstream to other areas particularly the brain and CNS, this can lead to a more severe disease

Flu like illness

94
Q

How is Coccidiodomycosis diagnosed?

A

Through Serology

  • Enzyme Immunoassay
  • Immunodiffusion
  • Complement fixation
95
Q

How is talaromycosis diagnosed?

A
  • Antigen detection assays

- PCR based assays

96
Q

What are the 7 limitations of current antifungal agents?

A
  1. Spectrum of activity
  2. Pharmacokinetic (PK - time course of drug in body) properties
  3. Pharmacodynamic (PD - rate and extent of pathogen killing) properties
  4. Dosing
  5. Toxicity
  6. Interactions with other drugs
  7. Cost
97
Q

What are the 5 sites of action of antifungal drugs?

A
  1. Nuclear division
  2. DNA synthesis
  3. Protein synthesis
  4. Cell Wall
  5. Cell Membrane
98
Q

What type of drug inhibits cell walls?

A

Echinocandins

Considered relatively safe and has few side effects (headaches, fever, hypertoxicity)

Examples:
Caspofungin, Micafungin, Anidulafungin

99
Q

What type of drugs inhibits cell membrane?

A

Azoles and Polyenes

Examples:
Fluconazole, Itraconazole, Voriconazole, Posaconazole, Isavuconazole

These all target the fungal cytochrome P450 enzyme

All considered to the fungistatic (inhibit the growth of fungi)

Examples of polyenes:
Amphotericin B

This drug can damage the cells by increasing cell permeability

100
Q

What type of drug inhibits DNA and protein synthesis?

A

Flucytosine

101
Q

What are the 5 working steps of flucytosine?

A
  1. Enters fungal cell via Cytosine permase
  2. Cytosine deaminase, 5FC to 5-fluorouracil
  3. Incorporation into RNA - inhibits protein synthesis
  4. Conversion to fluorodeoxyuridine monophosphate inhibits DNA synthesis
  5. Resistance occurs via mutations in enzymes involved in uptake or conversion
102
Q

What are the 5 factors that affect antifungal susceptibility testing?

A
  1. Inoculum – more fungus, usually higher MIC
  2. pH – lower pH, usually higher MIC
  3. Medium
  4. Incubation temperature
  5. Incubation duration – longer incubations, usually higher MIC
103
Q

What are the 3 methods available for clinical resistance?

A
  • E tests
    • Consist of simple plate method and incubation of 24-72 hours
  • Yeast One Sensititre
    • Microtitre plate assay
    • The colour change indicates growth after 24 hour incubation
  • Standard methodology (broth microdilution)
    • Light suspension of yeast/mould
    • Microtitre plate read visually
104
Q

What are the mechanisms of resistance to antifungal drugs?

A
  1. Decreased effective drug concentrations

a) Active efflux
e.g. ATP-binding cassette (ABC) transporters
↑ efflux reduces drug accumulation in cells
b) Drug target overexpressed
effective drug concentration needs to be increased to saturate target molecules
c) Drug sequestration
Biofilms associated with resistance. Biofilm matrix has capacity to sequester drugs - extracellular
Sequestering in vacuoles - intracellular
d) Poor drug metabolization
Mutation in enzyme in metabolic pathway

  1. Drug target alterations
    - Azoles and Echinocandins
  2. Metabolic bypass mechanisms
    - Loss or strong decrease of specific function
    - Azoles and Amphotercicin B

Eukaryotic Microbio (4 decks)

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