Mycology Flashcards
(104 cards)
1
Q
What are fungi?
A
They are eukaryotic organisms
They arose around 1 billion years ago
2
Q
What are the attributes that make a fungus a fungus?
A
- Main feeding body either comprised of microscopic filamentous tubes (hyphae) or individual yeast cells
- Do not move due to rigid cell walls
- Obtain energy from digestion of organic matter (heterotrophs)
- Saprophytes – dead remains
- Parasites – living organisms, harming them
- Mutualists (symbionts) mutualistically beneficial - Produce a huge range of spores
- Sexual or asexual reproduction
- Dispersal
- Survival
3
Q
How many species of fungi are there?
A
1.5 to 3 million species
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
5
Q
What are individual copies separated by?
A
By a sequence called the intergenic spacer region (IGS)
6
Q
Name three useful genes that encode proteins?
A
- Translation factor 1a
- B-tubulin, actin
- RNA pol II (RPB1 and RPB2)
7
Q
Which subunit is used to study distantly related organisms?
A
18S subunit (small subunit)
8
Q
Which subunit is used to study yeast ID?
A
28S subunit (large subunit)
9
Q
What is used as a DNA barcode for fungal identification?
A
ITS1 and ITS2
10
Q
What is found in all major lineages in the fungi tree of life?
A
Fungi that infect vertabrates
11
Q
What are the sexual and asexual forms of fungi called?
A
Sexual = telomorph
Asexual = anamorph
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’
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
14
Q
What is the lifecycle of a Coprinus comatus?
A
- Fruit body
- Young basidia
- Mature basidum
- Basdiospores
- Homokaryotic hyphae
- Heterokaryotic hyphae
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)
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
17
Q
Where are sexual forms on phylum ascomycota found?
A
They are identified in most ascomycetes
18
Q
What do the sexual organs contain?
A
Asci
These are characteristic spore producing cells
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
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
21
Q
What contains 1% of described species?
A
Zygomyectes
22
Q
What is the lifecycle of a zygomycete?
A
- Zygophores of compatible hyphae meet → gametangia
- Gametangia – plasmogamy
(cytoplasm fusion without nuclei fusion) - Zygote formed (heterokaryotic)
- Zygote → zygospore
(thick walled – survive harsh environments) - Karyogamy (nuclei fuse)
- Favourable conditions → meiosis → sporangiophore bearing sporangium
- Spores released
- Germinate → mating type + and mating type – mycelium
- Asexual reproduction – sporangiophores with sporangia formed directly from mycelium – all spores = genetically identical
23
Q
What is a dimorphic fungi?
A
They have both yeast and filamentous forms
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
25
Do saccharomyces cerevisae exist as haploid or diploid?
Both
They are capable of asexual reproduction by budding
26
What do haploid cells do?
Bud next to scar from preceding daughter cell
27
What do diploid cells do?
Buds form at opposite poles, alternating from one end to the other from division to division
28
What method of reproduction is rarer than budding?
Fission
Fission relies of a model organism with 3 chromosomes
29
Which fungal pathogens reproduce via budding?
- Candida
- Cryptococcus
- Histoplasma
- Blastomyces
- Paracoccidioides
30
What fungal pathogen reproduce via fission?
- Talaromyces marneffei
31
What is a microconidia?
Simple single celled
32
What is a macroconidia?
Larger and multi-celled
33
Which fungi produce both microconidia and macroconidia?
Fusarium
34
What are the characteristics of eukaryotic organisms?
- 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
35
What does the fungal cell structure contain?
- 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
36
What temperature do fungi grow at?
- Body temperature (37.5C)
37
What are the factors of fungi metabolism?
- grow at body temperature
- often at rather low oxygen tensions
- must obtain nutrients from human host
38
What is the most preferred carbon source for most fungi?
Glucose
39
What are some non-glucose based carbon sources?
- Gained by active hydrolysis of host proteins or phospholipids
- Many pathogens produce proteases, lipases and phospholipases
40
What is present at very low concentrations in fungi?
- 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
41
How does metabolism affect pathogenicity?
It influences pathogenicity at multiple levels
Contributes directly by supporting fungal growth
Affects antifungal drug susceptibility
42
How does metabolism contribute indirectly to pathogenicity?
- cell wall remodelling
- enhancing stress resistance
- modulating expression of key virulence factors
- affecting efficacy of immune surveillance by innate immune cells
43
What is pathogenesis?
The ability of an organism to cause diseases
44
What is virulence?
The relative ability of an organism to cause disease
45
What is virulence factors?
Components that permit it to cause disease
46
What is virulence attributes?
Components that have arisen through evolution in natural environment
47
What are the 6 mechanisms of tissue damage in fungal infection?
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
What are the 4 types of human fungal infection?
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
What is the emerging importance of fungal diseases?
~ 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
What are the contributing factors to this?
- 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
What are the burdens of fungal diseases?
- 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
How many people die every hour from fungal infection according to GAFFI?
150 people
53
What is the molecular epidemiology for fungi?
- 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
What are the characteristics of Candida?
- Most well known fungal pathogen
| - More than 150 disparately related species
55
What are some candida species commonly implicated in human infections?
- C. albincans
- C. alabrata
- C. parapsilosis
- C. tropicalis
56
Where do candida organisms primarily reside?
- in gastrointestinal tract
- vagina
- urethra
- on skin and under fingernails
57
What is Candida auris?
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
What is the most similar species to candida auris?
Candida lustaniae @ 82%
59
What adaptations do candida make to human microflora?
- 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
What is the morbidity and mortality rate for candidosis and what is the source of infection?
30 to 60%
The source of infection is often the patient
61
What are the risk factors of Haematogenous candidosis?
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
How are candida infections diagnosed?
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
What biochemical tests are done to determine culture of candida?
- API-20C strip
- ID 32C, API Candida kit
- AuxaColor 2
64
What is the germ tube test?
The formation of unconstricted filaments in response to serum
65
What is cryptococcus?
More than 70 species
Round or oval yeast like cells, cultures generally mucoid on solid media
66
How do cryptococcus reproduce?
By multilateral budding
67
What is the pathogenesis and epidemiology of Cryptococcus?
- 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
What is cryptococcus neoformans virulence factor?
- High temperature (37-39C)
- Extracellular polysaccharide capsule
- Melanin
69
What are the 6 steps of infections inside macrophages?
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
Where does primary cryptococcal disease primarily occur?
In the lungs
71
Where is the foci (central site) of infection in cryptococcus?
- CNS
- Eyes
- Lymph nodes
- Skin
72
What is cryptococcus morphology?
- Anamorphic form (asexual)
| - Grow in 48-72 hours on routine fungal culture media
73
How are cryptococcus characterised?
- From biochemical traits
- - Ability to assimilate inositol as sole carbon source
- - Produce urease
- - React with diazonium blue B (yellow Asco, red Basidio)
74
How do we distinguish C. gattii and C. neoformans?
By using CGB media
C. gattii turns into a deep blue colour
75
What is aspergillus?
- Diverse genus
- Spoil food
- Mycotoxin producers
- Commercially important (citric acid, soy sauce, sake, miso, lovastatin)
76
What is the ecology of aspergillus?
- 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
What did the international commission of Penicillium and Aspergillus decide to do in 2012?
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
What are cryptic species?
- Morphologically similar but genetically distinct
| - Some of these cryptic species are more resistant to antifungal drugs than corresponding type species
79
What is complex?
Cultured and no molecular identification
80
What is section?
Taxonomically correct terminology if molecular identification has occurred
81
What are some adaptations that facilitate becoming opportunistic pathogens?
- 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
What are the 3 consequences of exposure to airborne Aspergillus to the nasal cavity?
1. Allergies
2. Chronic aspergillosis (More than 3 months)
3. Invasive aspergillosis
83
What is allergic bronchopulmonary aspergillosis (ABPA)?
- 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
What is invasive aspergillosis (IA)?
- 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
What is invasive pulmonary aspergillosis (IPA)?
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
How does invasive aspergillosis progress into the body?
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
What are some non-culture based diagnosis?
- Biomarkers and molecular techniques (cut time to diagnose)
- Galactmannan antigen (component of cell wall)
- PCR
88
What is Zygomycosis?
- Reproduce sexually by fusion of gametangia to form zygospores
asexually by sporangiospores
- Zygomycosis infections by members of Mucorales and Entomophthorales
89
What are the differences between Mucorales and Entomiphthorales?
- 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
How are mucoraceous mould infections diagnosed?
- Direct microscopy / tissue stained with Calcofluor
- Histology
- Diagnostic PCR assays
- Isolation and subsequent identification of pathogen for full diagnosis
91
What are the 6 endemic regions where Ascomycota arises the most?
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
How is histoplasmosis diagnosed?
- Through growth of fungus from body fluids or tissues
- Immunodiagnosis
- - Immunodiffusion
- - Complement fixation
- - Antigen tests - including EIA
93
How does Coccidiodomycosis affect the body?
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
How is Coccidiodomycosis diagnosed?
Through Serology
- Enzyme Immunoassay
- Immunodiffusion
- Complement fixation
95
How is talaromycosis diagnosed?
- Antigen detection assays
| - PCR based assays
96
What are the 7 limitations of current antifungal agents?
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
What are the 5 sites of action of antifungal drugs?
1. Nuclear division
2. DNA synthesis
3. Protein synthesis
4. Cell Wall
5. Cell Membrane
98
What type of drug inhibits cell walls?
Echinocandins
Considered relatively safe and has few side effects (headaches, fever, hypertoxicity)
Examples:
Caspofungin, Micafungin, Anidulafungin
99
What type of drugs inhibits cell membrane?
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
What type of drug inhibits DNA and protein synthesis?
Flucytosine
101
What are the 5 working steps of flucytosine?
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
What are the 5 factors that affect antifungal susceptibility testing?
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
What are the 3 methods available for clinical resistance?
- 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
What are the mechanisms of resistance to antifungal drugs?
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
2. Drug target alterations
- Azoles and Echinocandins
3. Metabolic bypass mechanisms
- Loss or strong decrease of specific function
- Azoles and Amphotercicin B
