MYCOLOGY
degrade organic substrates into soluble
 Mykos (mushroom)
 Study of fungi which include molds and
yeasts
General Characteristics
 >200,000 valid species of fungi exist
 Only 100 – 150 species are generally
recognized
 Approximately 25 spcs cause human
disease
 General habitat are water soil and
decaying organic matter
 Variable size and shape
 Single-celled or multi-celled.
 Eukaryotic organisms, each fungal cell
has at least a membrane bound nucleus
and organelles.
 Exist as Parasites or saprophytes
REPRODUCTION:
 Asexual – offspring arise from a single
organism, and inherit the genes of that
parent only.
- it does not involve fusion of
gametes and almost never changes the
number of chromosomes.
 Sexual – two morphologically distinct
types of specialize reproductive cells
called gametes fuse together.
 Parasexual – peculiar to fungi and
single-celled organisms.
- nonsexual mechanism of
parasexuality for transferring genetic
material without meiosis or the
development of sexual structures
Nutritional requirements:
 Chemoheterotrophs – obtain their
nutrients by absorbing chemicals found
in the environment.
 Fungi survive by secreting enzymes that
nutrients
Fungi differ from bacteria:
 Fungi grow best with a pH of 5
 Almost all molds are aerobic; most
yeasts are facultative anaerobes
 Most fungi are resistant to osmotic
pressure than bacteria
 Fungi can grow on substances with a
very low moisture content
 Fungi requires less nitrogen than
bacteria for growth
 Fungi are often capable of metabolizing
complex carbohydrates
Lignin (component of wood)
Harmful effects of fungi:
 Contaminants of food and therefore are
important cause of spoilage of food
 Cause human diseases in 3 general
ways:
- Fungus allergy
- Mycotoxicoses: aflatoxic & amatoxin
- Mycoses
Beneficial effects of fungi:
 Yeast (saccharomyces)
 Preparation of vaccines (Hepatitis B
Vaccines)
 Source of drugs (penicillin)
 Higher fungi, mostly Basidiomycetes
may be eaten directly as mushrooms
 Saprophytic fungi in soil produce
degradative enzymes which are
essential for the biologic recycling of
organic matter.
MORPHOLOGY Reproduction:

 Yeasts:  Teleomorphis – the sexual

- unicellular growth of fungi stage of a fungus
- Spherical or ellipsoidal ( 3-  Anamorphis – the asexual
15 micra) stage of a fungus.
- Most reproduce by budding
(blastoconidia), few by Fungi imperfecti:
binary fission.
 fungi that do not exhibit sexual stage
 Pseudohyphae – chain of elongated
 most fungi of medical importance are
yeast cells that resemble hyphae
imperfecti fungi
 Colonies are pasty, opaque, 0.3 – 5mm
in diameter
 Few species produce pigments but
most are cream-colored
 Yeast have similar microscopic and
COLLECTION AND PROCESSING OF
colonial characteristics
CLINICAL SPECIMENS FOR FUNGAL
STUDIES.

 Molds:
- Produce multicellular,
BONE MARROW
filamentous colonies
- Irregular & dry colonies  Absence of normal fungal flora
consisting of branching
 Aspirate o.5mL marrow, then to BHI
cylindrical tubules varying in
broth
diameter from 2 – 10 micra,
called hyphae CEREBROSPINAL FLUID
- Hypha grow to form
filamentous mass of  Absence of normal fungal flora
intertwining strands called a  Collect in sterile tubes by lumbar
mycelium. puncture
 If volume is more than 2mL, centrifuge
Dimorphism – ability of some fungi (pathogenic and use sediments for slides and plating
species) to grow in 2 forms under different
 If less than 2mL, use uncentrifuged
environmental conditions:
specimen
 Grow as:
CUTANEOUS
 Yeast form at 37°C
 Mold form at room temperature  HAIR
o Have contaminants
Dimorphic fungi: o Pluck by roots by sterile
 Sporothrix schenkii forceps; select that fluoresce
or are broken and scaly
 Coccidioides immtis
 NAIL
 Histoplasma capsulatum
o No normal flora
 Blastomyces dermatitidis
o Clean nails with 70% alcohol,
 Parcoccidioides brazeliense
scrape the discolored area,
 discard outer layer collect IDENTIFICATION METHOD:
inner infected nail
o May also collect using sterile  3 Methods
nail clipper 1. Microscopic
o Place nail in a sterile petri 2. Culture
dish, cut into small pieces 3. Serologic test
o Examine microscopically
using KOH
i. Wet Mount

 SKIN a. Saline Mount

o Few Candida and o Quick , simple method
contaminants to observe fungal
o Clean skin with 70% alcohol, elements: budding
scrape outer edge of ring in yeast, hyphae &
case of suspected ringworm, pseudohyphae
or scrape area of active o Spx + 1 drop of sterile
infection saline
o Examine microscopically o Apply coverslip and
using KOH examine under LP & HP
o Major disadvantage:
 MUCOCUTANEOUS lack of contrast
o No normal fungal flora
o Collect by scraping plaque b. KOH Preparation
with sterile tongue depressor o Used to dissolve
especially if Candida is keratin in skin, hair or
suspected nail specimens
o Keratin may obscure
the fungal elements in
 THROAT these specimen
o Few yeast, few contaminants o OH acts as cleaning
o Collect with 2 sterile swabs, agent, it eliminates
debris and makes
scrape off and collect with
fungal elements
sterile tongue depressor if
prominent
Candida is suspected

c. Lactophenol
o Lactic acid - preserve
 URINE the fungal structures
o Avoid 24-hour collection o Phenol - is a killing
o Centrifuge and use sediment agent
for microscopic exam and o Cotton blue – color
plating fungal structures
o Process within 2 hours or
refrigerate to avoid bacterial
overgrowth
o Colony count of .100,000/mL
esp of Candida is significant

d. India Ink Preparation
o Used to identify the
capsule of the yeast
Used to identify the
capsule of the yeast
Cryptococcus
neoformans
o CSF can be directly
examined by adding
one drop of fluid to one
drop India ink
o Exam microscopically
and capsule appear as
clear halos against a
dark background
ii. Fluorescence
a. Calcofluor White Stain
o Calcofluor binds to
chitin in the fungal cell
wall giving a brilliant
fluorescence under the
fluorescent microscope
b. Wood’s Lamp (UV light)
o Infected hair and skin
will fluoresce when
examined in the dark
iii. Staining
a. Gram Stain
o Fungi stain (+) but often
stain poorly
o Useful for Candida
Pityriasis versicolor ( Tinea versicolor)
 A chronic and nonirritating superficial
infection of the stratum corneum
 Cxd by brownish scaly area on light-
skinned and lighter areas on dark-
skinned persons
 Found on the trunk, arms, shoulders,
face and neck
 Etiologic Agent: Malassezia furfur
(Pityrospurum orbiculare)
o ipophilic and grows in areas
where sebum and skin oil
accumulates
o Seen in warmer environments
and is associated with poor
hygiene
Black Piedra
 Hard, brown-black crust on the outside
of the hair shaft
 Primarily involve the scalp hair, rarely
axillary and pubic hair
 Black piedra-black nodule arranged
irregularly on the hair shaft
 Etiologic Agent : Piedraia hortae
White Piedra
 Produces light brown, soft nodules
especially on the beard or moustache
 Etiologic Agent: Trichosporon beigelii
 Microscopic
- Direct wet mount with KOH show hyaline
hyphae and numerous rectangular
arthroconidia, occasional blastoconidia in
chains or clusters
 Culture
- SDA grow as cream-colored, wrinkled
colonies
 o Location of lesions: inerdigital
spaces on feet of persons
FUNGAL AGENTS CAUSING CUTANEOUS
wearing shoes
MYCOSES OR DERMATOPHYTOSIS
o Clinical features:
- Acute: itching, red
vesicular
Cutaneous Mycoses/Dermatophytoses - Chronic: itching,
scaling, fissures
 Dermatophytes parasitize the nonliving,
cornified layer of the skin
- Secrete keratinases which are
proteolytic enzymes that digest
keratin
FUNGAL AGENTS CAUSING
- Classified according to its
SUBCUTANEOUS MYCOSES
habitat:
 Zoophilic
 Anthropophilic Subcutaneous Mycoses
 Geophilic
 Caused by exogenous fungi that
 3 genera associated with human normally in nature mostly in soil and
infection: identified on the basis of their vegetation
colonial appearance and microscopic  Portal of entry
morphology - Skin or subcutaneous
tissue by traumatic
1. Microsporum inoculation with
2. Trichophyton contaminated material
3. Epidermophyton  Causes chronic infections
 TYPES:
 Microsporum audounii 1. Sporotrichosis
o Anthropophilic 2. Mycetoma
o Infect Hair and scalp 3. Chromoblastomycosis
4. Phaeohyphomycosis
o Important cause of tinea
capitis
 Sporotrichosis
Dermatophytosis (Tinea or Ringworm) o Chronic infection of the
subcutaneous tissues and
 Tinea capitis – scalp lymphatic
 Tinea barbae – beard or moustache o Acquired through trauma
(Barber’s itch) (thorns or splinters) usually to
 Tinea corporis – body the hand, arm or leg
 Tinea cruris – inguinal area or groin o Occupational hazard for
(Jock itch) farmers, miners, gardeners,
 Tinea pedis – athlete’s foot florist
 Tinea ungium – nail (Onychomycosis) o Macroscopic
- Rapid growing (3-5 days)
- White, pasty, moist
colony that later
 Tinea pedis – athlete’s foot
 becomes brown, black,
wrinkled or leathery
- The yeast phase
(inhibited on antibiotic
media). Grows on BHI at
37°C as soft, white,
cream-to-tan-colored
colonies
 Mycetoma
- Other names: Madura foot or
Maduromycosis
- Traumatic inoculation with
several saprophytic fungi,
commonly involving the lower
extremities but may occur in any
part of the body
 Pseudoallesheria boydii
- Ascomycota group
- Soil, standing water and
sewage
- Humans acquire
infection by traumatic
inoculation into the skin
and subcutaneous
tissues
- Clinical specimens:
Granules from the
lesions
 Chromoblastomycosis
o Traumatic inoculation into the
subcutaneous tissue
o Chronic infection producing
warty (non-healing, hard) or
cauliflower-like lesions mostly
in the lower extremities
 Phaeohyphomycosis
o it is characterized by darkly
pigmented, septate hyphae; a
yeast phase may be observed
in tissue
o subcutaneous and brain
abscess are also seen usually
opportunistic
o Etiologic Agents:
- Exophiala jaenselmei,
E. dermatitidis
- Alternaria
- Bipolaris
- Drechslera
- Curvularia
FUNGAL AGENT CAUSING SYSTEMIC AND
OPPORTUNISTIC MYCOSES
PRIMARY SYTEMIC MYCOSES
 Coccidioidomycosis
 Histoplasmosis
 Blastomycosis
 Paracoccidioidomycosis
 Generally caused by dimorphic fungi
OPPORTUNISTIC MYCOSES
 Candidiasis, systemic
 Cryptococcosis
 Aspergellosis
 Mucormycosis
 Coccidioidomycosis
o Acquired through inhalation of the
infective arthroconidia
o Approximately 60% are
asymptomatic and self-limited
respiratory tract infections
o Infection may become
disseminated to visceral organs,
meninges, bone, skin, lymph
nodes and subcutaneous tissue
 oConsidered as the most infectious
fungi of all fungi
o Extreme caution should be
observed in handling cultures of
this organism
 Safety Precautions in handling
C. immitis cultures:
- if culture plates are
used, they should be
handled only in
biologic safety cabinet
(BSC)
- cultures should be
sealed in tape if the
specimen is
suspected of
containing C. immitis
- tissues or scrapings of
 Histoplasmosis
o A chronic granulomatous
infection that is primary and
begins in the lungs and may
produce cavitary lesion that
resemble tuberculosis
o Infection may disseminate to
the lymphatic tissue, liver,
spleen, kidneys, meninges
o Acquired by inhalation of
infective conidia from the
environment
o 95% of infection are
asymptomatic and self-limited
o Considered as the most
prevalent pulmonary mycosis
of humans and animals
 Blastomycosis
o Etiologic Agent:
Blastomyces dermatitidis
- Direct microscopic
examination of tissues or
body fluids
 Large, spherical,thick-
walled yeast cells 8 - 15µ
usually with a single bud
that is connected to its
parent cell by a broad
base.
 Paracoccidioidomycosis
o Chronic granulomatous
infection begins as a primary
pulmonary infection
o Usually asymptomatic but
may disseminate to produce
ulcerative lesion of mucous
membranes of the nasal
cavity, oral, gingival and
conjunctiva
o Etiologic Agent:
Paracoccidioides brasiliensis
o Direct microscopic
examination of sputum,
ulcerative lesions
 Large, round or oval
yeast cell, 8-40µ,
producing multiple buds
and each is attached to
the parent cell by a
narrow base
 “Mariner’s wheel”
Candidiasis
o Most frequently encountered fungal
infection
o Etiologic agent:
 Candida albicans – most frequent
 C. tropicalis
 C. parapsilosis
 C. glabrata
o Candida albicans and other species are
part of the normal flora, seen in the
oropharynx, GIT, GUT, skin
o Infections are believed to be
endogenous in origin
o Candida infections in normal and
immunocompromised hosts
 Intertriginous candidiasis
 Onychomycosis and paronychia
 Mucocutaneous and junction of
lips
 Oral thrush
  Vulvovaginitis o direct microscopic
 Pulmonary infection examination
 Eye infection  spherical, single or multiple
 Endocarditis budding, thick-walled yeast
 Meningitis cell surround by a wide,
 Fungemia and disseminated refractile polysaccharide
capsule
infection
- Most commonly seen in
immunocompromised patients
- Onychomycosis and
Aspergillosis
esophagitis caused Candida
albicans are very coomon in
 an opportunistic infection causing
AID’s patients
disseminated infection in
 Predisposing factors for immunocompromised patients
candiasis  also cause various other infections
- Alteration in the normal including invasive lung infection,
skin and mucous pulmonary fungus ball (tangled mass of
membrane barriers hyphae). Allergic pulmonary
- Prolonged antibiotic aspergillosis, onychomycosis, keratitis
administration  acquired through inhalation
- Use of immunosuppressive
Zygomycosis (Mucormycosis)
drugs
- Diseases of the immune  less common cause of infection as
system compared to Aspergillosis
 acquired by inhalation
 Rhinocerebral infection involving nasal
Cryptococcosis mucosa, palate, sinuses and brain

 a subacute or chronic fungal Penicillium

infection that has several
manifestations  When clinically significant, cilinical
 disseminated disease with or manifestations include:
without meningitis in - Bronchopulmonary
immunocompromised patients - Endocarditis
- Cutaneous ulcers of extremities.
 meningitis occur in 2/3 of
patients with disseminated  Phialides
infection  Metulae
 exit as saprophyte in nature
 often found associated with
pigeon, bat, or bird droppings Fusarium
as well as decaying vegetation,
fruits, plants  Other infections
 acquired through inhalation - Sinusitis
 primarily affecting lungs, then - Wound (burn) infections
disseminate to meninges and - Allergic fungal sinusitis
other sites - Respiratory tract infections
 Etiologic Agent: Cryptococcus
neoformans
Pneumocystis jeroveci (atypical fungus) subunits arranged in a
precisely defined
 Opportunistic atypical fungus that is a fashion
common cause of pneumonia in - Each protein subunit is
immunocompromised patients known as capsomere
 Differ from fungi:
- Cell membrane contains cholesterol
- Trophozoite and cyst (octonucleate
cyst)
CLASSIFICATION OF VIRUSES (ANIMAL
VIROLOGY VIRUSES)

 DNA Viruses
 Study of viruses
- Are obligate  RNA Viruses
intracellular parasites,
which are unable to
multiply by binary  DNA Viruses
fission - Poxviridae
- Herpesviridae
 ASEXUAL REPRODUCTION - Adenoviridae
- Bacteria reproduce by - Papovaviridae
BINARY FISSION  Papillomaviridae
 Dmitri Iwanowski (1892)  Polyomaviridae
- First noted the - Hepadnaviridae
filterable organism, the - Parvoviridae
tobacco mosaic
viruse (TMV)
 Wendell Stanley (1935)
 RNA Viruses
- Confirmed that the
- Picornaviridae
filerable organism is
- Caliciviridae
TMV
- Togaviridae
- Flaviviradae
- Coronaviridae
ORIGIN OF VIRUSES - Reoviridae
- Astroviridae
 Derived from DNA or RNA - Filoviridae
nucleic acid components of host - Paramyxoviridae
cells that have acquired the - Orthomyxoviridae
ability to exist independently - Bunyaviridae
 May be degenerate forms of - Arenaviridae
intracellular parasites - Rhabdoviridae
 VIRION – the complete virus - Retroviridae
particle
 CAPSID – protein coat Prions
- Encloses the genome
 Infectious particles composed of
or genetic material of
abnormal proteins (PrP)
either DNA or RNA
 Abundant in neurons
- Composed of
repeating, identical  Cause of transmissible spongiform
encephalopathy
 - Humans: Kuru, Creutzfeldt-
Jakob disease
- Animals: Scrapie (goat and
sheeps),Bovine spongiform
encephalopathy (Mad cow
disease)
 Hepatitis B virus (HBV)
- Primary hepatocellular
carcinoma
 Human Herpesvirus 8 (Kaposi
sarcoma-associated herpesvirus)

 Human T cell Leukemia Virus (HTLV)

 Hepatitis C virus
ANTIVIRAL AGENTS
- Primary hepatocellular
 Analogues of Ribonucleosides and
carcinoma
Deoxyribomucleosides: inhibit viral
RNA and DNA synthesis
 Hepatitis D (Delta Agent)
 Acyclovir: highly specific for
- Primary hepatocellular
Herpes simplex and Varicella
carcinoma
Zoster Virus
 Less active against CMV
and EBV
 Poxviridae
 Ganciclovir: powerful inhibitor  Orthopoxviruses:
of HSV multiplication - Variola (Human)
 The best inhibitor of CMV - Vaccinia (Human, water buffalo)
- Monkeypox (rodents, monkeys)
 Zidovudine (AZT): inhibitor of - Cowpox (cows)
retrovirus reverse transcriptase

 Interferon
 Herpesviridae
 Antiviral, immunoregulatory,
 General characteristics:
antiproliferative
- Produce skin lesions
 Antitumor drug
- Cause latent infection
 Hepatitis infection
- Oncogenic potentials
-
 Human Herpesvirus Classification:
DNA Tumor Viruses  Alphaherpesvirus
 Herpes simplex
 Human Papillomavirus (HPV) virus (HSV) 1 & 2
- Cervical carcinoma, vaginal and  Varicella-Zoster
vulvar carcinoma, penile Virus (VSZ)
carcinoma  Betaherpesvirus
 Cytomegalovirus
 Epstein-Barr Virus (EBV) (CMV)
- Burkitt’s lymphoma and  Reseolovirus
nasopharyngeal carcinoma (human
herpesvirus 6 & 7)
  Reseolovirus (human herpesvirus 6 & 7)  Non-enveloped
- Biologic criteria:  (+) sense
gammaherpesviruses because  Icosahedral
they infect lymphocytes (T  28 – 30 nm
lymphotropism)

 Gammaherpesvirus
 Epstein-Barr virus  Filoviridae
(EBV)  Singe-stranded genome
 Human herpes 6  Long, filamentous (helical) capsid
(exanthem  Enveloped
subitum or
Roseola infantum)
 Adenoviridae
 Paramyxoviridae
 Double-stranded DNA genome
 Human pathogens:
 Icosahedral capsid
- Measles virus or Rubeola
 Non-enveloped  Transmission:
 70 – 70 nm Contact with
respiratory secretions;
extremely contagious
 Picornaviridae - Mumps Virus
 Human enteroviruses  Transmission:
- Human Hepatitis A virus  Person-to-
person contact
(Human enterovirus 72)
 IP is 2-6 weeks  Presumably
respiratory
 Human Rhinoviruses
droplets
- 113 seotypes (Common colds
infection) DISEASE:
- Foot-and-mouth disease
(Aphthovirus) in lower animals  Mumps (epidemic
 DISEASE: Parotitis)
- Poliomyelitis (polio)  Orthomyxoviridae
- Herpangina (coxsackie A)  Influenza virus infections in humans
- Pleurodynia (Coxsackie B) - Pathogenesis and pathology
o Airborne and contact with
contaminated hands or
surfaces
 Calciviridae o Infects respiratory
 Human pathogens epithelium:
- Hepatitis E virus (HEV)  Lowers resistance to
 Cause hepatitis similar secondary bacterial
clinically to Hepatitis A invaders
 Moratlity rate is 10-20% o IP: 1 – 4 days
in pregnant women  Influenza viruses types A, B, C
- Influenza A
o The most common
serotype causing
 Astroviridae
influenza epidemics
 Single-stranded
 o Avian flu: H5N1
o Swine flu: H1N1
 Coronaviridae
 Outstanding characteristics:
- Cause colds and SARS
 Togaviridae - Display high frequency of
 Genus alphaviruses: Mosquito- recombination
borne viruses
- Eastern, Western, Venezuelan
equine encephalitis viruses
 Rhabdoviridae
- Chikungunya virus
 Bullet-shaped
 Enveloped helical nucleocapsid
 180 x 75 nm
 Replication: cytoplasm
 Retroviridae
 Chikungunya
 it is a debilitation, but non-fatal, viral  Human Retroviruses
(chikungunya virus, classified family: Togaviridae, - Human Immunodeficiency 1
genus Alphavirus) illnessthat is spread by and 2 (HIV)
the bite of an infected Aedes (Aedes  Viruses encodes its
aegypti, aedes albopictus) mosquito. genetic information in
 1952 in Tanzania RNA and uses a
 Chikungunya means that which unique viral enzyme
“contorts or bends up” – stooped call reverse
posture of patients who are afflicted transcriptase to copy
with the severe joint pain. genome into DNA
 Latency: CD4+ T cells
 Flaviviridae  Clinical manifestations
 Mosquito borne (CDC)
- Dengue virus  Chronic or Latent
 4 serotypes: 1, 2, 3, 4 Latenct and ARC
 Transmission: bite of Relative
aedes aegypti and containment of
the virus
aedes albopictus

DISEASE:

 Classical Dengue
Fever; Dengue
hemorrhagic
fever/Dengue shock
syndrome
 Hepatitis C virus (HCV)
- Hepatitis C infection previously
referred as non-A, non-B
hepatitis
- Responsible for 90% of post-
transfusion hepatitis
- Chronic infection