USTMED

UST FACULTY OF MEDICINE

Basics of Medical Microbiology & Parasitology
& SURGERY SecC2021 Justine Val Jade B. Lacaba BACTERIOLOGY, VIROLOGY, MYCOLOGY, PARASITOLOGY 1
ILTΣΒΤΦ ILTΣΒΤΦ ILTΣΒΤΦ

BASICS OF MEDICAL MICROBIOLOGY & PARASITOLOGY

I. General Classification of Microbes III. Basics of Virology

A. Microorganisms A. Viral Structure
i. Prokaryotes B. Viral Genetics
ii. Eukaryotes C. Viral Characteristics
B. Acellular Infectious Agents D. Viral Pathogenesis
i. Viruses E. Diagnostic Virology
ii. Viroids IV. Basics of Mycology
iii. Prions A. Fungal Structure & Function
II. Basics of Bacteriology B. Fungal Reproduction
A. Bacterial Cell Structure C. Fungal Classification
B. Bacterial Growth D. Mycotic Pathogenesis
C. Metabolic Characteristics E. Diagnostic Mycology
D. Bacterial Genetics V. Basics of Parasitology
E. Normal Microbiota A. Characteristics of Parasites & Hosts
F. Bacterial Pathogenesis B. Parasitic Arthropods
G. Diagnostic Bacteriology C. Parasitic Protozoans
D. Parasitic Helminths
C. Parasitic Pathogenesis
D. Diagnostic Parasitology

DISCLAIMER
These notes are intended for the use of Written Revalida Review and are
NOT substitutes for learning for 2nd Year Microbiology & Parasitology in
USTMed.

These notes only cover the BASIC INTRODUCTORY concepts for each
microbial group and does NOT include ALL topics taught in the
Microbiology & Parasitology Curriculum of the UST-FMS.

These notes were originally made merely for the author’s own personal
use. Grammatical errors are to be expected. Use at your own risk.

The authors claim no warranties with respect to the accuracy and

completeness of the contents of these notes.

All information in these notes are gathered from the sources listed below.
Some pictures were obtained from the internet but most are sourced
from the personal notes of the author

No Copyright Infringement Intended

MAJOR SOURCES

UST-FMS Microbiology & Parasitology Transes

TopNotch Micro-Para Handouts 2019, 2020
Jawetz Medical Microbiology, 27th Ed
BRS Microbiology & Immunology, 6th Ed
Review of Medical Microbiology & Immunology, 14th Ed
Clinical Microbiology Made Ridiculously Simple, 6th Ed

NOTES BY LACABA, Justine Val Jade B.

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General Classification of Microbes 01

MICROORGANISMS

I. BASIC PRINCIPLES
A. Microbiology is the study of microorganisms
B. Microorganisms
a. a large group of microscopic organisms that exist as single cells or cell clusters
b. includes Prokaryotes (Bacteria) and Eukaryotes (Protozoa, Fungi, Algae)
C. Acellular Infectious Agents
a. biological entities that lack the basic unit of life: the cell
b. gain biological activity when parasitizing a host cell
c. includes viruses, viroids, and prions

II. PROKARYOTES
A. small sized microorganisms without nuclear membrane, only has nucleoid
B. differs from eukaryotes according to the following (Table 1.1)
C. two major subdivisions of Prokaryotes
a. Bacteria
i. has a peptidoglycan cell wall & phospholipid cell membrane
ii. 70S ribosomes consists of 30S and 50S subunit
iii. DNA contains EXONS only
b. Archaebacteria
i. unique lipid cell membrane consisting of isoprenoids
1. allows archaebacteria to withstand extreme conditions
ii. presence of INTRONS within cells
1. segments of DNA that interrupts informational DNA within genes
2. found in both archaebacteria and eukaryotes

TABLE 1.1 Comparison between Prokaryotes & Eukaryotes

Prokaryotes Eukaryotes
DNA within nuclear membrane? NO, only nucleoid YES
Mitotic Division? NO YES
DNA associated with histones? NO YES
Chromosome Number? 1 (most) >1
Membrane-bound Organelles? NO YES
Size of Ribosome? 30S + 50S = 70S* 40S + 60S = 80S*
Cell wall with peptidoglycan? YES NO
*Svedberg Unit (S): non-SI unit for sedimentation rate at which particle of a given size travel to the bottom under centrifugal
force; technically a measure of time: the smaller the subunit, the faster the sedimentation rate

III. EUKARYOTES
A. has a true nucleus and membrane-bound organelles
B. with microtubules & microfilaments, comprising complex intracellular cytoskeleton
C. Protists are microbial eukaryotes and contain four major groups:
a. Algae
i. photosynthetic eukaryotic organisms containing chlorophyll
ii. used to denote all organisms that produce O2 as a product of photosynthesis
iii. many algal species are unicellular, some may form large multicellular structures
iv. includes dinoflagellates, previously included cyanobacteria
b. Protozoa
i. unicellular non-photosynthetic (heterotrophic) protists
ii. includes flagellates, amoebae, ciliates, sporozoa
c. Fungi
i. non-photosynthetic protists
ii. may have coenocytes – multinucleated mass of continuous cytoplasm
iii. includes the following:
1. molds - with mycelial form
2. yeasts – do not form mycelium, grow as single units that bud, with transitional form
d. Slime Molds
i. diverse forms
ii. characterized by presence of plasmodium
1. Plasmodium is an ameboid multinucleate mass of cytoplasm, analogous to mycelium

NOTES BY LACABA, Justine Val Jade B.

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ACELLULAR INFECTIOUS AGENTS

TABLE 1.2 Comparison between Viruses, Viroids, and Prions

Viruses Viroids Prions
obligate intracellular agents obligate intracellular agents abnormal form of cellular protein
consist of either RNA or DNA consist only of RNA consist only of protein
surrounded by a protein coat no protein coat no DNA or RNA

I. VIRUSES
A. lack many attributes of cells
a. does not replicate alone
b. only replicated when it infects a host or a living cell
B. known to infect all cells, including microbial cells
a. Virophage – virus that infects other viruses
b. Bacteriophage – virus that infects bacteria
c. Viroids – small circular ssRNA molecules causing transmissible plant diseases
C. viral particles are generally small
a. contains a nucleic acid molecule, either DNA or RNA, with intermediate mRNA
b. enclosed in a protein coat aka capsid

II. PRIONS
A. noncellular infectious proteins
a. same amino acid sequence as normal human cell surface proteins but misfolded
i. normal proteins have more α helices, pathological prions have β sheets
b. has the ability to transmit its misfolded shape onto normal variants of the same protein
B. contain no nucleic acids, does not require DNA as genetic material
C. cause transmissible neurodegenerative diseases in humans & animals

III. PRION DISEASES

A. Human and Animal Prion Diseases
a. Human Prion Diseases
i. Creutzfeld-Jakob Disease – due to infection, manifest as ↓cortical function (eg dementia)
ii. Kuru – due to cannibalism, manifest as ↓cerebellar function (dysdiadochokinesia, ataxia)
iii. Gerstmann-Staussler-Scheinker (GSS Syndrome)
iv. Fatal Familial Insomnia (FFI)
v. Sporadic Fatal Insomnia
b. Animal Prion Diseases
i. Scrapie (sheep and goats)
ii. Transmissible Mink Encephalopathy
iii. Bovine Spongiform encephalopathy (BSE) – aka mad cow disease
iv. Chronic wasting disease (mule, deer, elk)
B. Transmission of Prion Diseases
a. sporadic
b. infection
i. skin cuts
ii. transplant of contaminated tissues (cornea)
iii. use of contaminated medical devices (brain electrodes)
iv. ingestion if infected tissue (cannibalism causes Kuru)
c. inherited syndrome
C. Pathogenesis of Prion Diseases (see Figure)
D. Susceptible population
a. women and children of Fore tribe in jungles of New Guinea
b. neurosurgeons & brain surgery patients
c. transplant surgeons and transplant patients
E. Spectrum of Disease
a. progressive neurodegenerative disease
i. loss of muscle control, shivering, myoclonic jerks, tremors, loss of coordination
ii. rapidly progressive dementia
iii. death
F. Treatment and Prevention
a. no treatment available
b. cessation of ritual cannibalism, elimination of contaminated animal products
c. disinfection of neurosurgical tools and electrodes
i. standard autoclave: 121°C, 15-20 minutes, 15psi
ii. prion control: extended to 1 hour

NOTES BY LACABA, Justine Val Jade B.

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BASICS OF BACTERIOLOGY 02

BACTERIAL CELL STRUCTURE

I. BACTERIAL MORPHOLOGY
A. Bacteria have FOUR major shapes
a. Cocci: spherical
b. Bacilli: rods, short bacilli are called coccobacilli
c. Spiral forms: comma-shaped, S-shaped, or spiral-shaped
d. Pleomorphic: lacking distinct shape
B. Cell Grouping results when cells remain temporarily attached after division
a. Cocci: clusters, chains (streptococci), pairs (diplococci), cubical bundles (sarcinae), flat plates
b. Bacilli: pairs, chains, palisade (occur in diphtheria due to repeated whipping motion)

II. BACTERIAL CELL WALL & MEMBRANE

A. Cell wall
a. all bacteria have a cell wall composed of peptidoglycan
i. except mycoplasma which do not have cell walls at all
b. peptidoglycan: sugar backbone (glycan) + peptide side chains (peptido)
i. crossed linked by tanspeptidase reaction
ii. complex polymer consisting of NAG and NAM connected by β1→4 linkages
B. Porins
a. channels found in the outer membrane of gram negative bacteria
b. allow passage of small, essential hydrophilic molecules (sugars, amino acids, vitamins)
i. also allow passage of many antimicrobial agents such as Penicillins
C. Gram Staining
a. most bacteria are classified as gram positive or gam negative according to response to stain
i. Gram Positive
1. retains crystal violet ● Gram Stain Results (MRS)
2. looks blue/purple under microscope ○ Gram Positive: positively BLUE over you
3. crystal violet (CV+) complexes with I- as CV-I complex which binds to teichoic acid ○ Gram Negative: no RED commies
ii. Gram Negative
1. does not retain dye-iodine complex, counterstained with safranin red
2. looks red under the microscope
3. thin peptidoglycan become leaky upon alcohol treatment, releasing CV-I complexes
b. procedure of gram staining
(1) Primary Stain: pour on crystal violet and wait 60 seconds
(2) Mordant: wash off with water and flood with iodine solution, wait 60 seconds
(3) Decolorizing Agent: wash off with water and then “decolorize” with 95% alcohol
(4) Counter-stain: counter-stain with safranin red, wait 30 seconds, wash off with water
D. Gram Positive vs Gram Negative Cell Walls (see Table 2.1)
a. Gram Positive
i. has thick peptidoglycan layer with one cell membrane beneath
ii. teichoic acids encompass wall, membrane, or capsular polymers
1. Lipoteichoic acid – covalently linked to membrane glycolipid
2. Wall Teichoic acid – covalently linked to peptidoglycan
b. Gram Negative
i. has thin peptidoglycan layer in periplasmic space
1. periplasmic space is located between outer and inner cell membrane
ii. lipopolysaccharide (endotoxin) on the outer membrane
1. consists of Lipid A and O antigen → induction of IL-1 and TNF, cause fever
2. all gram positive bacteria have NO endotoxin except Listeria monocytogenes

TABLE 2.1 Comparison between Gram Positive & Gram Negative Cell Wall
Gram Positive Gram Negative
Gram Stain Purple Reddish-Pink
Peptidoglycan Thick Layer Thin Layer
Outer Membrane Absent Present
Periplasm Absent Present
Teichoic Acid Present Absent
Lipopolysaccharide Absent Present
Absent Present
Porin
*unnecessary, because no outer membrane *passage through outer membrane
Sensitivity to Penicillin Generally more susceptible Generally less susceptible
Sensitivity to Lysozyme* Yes No
*Lysozyme: enzymes that kill bacteria by cleaving the β1→4 glycosidic bonds between NAG & NAM of peptidoglycan

NOTES BY LACABA, Justine Val Jade B.

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E. Bacteria not Seen in Gram Stain (see Table 2.2) ● Types of Acid Fast Staining
○ Kinyoun: no heat applied (kinyoun kold)
○ Ziehl-Neelsen: uses heat (ziehl sizzling)
TABLE 2.2 Gram-Indeterminate Bacteria, Reasons, and Alternative Approach
Genus Reason Alternative Approach
Acid fast stain (Carbol fuchsin)
Mycobacteria Too much lipid in cell wall, dye cannot penetrate DON’T FORGET! All bacteria have cell walls
Malachite green/methylene blue counterstain
composed of peptidoglycan except
Spirochetes too thin to see Darkfield microscopy
Mycoplasma
Mycoplasma no cell wall, very small None (serologies)
Legionella poor uptake of red counterstain Silver stain
Chlamydia intracellular, very small Giemsa Stain (find inclusion bodies)
Rickettsia intracellular, very small Giemsa/Tissue Stain

II. COMPONENTS OF BACTERIA (see Table 2.3)

A. Essential Components
a. structures of bacterium that they cannot live without
b. acquired from chromosome via binary fission
B. Non-Essential Bacterial Components
a. accessory structures that may or may not be possessed
b. acquired from genetic mobile elements via conjugation, transduction, transformation
c. presence of non-essential components usually confers virulence, more pathogenic

TABLE 2.3 Components of Bacteria

Component Description Function
Essential Components
Cell Wall
Cytoplasmic Membrane lipoprotein bilayer with steroids site of oxidative & transport enzymes
Ribosome RNA & protein in 50S & 30S subunits protein synthesis
Nucleoid contains DNA genetic material
Mesosome invagination of plasma membrane participate in cell division & secretion
Periplasmic Space space between plasma & outer membrane contain hydrolytic enzymes (eg β lactamase)
Non-Essential Components
Capsule polysaccharide protects against phagocytosis
Pilus or Fimbria glycoprotein attachment, conjugation
Glycocalyx polysaccharide mediates adherence to surfaces
Flagellum protein motility
Spore Keratin-like coat, dipiclonic acid resistance to heat & chemicals
Plasmid DNA genes for antibiotic resistance & toxins
Granule glycogen, lipid, polyphosphates site of nutrients in cytoplasm

IV. FLAGELLA
A. helically-shaped structures containing the protein flagellin
B. hook (base of flagella) is attached via basal body
a. basal body spans the entire cell wall and cytoplasmic membranes
b. rotates in clockwise or counterclockwise direction, spinning the flagellum
C. Types of Flagellum
a. Monotrichous – single polar flagellum (eg Vibrio cholerae)
b. Amphitrichous – single flagellum on both ends
c. Lophotrichous – tufts of flagella at one or both sides
d. Peritrichous – numerous flagella all over the bacterial body (eg E. coli, P. mirabilis)

IV. PILI
A. hair-like appendage on surface of bacteria
B. shorter than flagella and do not move
C. Types of Pili
a. Attachment Pili (Fimbriae) – serve as adherence factors for virulence or biofilm formation
b. Conjugative Pili (Sex/F Pili) – allow transfer of DNA between bacteria via conjugation

V. CAPSULE
A. protective wall coating around the bacteria
DON’T FORGET! All bacterial capsules
B. usually composed of polysaccharide consist of polysaccharides except B. anthracis
a. Bacillus anthracis cell wall is composed of polypeptide of D-glutamate which consists of poly-D-glutamate
C. protects bacteria against phagocytosis by macrophage & neutrophils
D. Tests for Visualizing Capsule
a. India Ink Stain – capsule appears as transparent halo around the cell (Cryptococcus)
b. Quellung Reaction – Ab binds to capsule → opaque and appear to enlarge (S. pneumoniae)

VI. PLASMIDS
A. extrachromosomal, circular dsDNA capable of replicating independently of chromosome
B. can sometimes be integrated into bacterial chromosome → episomes
C. Conjugation: donor transfers plasmid to recipient via conjugation pilus
D. Significance of Plasmids
a. antibiotic resistance d. Pili (Fimbriae)
b. resistance to heavy metals e. Exotoxins & Enterotoxins
c. resistance to UV light f. Bacteriocins – bacterial toxins toxic to other acteria

NOTES BY LACABA, Justine Val Jade B.

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VII. ENDOSPORES
A. metabolically dormant forms of bacteria
B. formed only by 2 genera of bacteria (both are Gram Positive): Bacillus & Clostridium
C. resistant to heat (boiling), cold, drying (dessication), and chemical agents
a. forms when there is shortage of nutrients, from a mother cell that underwent autolysis
b. destroyed by autoclave od 121°C for 15 minutes
c. heat resistance is conferred by the presence of Calcium dipicolinate
D. multilayered protective coat consisting of (inside to outside):
(1) core – spore protoplasm, contains chromosome & systems for protein & ATP synthesis
(2) cell membrane
(2) spore wall - thick peptidoglycan cell wall of the vegetative cell
(3) cortex – thickest layer of peptidoglycan, sensitive to lysozyme & autolysis
(4) keratin spore coat – keratin-like, impermeable (antibiotic resistant)
(4) exosporium
E. Sporulation (see figure)
a. formation of endospore due to decrease in nutrients
b. occurs at the terminal end of the log phase
F. Germination
a. Activation – by nutrition-rich medium or spore-coat damage
b. Initiation – binding of effector activates autolysin, degrades cortex proteoglycan
i. calcium dipicolinate is released, spore constituents are degraded by hydrolytic enzymes
c. Outgrowth
i. spore protoplast + surrounding wall → vegetative cell (result of spore degradation)
ii. period of active biosynthesis ending in cell division

BACTERIAL GROWTH

I. BASIC PRINCPLES
A. growth – defined in terms of increase in cell number rather than cell size
a. increase in cell number occur via binary fission
B. bacterial growth is a coordinated process of:
a. increase in individual cell mass and size and duplication of chromosome
b. followed by cell division

II. BACTERIAL GROWTH CYCLE

A. Phase 1: Lag Phase
a. character: no cell division, no increase in mass (zero growth rate)
b. depleted metabolites from previous unfavorable condition, adapt to new environment
c. vigorous metabolic activity occurs but cells do not divide (no net increase in mass)
B. Phase 2: Log (Exponential) Phase
a. character: microbes are dividing at maximum growth rate (constant growth rate)
b. exhibit constant growth rate and increase in new cell material
c. continues until one or more nutrient in medium becomes exhausted
C. Phase 3: Stationary (Plateau) Phase
a. character: total number of viable microbes remain constant (zero growth rate)
b. cell death balanced by formation of new cells
c. due to exhaustion of nutrients or accumulation of toxic products
d. phase where β-lactams act
D. Phase 4: Decline (Death) Phase
a. character: negative growth rate
b. most undergo cell death due to exhaustion of nutrients

III. CONTROL OF BACTERIAL CELL GROWTH

A. Methods of Control
a. Sterilization
i. process of killing & removing ALL viable microbes, including spores
ii. example: autoclaving, recall that prions require 1 hour instead of just 15 minutes
b. Disinfection
i. process of killing some but NOT ALL viable microbes in inanimate objects
ii. example: application of rubbing alcohol to inanimate objects
c. Antisepsis
i. disinfection of tissue/skin (patient), removal of microbial flora (HCW)
ii. example: preoperative skin preparation, hand rubbing with alcohol
d. Sanitization
i. reduction of microbial contamination to an acceptable “safe” level
ii. terminology used in food safety
e. Degerming or Cleaning
i. physical removal of microorganisms using soaps or detergents
ii. example: handwashing with soap and running water

NOTES BY LACABA, Justine Val Jade B.

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B. Germicide and Sporicide

a. Germicide – biocides capable of killing germs in general
b. Sporicide – biocides capable of killing spores
C. Effects of Bactericidal & Bacteriostatic Antimicrobials
a. Bactericidal Antimicrobial
i. example: cell wall synthesis inhibitors (β-lactams, glycopeptides)
ii. acts on log phase, cause a decrease in cell number
a. Bacteriostatic Antimicrobial
i. example: protein synthesis inhibitors
ii. acts on log phase, cause a plateau in growth
D. Specific Actions of Selected Biocides
a. Heat – preferred method due to ease of use
i. Dry Heat – incineration using Bunsen burner or hot air oven for 1 hour
ii. Autoclaving (121°C 15psi for 15-20 minutes) – most effective for sterilization
iii. Boiling Water – kill vegetative bacteria but not all spores, most effective up until 2 mins
iv. Pasteurization (62.8-65.6°C for 30 min) – eliminate pathogenis in small numbers in fluids
b. Radiation
i. UV Radiation (260nm) – thymidine dimer formation in DNA, not sporicidal
ii. Gamma Irradiation (<1nm) – free radical formation, used for sterilizing
c. Chemical Agents (see Figure)

METABOLIC CHARACTERISTICS

I. BASIC PRINCIPLES
A. Requirements for growth:
a. Organic Matter comprises most of the dry weight of microorganism
i. Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur
b. Inorganic Ions
ii. Sodium, Potassium, Calcium, Chloride, Magnesium, Iron

II. SOURCES OF METABOLIC ENERGY

A. Fermentation
a. ATP synthesis done exclusively via substrate-level phosphorylation
b. not coupled with electron transfer
B. Respiration
a. reduction of an oxidant (eg O2) through electron carriers (O2 → H2O)
b. formation of proton motive force that is used in ATP synthesis
C. Photosynthesis
a. reduction of an oxidant (CO2 → Glucose)
b. production of O2 in the process

III. FACTORS AFFECTING GROWTH (see Table 2.4)

A. Hydrogen Concentration (pH) – internal pH maintained by pumping protons in & out of cell
B. Temperature – thermal stability is expressed in 2 ways
a. Heat Shock
i. transient synthesis of heat shock proteins in response to sudden temperature rise
ii. stabilization of heat sensitive proteins, become unusually heat resistant
b. Cold Shock
i. killing of cells by rapid cooling
C. Aeration
a. oxygen metabolism generates toxic products such as superoxide & hydrogen peroxide
b. enzymes such as superoxide dismutase, catalase, and peroxidase to survive aerobic life
D. Ion Strength & Osmotic Pressure
a. osmolality can be regulated by active transport of K into the cell
b. internal ionic strength is kept constant by compensating excretion of (+) charged putrescine

TABLE 2.4 Classification According to Factors Affecting Growth

Classification Description Classification Description
Hydrogen Ion Concentration Aeration
Alkalophile grow best at pH 10.3 Aerotolerant anaerobic indifferent to O2
Neutralophile grow best at pH 6.0-8.0 Obligate Aerobe dependent on O2 for ATP generation
Acidophile grow best at 3.0 Facultative Aerobe use O2 if present, can switch to fermentation
Temperature Microaerophile fermentation, tolerate low amt O2 (2-10%)
Hyperthermophilic above boiling water temp Obligate Anaerobe can’t grow in O2 (lack antioxidant enzymes)
Thermophilic grow best at 50-60°C Ion Strength & Osmotic Pressure
Mesophilic grow best at 30-37°C Halophilic require high Na concentration
Psychrophilic grow best at 15-20°C Osmophilic require high osmotic pressure

NOTES BY LACABA, Justine Val Jade B.

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BACTERIAL GENETICS

I. GENOME ORGANIZATION
A. Genome is the totality of all genetic information in an organism (all genes)
B. Chromosomal DNA
a. self-replication genetic element (aka replicon)
b. essential for replication
C. Extrachromosomal DNA – nonessential replicon but aids in survival
a. Plasmid
i. replicates independently compared to chromosome
ii. encodes trains nonessential to viability
iii. advantages: promote antibiotic resistance, produce toxins
b. Bacteriophage
i. viral DNA integrated to eukaryotic genome = provirus
ii. phage DNA integrated to bacterial genome or episome = prophage
D. Transposons (aka transposable elements, mobile genetic elements, jumping genes)
a. DNA pieces that readily moves from one site to another (DNA, plasmids, bacteriophages)
b. codes for drug-resistant enzymes, toxins, or metabolic enzymes
i. cause mutations in genes, altering the expression of nearby genes
c. TWO methods of transposition
i. Direct Transposition (cut-and-paste)
ii. Replicative Transposition (copy-and-paste)

II. MECHANISMS OF GENE TRANSFER

A. Vertical Gene Transfer – inherit from parental genes
a. Binary Fission
i. method of asexual reproduction of single-celled organisms
ii. replication of DNA followed by cytokinesis by formation of transverse septum
B. Horizontal Gene Transfer – from one organism to another
a. Transduction
i. mediator: phage-mediated (virus to bacteria)
ii. mechanism: donor DNA packaged in phage coat, transfer to recipient like phage infection
b. Transformation
i. mediator: direct naked DNA uptake, direct inoculation
ii. natural transformation – active process, require protein synthesized by recipient
iii. forced transformation – treatment with ↑salt & temp → ↑competence for plasmid uptake
c. Conjugation
i. mediator: F(+) “Male” bacteria (bacteria to bacteria)
ii. mechanism of conjugation
(1) sex pilus of F(+) bacteria is inserted into F(-) bacteria
(2) F(-) bacteria receive ssDNA (only one strand of DNA)
(3) F(-) bacteria becomes F(+), synthesize complementary strand to the acquired D

III. GENE CLONING

A. isolation of desired gene using restriction enzymes producing sticky ends
B. DNA fragments are incorporated into plasmids by DNA ligase
C. plasmids are incorporated into bacterial host cells via transformation

IV. BLOTTING TECHNIQUES

A. Principles of Blotting
a. target molecules are separated according to size & charge by gel electrophoresis
b. separated molecules are transferred to a membrane
c. membrane is queried with a probe directed against specific molecule of interest
B. Types of Blotting Techniques
a. Southern Blot DNA
b. Norther Blot RNA
c. Western Blot protein
d. Eastern Blot post-translationally modified proteins
e. South-Western Blot DNA-binding proteins
C. HIV Testing
a. type of western blot, detects key proteins: p24, gp41, gp120
b. Results of HIV Testing
i. Indeterminate – 1/3 matches
ii. Negative – 0/3 matches
iii. Positive - ≥2/3 matches

NOTES BY LACABA, Justine Val Jade B.

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NORMAL MICROBIOTA

I. BASIC PRINCIPLES
A. normal microbiota are microorganisms that are permanent residents of the body
B. low-virulence organisms in their usual anatomic site
C. Resident vs Transient Microbiota
a. Resident – stay permanently, fixed types of organisms regularly found in a given area
b. Transient – temporary, non-pathogenic or potentially pathogenic, derived from environment

II. ROLE OF RESIDENT MICROBIOTA

A. either commensals or mutualistic
B. presence is not essential to life but some have role in maintaining health
a. Vitamin K Synthesis – resident GI microbiota
b. Bacterial Interference – prevent pathogens by competition with binding sites & nutrients
C. members of normal microbiota may produce disease if found in UNUSUAL anatomic sites
a. S. viridans in the URT → introduced to blood in tooth extraction, infective endocarditis
b. E. coli in the urethra → urinary tract infection
D. overgrowth of potentially pathogenic normal flora occur when:
a. composition of flora changes (eg Clindamycin use → risk for C. difficile infection)
b. changes in local environment (low stomach pH → risk for H. pylori infection)
c. immunocompromised (AIDS → risk for P. jirovecii pneumonia)

III. COMMON NORMAL MICROBIOTA (see Table at the margin)

BACTERIAL PATHOGENESIS

I. CHARACTERISTICS OF PATHOGENIC BACTERIA

A. 6 Characteristics of Pathogenic Bacteria
a. Transmissibility d. Toxigenicity
b. Adherence to host cells e. Immune system evasion
c. Invasion of host cells and tissues f. Resistance to antimicrobials & disinfectants
B. Koch’s Postulates
a. The 4 Postulates
(1) the microorganism should be found in all cases of the disease in question
and its distribution in the body should be in accordance with the lesions observed
(2) the microorganisms should be grown in pure culture in vitro for several generations
(3) when such culture is inoculated into susceptible animal species,
the typical disease must result
(4) the microorganism must again be isolated from such experimentally produced disease
b. Exceptions to the Koch’s Postulate
i. Treponema pallidum – does not grow in vitro
ii. Mycobacterium leprae – does not grow in vitro
iii. Neisseria gonorrheae – tropic to human, cannot be inoculated in animals

II. MODES OF TRANSMISSION

A. Human to Human
a. direct (sexual, transvaginal, contact) d. transplacental
b. fecal-oral transmission e. blood-borne (parenteral, IV)
c. inhalation of aerosols
B. Non-human to Human
a. soil, water
b. direct animal source, vector-borne, animal excreta
c. fomites

III. INFECTION-DISEASE STAGES

A. Incubation Stage
a. no signs or symptoms
b. bacteria is already inside and multiplying
B. Clinical Stage
a. peak of characteristic signs and symptoms of infection or disease
C. Stage of Decline
a. condition of host deteriorates possible to death
b. or signs and symptoms begin to subside as host improves
D. Convalescent Stage
a. full recovery of surviving host
b. or chronic infection may develop

NOTES BY LACABA, Justine Val Jade B.

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IV. TERMS RELATED TO PATHOGENICITY

A. Pathogenicity
a. absolute ability of an infectious agent to cause disease in a host
b. follows virulence
B. Infectivity
a. ability of an agent to cause infection
b. measured by number of infectious particles required
C. Toxigenicity
a. ability of an agent to produce exotoxins or endotoxins
D. Virulence
a. measure of pathogenicity (degree or intensity of pathogenicity)
b. severity of the disease after infection occurs, measured by case fatality rate

V. VIRULENCE FACTORS
A. determine degree to which the pathogen causes damage, invasion, infectivity
B. characteristics of pathogen that allows it to adhere, colonize, & invade tissue
C. Includes the Following:
a. Adherence Factors d. Antiphagocytic Factors
b. Enzymes for Bacterial Invasion e. Intraphagocytic Pathogenicity
c. Exotoxins and Endotoxins f. Biofilm Formation

VI. ADHERENCE FACTORS

A. Pili
a. thick rodlike appendages
b. help mediate attachment of bacteria to host cell surfaces
c. examples of pili
i. E. coli Type I Pili – adhere to epithelial cell receptors, bind to D-mannose
ii. E.coli P Pili – attach to P blood group antigen, causing UTI, bind to galactose
B. Fimbriae
a. shorter “hairlike” structures extending from bacterial cell surface
b. S. pyogenes fimbriae
i. Lipoteichoic Acid & Protein F – adhere to buccal epithelial cells
ii. M protein – antiphagocytic molecule
C. Glycocalyx
a. mediates strong adherence to surface of human cells
D. Curli
a. surface proteins that mediate binding to endothelium & fibronectin

VII. ENZYMES IN BACTERIAL INVASION

A. Collagenase & Hyaluronidase
a. promotes spread of infection through tissue
b. collagenase degrades collagen
c. hyaluronidase hydrolyzes hyaluronic acid of connective tissue ground substance
i. also known as spreading factor, allows development of cellulitis from a furuncle
B. Coagulase
a. coagulate plasma, formation of fibrin walls around S. aureus infections
b. help in persistence in tissues as well as protect from phagocytosis
C. Fibrinolysin (Streptokinase)
a. produced by hemolytic streptococci
b. activates plasminogen to plasmin → dissolve coagulated plasma → allow spread to tissues
D. Cytolysin
a. produced by bacteria which act on blood cells
b. Hemolysins – dissolve RBC
i. Streptolysin O oxygen labile antigenic
ii. Streptolysin S oxygen stable non-antigenic
c. Leucocidins – kill neutrophilic leukocytes & macrophages
i. Panton-Valentine Leucocidin
E. Streptolysin – formed by GABHS
F. IgA1 Proteases
a. splits IgA1 at PRO-THR or PRO-SER bonds → inactivation of antibody activity
b. found in N. gonorrheae, N. meningitidis, H. influenzae, S. pneumoniae

VIII. ANTIPHAGOCYTIC FACTORS

A. Capsule – protects against phagocytosis
B. Cell Wall Proteins
a. antiphagocytic M protein of S. pyogenes
b. Protein A of S. aureus – binds Fc portion of IgG
C. antiphagocytic pili - N. gonorrhoeae
D. soluble factors that inhibit chemotaxis of WBC – Bordetella

NOTES BY LACABA, Justine Val Jade B.

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IX. EXOTOXINS
A. proteins or peptides excreted by living bacteria
B. can be excreted by BOTH gram positive and gram negative bacteria
C. there are several types of exotoxins (See Table 2.5):
a. Neurotoxins – acts on nerves or motor end plates, causing paralysis
b. Enterotoxins – act on the GI tract, causing infectious diarrhea or food poisoning
c. Pyrogenic Exotoxins – stimulate release of cytokines, causing rash, fever, and toxic shock
d. Tissue Invasive Exotoxins – allow bacteria to destroy tissue and spread
e. Miscellaneous Toxins – cause disease unique to the individual bacterium
D. A-B subunit structure
a. some exotoxins have 2 subunits bonded together by disulfide bridges
i. found in exotoxins of B. anthracis, C. botulinum, C. diphtheriae, V. cholerae, etc.
b. B subunit – binds to target cell (H aka heavy for tetanospasmin)
c. A subunit – enters the cell and exerts toxic effect (L aka light for tetanospasmin)

TABLE 2.5 Important Exotoxins and their Mechanisms of Action (combined form MRS and BRS tables)
Organism Toxin Gene Mechanism Biological Effect Results
NEUROTOXINS
Clostridium tetani Tetanospasmin plasmid 1. H (heavy) subunit: binds to neuronal Inhibits inhibitory Tetanus: continuous
gangliosides neurotransmitter release motor neuron activity,
2. L (light) subunit: block release of GABA lockjaw, tetanic paralysis
from inhibitory interneurons of respiratory muscles
Clostridium botulinum Botulinum Toxin phage 1. inhibit Ach release from motor neurons at Inhibits acetylcholine Botulism: flaccid
the NMJ release paralysis
ENTEROTOXINS – Infectious Diarrhea
Vibrio cholerae Choleragen chromosome 1. Five B subunits: binds to GM1 ganglioside Increase cAMP synthesis Cholera: osmotic watery
on intestinal cell membrane Enhance Cl excretion diarrhea with
2. Two A subunits: ADP-ribosylation of GTP- Inhibit Na reabsorption dehydration
binding protein, ↑cAMP
1. E. coli E. coli heat labile toxin (LT) plasmid similar to choleragen osmotic watery diarrhea
2. Campylobacter jejuni *structurally similar to choleragen
3. Bacillus cereus
1. E. coli E. coli heat stable toxin (ST) plasmid 1. binds receptor in intestinal brush border Increase cGMP synthesis osmotic watery diarrhea
2. Y. enterocolitica 2. activates guanylate cyclase forming cGMP Inhibition of NaCl
reabsorption
1. Shigella dysenteriae 1. Shiga Toxin 1. plasmid 1. Five B subunits: bind intestinal epithelium Inhibition of protein Bloody diarrhea, HUS
2. EHEC 2. Shiga-like Toxin (Vero Toxin) 2. chromosome 2. A subunit: inhibit protein synthesis by synthesis
3. EIEC or phage inactivation of 60S
3. kills epithelial cells, sloughing off
ENTEROTOXINS – Bacterial Food Poisoning
Staphylococcus aureus Staphylococcal heat stable toxin phage Release of cytokines Superantigen* Diarrhea & vomiting that
Aka Staphylococcus enterotoxin lasts <24 hours
Bacillus cereus Heat stable toxin 1. vomiting <24 hours
2. limited diarrhea
PYROGENIC TOXINS
Streptococcus pyogenes Streptococcus pyrogenic toxin phage Activate endogenous mediators of sepsis eg Superantigen* Scarlet fever
Group A Streptococci Aka Erythrogenic Toxin IL1
Staphylococcus aureus Toxic Shock Syndrome Toxin-1 chromosome Activate endogenous mediators of sepsis eg Superantigen* Toxic Shock Syndrome:
IL1 fever, rash, diarrhea,
desquamation, hypoTN
TISSUE INVASIVE TOXINS
Streptococcus pyogenes 1. Hemolysin/Streptolysin O & S 1. Lyse RBC Abscess, skin infections
2. Streptokinase 2. activate plasminogen, lyse fibrin clots Systemic infections
3. DNAases 3. hydrolyzes DNA
4. Hyaluronifase 4. breaks down proteoglycans
5. NADase 5. hydrolyzes NAD
Staphylococcus aureus Many of the above and: Abscess, skin infections
1. Lipases 1. hydrolyze lipids Systemic infections
2. Penicillinase 2. destroy penicillin
3. Staphylokinase 3. activate plasminogen, lyse fibrin clots
4. Panton-Valentine Leucocidin 4. lyses WBC
5. Exfoliatin 5. epithelial cell lysis 5. Staphylococcal Scalded
6. Factors that bind complement 6. cripples host complement defense Skin Syndrome (infants)
Clostridium perfringens alpha Toxin chromosome & Lecithinase activity: hydrolyze lecithin in cell Gas gangrene
*More than 12 lethal toxins named by plasmid membranes, causing cell death
Greek letters, α is the most lethal and
important
MISCELLANEOUS TOXINS
Bacillus Anthracis Anthrax Toxin has 3 components plasmid 1. PA (B subunit): binds and allows entry of Increase cAMP synthesis Anthrax
1. Protective Antigen (PA) EF into the cell
2. Edema Factor (EF) 2. EF (A subunit): calmodulin-dependent AC
3. Lethal Factor (LF) ↑cAMP, impair neutrophil function, cause
massive edema
3. LF: Zn metalloprotease that inactivates
protein kinase, stimulate M1 to release TNF
& IL-1β
C. diphtheriae Diphtheria Toxin phage 1. B subunit: binds to heart and neural tissue Inhibition of protein Diphtheria: myocarditis,
2. A subunit: ADP-ribosylates EF2, inhibiting synthesis peripheral nerve palsies,
translation of mRNA into proteins CNS effects
Bordetella pertussis Four Toxins: 1. chromosome 1. Pertussis Toxin 1. Increase cAMP Whooping cough
1. Pertussis Toxin ○ B subunit: binds to target cells synthesis
2. Extracytoplasmic adenylate cyclase ○ A subunit: activate Gs proteins ↑cAMP
3. Filamentous hemagglutinin 2. similar to EF, impair chemotaxis &
4. Tracheal cytotoxin phagocytosis
3. allow binding to ciliated epithelial cells
4. damages respiratory epithelial cells

Clostridium difficile 1. Toxin A 1. fluid secretion, mucosal inflammation, Pseudomembranous

2. Toxin B leading to diarrhea colitis
2. cytotoxic to colonic epithelial cells
P. aeruginosa Pseudomonas Exotoxin A chromosome ADP-ribosylates EF2, inhibiting translation Inhibition of protein
of mRNA into proteins (same as diphtheria) synthesis

NOTES BY LACABA, Justine Val Jade B.

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IX. ENDOTOXIN
A. lipopolysaccharides located in the outer membrane of gram negative bacteria DON’T FORGET! gram positive bacteria have
B. only found in gram negative bacteria NO endotoxin except Listeria monocytogenes
a. all gram positive bacteria have no endotoxin except Listeria monocytogenes
C. Lipid A
a. most toxic component of LPS
b. has the following effects:
i. induce overproduction of cytokines such as TND and IL-1
ii. activates complement cascade
iii. activates coagulation cascade, resulting in DIC
D. endotoxins differ from exotoxins (see Table 2.6)

TABLE 2.6 Endotoxin vs Exotoxin

Exotoxin Endotoxin
Source Gram positive & Gram negative Gram negative & Listeria
Secreted from cell? Yes No
Chemistry polypeptide Lipopolysaccharide
Location of Genes chromosome, plasmid, phage Chromosome only
Toxicity High Low
Antigenicity High Low
Vaccines Toxoids used as vaccines No vaccine available DON’T FORGET! all exotoxins are heat labile
Heat Stability Destroyed rapidly at 60°C Stable at 100°C for 1 hour except Staphylococcal enterotoxin
Typical Diseases Tetanus, Botulism Meningococcemia

X. BIOFILM FORMATION
A. aggregate of interactive bacteria attached to solid surface or to each other
B. encased in an exopolysaccharide matrix
a. provide protection from host immune mechanism
b. also functions as diffusion barrier for some antimicrobials
C. important in human infections that are persistent and difficult to treat
a. S. epidermidis and S. aureus infections
i. central venous catheters, eye infections with intraocular lenses, prosthetic joint infections
c. P. aeruginosa in cystic fibrosis patients

DIAGNOSTIC BACTERIOLOGY

I. MICORBIOLOGIC EXAMINATION
A. Microbial Culture
B. Microbial Identification
a. bacterial microscopy: colony and cellular morphology
b. culture: growth characteristics under various conditions (utilization of susbtrates)
c. biochemical tests: enzymatic activity
d. immunologic testing: serotyping, serogroups, serovars
e. genetic probes
C. Serodiagnosis
f. high or rising titers of specific IgG antibodies
g. presence of specific IgM antibodies may suggest or confirm diagnosis
D. Antimicrobial Susceptibility
h. in vitro testing to susceptibility to antimicrobuals

II. STAINING
A. stains combine chemically with bacterial protoplasm, staining kills the cell
B. Acids vs Basic Staining
a. Basic Staining – colored cations + colorless anion → stains bacteria uniformly
b. Acid Staining – colored anion + colorless cation → stains background, not the bacteria
B. There are several types of staining (see Table 2.7)

TABLE 2.7 Types of Staining

Staining Stain Description
Gram Staining Crystal Violet, Safranin Red counterstain affinity for peptidoglycan cell wall
Acid Fast Staining Carbolfuchsin, Methylene Blue/Malachite Green counterstain AFB is red, the rest are blue/green
Negative Staining Nigrosin stains background with acidic cye
Flagella Staining Tannic Acid, Basic Fuchsin ↑diameter of flagella due to stain
Capsule Staining Negative staining with Crystal Violet cell is blue, capsule is paler blue
Nucleoid Staining Feulgen Stain Feulgen is DNA specific
Spore Staining Malachite Green, Carbolfuchsin

NOTES BY LACABA, Justine Val Jade B.

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III. MICROBIAL CULTURE

A. Cultivation is the propagation of microbes in media conducive to their growth
B. Culture Medium
a. nutritive substance in which cultures of microorganisms are grown
b. may be a gel or liquid medium
c. THREE situations in choice of technique and type of medium
i. Growing cells of given species – reproduce organism’s natural environment
ii. Examination of natural materials – plating under different sets of conditions
iii. Isolation of particular organism
1. Enrichment Medium – duplicate niche of desired microorganism
2. Differential Medium – cause particular colonies to have distinctive appearance
d. Specialized Media for Bacterial Growth (see Table 2.8)
C. Isolation of Microorganisms in Pure Culture
a. Plating
i. cells are immobilized in a gel medium such as agar to form isolated colonies
ii. Methods of Plating
1. Pour-Plate Method – suspension of cells is mixed with melted agar at 50°C
2. Streak-Plate Method – suspension of cells is streaked on agar with a wire loop
b. Dilution
i. serial dilution of cell suspension, each dilution are plated

TABLE 2.8 Specialized Media for Bacterial Growth

Bacteria Agar Bacteria Agar
Gram Positive Cocci Pseudomonads
Staphylococci Mannitol Salt P. aeruginosa Cetrimide
Group D Strep Bile esculin Respiratory Gram Negative Bacilli
Gram Positive Bacilli H. influenzae Chocolate + Factors X and V
C. perfringens B. pertussis B. pertussis Bordet-Gengou
C. diphtheriae L. pneumophilia L. pneumophilia Charcoal-yeast extract
Gram Negative Cocci Mycobacteria & Mycoplasma
N. gonorrhoeae Chocolate, Thayer-Martin M. tuberculosis Lowenstein Jensen
N. meningitidis Chocolate M. pneumoniae Eaton
Enterobacteriaceae (Gram Negative Rods) Spirochetes
Salmonella Xylose-Lysine-Deoxycholate (XLD) B. burgdorferi Barbour-Stoenner-Kelly (BSK)
Shigella Xylose-Lysine-Deoxycholate (XLD) L. interrogans EMJH/Fletcher’s Medium
Curved Gram Negative Bacilli *EMJH: Ellighausen-McCullough-Johnson-Harris
V. cholerae Thiosulfate Citrate Bile Salt (TCBS)
Campylobacter Skirrows
Helicobacter Skirrows

IV. MOLECULAR TESTS

A. highly specific, quite sensitive, much faster than culture
B. Techniques of Molecular Testing
a. nucleic acid amplification tests (NAATs)
b. nucleic acid probes
c. nucleic acid sequence analysis
C. used for bacteria that are difficult to culture
a. NAATs for N. gonorrhoeae and C. trachomatis
b. Gene Xpert MTB Rif for M. tuberculosis

NOTES BY LACABA, Justine Val Jade B.

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BASICS OF VIROLOGY 03

VIRAL STRUCTURE

I. BASIC PRINCIPLES
A. acellular infectious agents that are obligate intracellular parasites
B. has a size ranging from 20-300nm
C. Basic Structure
a. the complete virus particle is called a virion
b. viruses have nucleocapsids consisting of nucleic acid encased in a protein coat (capsid)
c. some may carry structural proteins and enzymes inside the capsid
d. may or may not have envelope (enveloped vs naked)
e. peplomers are glycoproteins that protrude outward on the surface of envelopes

II. CAPSIDS & VIRAL SYMMETRY

A. Capsid
a. protein coat encloses and stabilizes nucleic acids
b. consists of repeating capsomeres which represent clusters of polypeptides
c. capsomeres is an aggregation of protomers which are the basic building blocks of the coat
B. Types of Capsid Symmetry
a. Icosahedral (Spherical or Cubic) Symmetry
i. icosahedron with 20 faces of equilateral triangles and 12 vertices
ii. often consist of multiples of 60 structural units (protomers)
iii. all DNA viruses are icosahedral except poxvirus
b. Helical Symmetry
i. protein subunits are bound to nucleic acid in a periodic way, winding into a helix NOTE! Empty (Defective) Particles
ii. only RNA viruses have helical symmetry ○ capsid protein that do not contain genome
iii. most RNA viruses are helical except for the following which are icosahedral ○ only occur in icosahedral viruses because
1. Flaviviruses they are capable of self-assembly
2. Caliciviruses ○ never occurs in helical viruses because
protomers assemble only in presence of
3. Reoviruses genome (RNA)
4. Picornaviruses
5. Togaviruses
6. Hepevirus DON’T FORGET! all DNA viruses are
c. Complex Structures icosahedral except poxvirus which is complex
i. some virus particles do not exhibit simple cubic or helical symmetry DON’T FORGET! all helical viruses are RNA
ii. Poxviruses are brick-shaped with ridges on external surface & core with lateral bodies viruses

III. VIRAL PROTEINS

A. surface proteins – attachment to host cell receptors
B. DNA or RNA polymerases
C. matrix protein – proteins in matrix that mediate interaction between nucleocapsid & envelope
D. antigenic (serotypic variants) – evasion of host defenses

IV. VIRAL ENVELOPE

A. phospholipid bilayer that surrounds some viruses
i. the space between the nucleocapsid & envelope is called matrix or tegmentum
B. viruses can either be naked or enveloped
i. icosahedral viruses can either be naked or enveloped
DON’T FORGET! all helical viruses are
ii. all helical viruses are enveloped enveloped
C. acquired during vital maturation via budding through a cellular membrane
i. except herpes virus which obtains its envelope from the nuclear membrane
D. enveloped viruses are less stable and more easily inactivated
i. this is because ether & detergents destroys phospholipids
ii. meanwhile, naked viruses do not require an envelope and are thus more stable

TABLE 3.1 Naked DNA and RNA Viruses

NAKED DNA VIRUS NAKED RNA VIRUS MNEMONIC! Give PAPP smears and CPR to a
Papillomavirus Calicivirus naked hippie (hepevirus) – notice the first
Adenovirus Picornavirus letters of the ones on the table
Parvovirus Reovirus
Polyomavirus Hepevirus

NOTES BY LACABA, Justine Val Jade B.

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VIRAL GENETICS

I. VIRAL GENOME
A. all viruses are haploid except for retroviruses
B. genome consists of either RNA or DNA but never both MNEMONIC! BOAR are segmented viruses:
i. genomes can either be double stranded or single stranded Bunya, Orthomyxo, Arena, Reo
ii. RNA can either be positive sense or negative sense
C. contains genes necessary for replication but requires host to complete replication
D. Segmented Genome
i. genome occurs in multiple segments, each unique and all comprise the whole genome
ii. occurs in Bunyavirus, Orthomyxovirus, Arenavirus, Reovirus

II. OVERVIEW OF VIRAL REPLICATION

1. virus attaches to susceptible cells by interacting with specific molecules
2. penetration of the membrane via two ways:
a. chemokine receptors to induce membrane fusion
b. receptor mediated endocytosis
3. uncoating of the virus inside the cell, liberating nucleic acids & enzymes into cytosol
4. early transcription & translation lead to polypeptide synthesis using cell’s machinery
5. DNA synthesis, late transcription & translation produce molecules for progeny virions
6. condensation of macromolecules in cytoplasm lead to assembly of virions
7. virus exit cells via two ways:
a. cell lysis – liberation of progeny virus (usually by NAKED virus)
b. budding – nucleocapsid push through membrane, taking part of it (ENVELOPED virus)

III. VIRAL GENOME REPLICATION ACCORDING TO TYPE OF GENOME

A. Replication of DNA Virus
1. Viral DNA enters the nucleus
2. In the nucleus, it produces DNA via replication and (+) mRNA via transcription
a. mRNA exits to the cytoplasm where it undergoes transcription forming proteins
b. DNA also exits to the cytoplasm
3. In the cytoplasm, DNA and viral proteins assemble to form virion
B. Replication of Positive Sense RNA Virus
1. (+) Sense RNA enters the cytoplasm
2. In the cytoplasm, it produces:
a. viral proteins – because (+) RNA itself can act as mRNA for viral protein synthesis
b. (-) Sense RNA – produced in order to become template for more (+) RNA synthesis
3. still in the cytoplasm, (+) Sense RNA and viral proteins assemble to form virion
C. Replication of Negative Sense RNA Virus
1. (-) Sense RNA enters the cytoplasm
2. In the cytoplasm, it produces (+) RNA first via its own RNA-dependent polymerase
a. viral proteins – synthesized from the (+) RNA produced
b. (-) Sense RNA – synthesized from the (+) RNA produced
3. still in the cytoplasm, (-) Sense RNA and viral proteins assemble to form virion
D. Replication of Retrovirus NOTE! Hepatitis B is a DNA virus with reverse
1. RNA enters the cytoplasm transcriptase and the mRNA produced would serve
as a template for DNA synthesis via reverse
2. in the cytoplasm, it produces DNA first via reverse transcriptase, subsequently producing: transcription (progeny DNA is not derived from DNA
a. viral proteins – translated from mRNA derived from transcription of the DNA replication unlike for other DNA viruses)
b. RNA – produced using the mRNA as the template
3. still in the cytoplasm, RNA and viral proteins assemble to form virion

VIRAL CHARACTERISTICS

I. DNA VIRUSES
A. Characteristics & Exceptions
a. all have LINEAR DNA except Parvoviridae, Hepadnaviridae & Polyomaviridae
b. all are dsDNA except Parvoviridae (ssDNA)
c. all are NAKED viruses except Herpesviridae, Hepadnaviridae, and Poxviridae
d. all are ICOSAHEDRAL except Poxviridae (complex virus)
e. all replicate in the nucleus except Poxviridae (replicates in the cytoplasm)
B. Notable DNA Viruses
a. Poxvirus are the LARGEST DNA virus
b. Parvovirus are the SMALLEST DNA virus

NOTES BY LACABA, Justine Val Jade B.

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II. RNA VIRUSES

A. Characteristics & Exceptions
a. all are ssRNA except Reovirus and Rotavirus (dsRNA)
b. all are ENVELOPED viruses except Caliciviridae, Picornaviridae, Reoviridae & Hepeviridae
c. all are HELICAL except
1. Flaviviruses 4. Picornaviruses
2. Caliciviruses 5. Togaviruses
3. Reoviruses 6. Hepevirus
d. all replicate in cytoplasm except Orthomyxoviridae & Retroviridae
B. Notable RNA Viruses
a. Paramyxoviridae are the LARGEST DNA virus
b. Picornaviridae are the SMALLEST DNA virus

VIRAL PATHOGENESIS

I. PRINCIPLES OF VIRAL DISEASES

A. Viral Disease is a harmful abnormality resulting from viral infection of host
a. Clinical disease consists of overt signs and symptoms
b. Syndrome is a specific group of signs and symptoms
B. Important principles that pertain to viral disease
a. many viral infections are subclinical
b. the same disease syndrome may be produced by a variety of viruses
c. the same virus may produce a variety of diseases
d. outcome in any particular case is determined by viral & host factors
C. Viral Pathogenesis is a process that occurs when a virus infects a cell & causes cellular changes
a. disease pathogenesis – subset of events during an infection that cause disease manifestation
b. pathogenic – if a virus can infect and cause signs and symptoms
c. virulent – more virulent if it commonly produces more severe disease in susceptible host
D. Important Features of two general categories of acute viral diseases (see Table 3.2)

II. STEPS IN VIRAL PATHOGENESIS

A. Entry and Primary Replication
a. viruses attach and enter cells of one of the body surfaces
b. some can be introduced directly into tissues or bloodstream through wounds, needles
c. after entry, virus replicates to produce new virion (primary replication)
B. Viral Spread and Cell Tropism
a. some viruses produce disease at portal of entry
b. other spread via bloodstream (viremia) or lymphatics
c. virus may be free in plasma or exhibit organ and cell-type specificity (viral tropism)
i. tropism usually reflect presence of specific cell surface receptors (see Table 3.3)
C. Cell injury and Clinical Illness
a. destruction of virus-infected cells in target tissues & physiologic alterations
b. general symptoms may result from host response such as cytokine production
D. Recovery from Infection
a. host either succumb, recover, or establish chronic infections
b. Outcomes of Viral Infections
i. Death – viral infection takes over, producing virion replication and cell lysis
ii. Cytopathic Effect – visual or functional change in infected cells
iii. Commensal Symbiosis – infected cells appear normal, but produce large number of virus
iv. Transformation – activation or introduction of oncogenes leading to cancer
c. Persistent Viral Infections
i. Carrier State – produce virus for long periods of time, source of infection
ii. Latent Infection – virus survive but not produce infection, may reactivate
iii. Chronic Slow Infection – may cause disease only after many years (indolent)
E. Virus Shedding
a. occurs from body surface involve in entry
b. occurs at different stages of disease depending on particular agent involved
c. infected individual is infectious to contacts

TABLE 3.3 Receptors Used by Viruses

Virus Receptor
CMV Integrins (heparan sulfate)
EBV CD21
HIV CD4, CXCR4, CCR5
Parvovirus B19 P antigen on RBCs
Rabies Nicotinic Ach Receptors
Rhinovirus ICAM-1

NOTES BY LACABA, Justine Val Jade B.

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III. ROLE OF VIRAL GENETICS

A. mutations can produce antigenic, drug-resistant, or attenuated variants
B. Genomic Reassortment causes epidemics
i. Antigenic Drift – minor changes caused by point mutations (only in Influenza A)
ii. Antigenic Shift – drastic changes caused by genetic reassortment (Influenza A, B, C)
C. Complementation
i. one virus produces protein that can be used by another virus
ii. example: Hepatitis D superinfection or co-infection to Hepatitis B
D. Phenotypic Mixing
i. two different viruses infect the same cell

IV. VIRULENCE FACTORS

A. Cytokine Decoys – bind cytokines & block ability to interact with intender targets
B. Virokines – reduce expression of antigen presenting cells, inactivate component
C. Antigenic variants of surface proteins

V. VIRAL VACCINES
A. utilize adaptive immune response of host to prevent viral disease
B. the most cost-effective method of prevention of serious viral infections
C. Types of Viral Vaccines
a. Killed-Virus Vaccines
i. prepared from inactivated viruses with minimal damage to viral structural proteins
ii. induce humoral & cell-mediated immunity
ii. Advantage: no reversion to virulence
iii. Disadvantage: require boosting shots to maintain effectiveness
b. Live Attenuated Vaccines
i. use of restricted virus mutants that has antigenic overlap with wild types
ii. induce only humoral immunity
ii. Advantage: acts more like natural infection
iii. Disadvantage: risk of reversion to greater virulence, infects immunocompromised

DIAGNOSTIC VIROLOGY

I. PRESUMPTIVE IDENTIFICATION
A. Cytopathic effect – visual changes in infected cells
B. Hemadsorption – attachment of RBCs to surface of infected cells
C. Interference – interference with CPE by another virus
D. Decrease in acid production by infected, dying cells (using phenol red)

II. DEFINITIVE DIAGNOSIS

A. Complement Fixation D. Fluorescent antibody assay
B. Hemagglutination inhibition E. Radioimmunoassay
C. Neutralization F. ELISA

III. SEROLOGIC TESTS

A. Seroconversion: finding antibody in one who previously had none
a. Presence of IgM – can be used to diagnose current infection
b. Presence of IgG – cannot be used to diagnose current infection, may be due to past infection

IV. DETECTION OF VIRAL ANTIGENS

A. presence of viral proteins is commonly used in diagnosis
a. examples: p23 of HIV, HbSAg of Hepatitis B
B. presence of viral DNA or RNA is the gold standard in viral diagnosis

NOTES BY LACABA, Justine Val Jade B.

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BASICS OF MYCOLOGY 04

FUNGAL STRUCTURE & FUNCTION

I. BASIC PRINCPLES
A. General Characteristics
a. aerobic eukaryotes with true nucleus
i. most are obligate or facultative aerobes; none are obligate anaerobes
b. filamentous branched somatic structures surrounded by a true cell wall
B. has two types: yeast and molds (see below)
C. has no chlorophylls, require preformed organic compounds from their environment
a. Saprobes – live on dead organic material, some are opportunistic
b. Commensal colonizers – live in harmony, derive compounds from body surface
c. Pathogens – infect healthy, damage living cells for nutrition

II. FUNGAL CELL MEMBRANE & CELL WALL

A. Fungal Cell Wall
a. consists primarily of chitin (not proteoglycan as in bacteria)
i. chitin is a polysaccharide of N-acetylglucosamine and β-glucan
iI. β-glucan is the site of action of capsofungin
b. protect cells from osmotic shock, determine cell shape, and have antigenic components
B. Fungal Cell Membrane
a. contains ergosterol as its sterol component
i. humans have cholesterol, bacteria do not have sterols at all
b. ergosterol is the site of action of polyene and azole antifungals

III. FORMS OF FUNGI: YEAST & MOLD

A. Yeasts
a. grow as single cells
b. reproduce by asexual budding (blastoconidia)
B. Molds
a. grow as long filaments of (hyphae) and form a mat (mycelium)
b. hyphae grows by extension of tip of hypha (apical growth)
C. Thermally Dimorphic Fungi
a. forms different structures at different temperatures MNEMONIC! Mold in the cold, Yeast in the
heat!
b. exist as filament molds in environment and yeasts in human tissues at body temperature
i. includes: Blastomyces, Histoplasma, Coccidioides, Paracoccidioides and Sporothrix NOTE! Candida is dimorphic but is yeast in
the cold (20°) and mycelial in the heat (37°C)
III. HYPHAE & MYECLIA
A. Hyphae are filamentous cells of molds and mushrooms
a. hyphae are either septate or non-septate
i. Septate Hyphae
1. have septations or cross walls at regular intervals
2. septa determines flow of fluids along the fungus
3. more evolved than non-septate; in ascomycetes, basidiomycetes, deutreromycetes
ii. Non-septate Hyphae
1. lacks transverse walls that divide the hyphae, multinucleated coenocytic
2. nuclear material are allowed to flow uninterruptedly throughout the filament
3. more primitive than septate, found in phycomycetes
b. hyphae can either by hyaline or dematiaceous
i. Hyaline Hyphae – colorless under the microscope
ii. Dematiaceous Hyphae – dark colored under the microscope
B. Pseudohyphae
a. hyphae with sausage-like constrictions at septations
b. formed by yeasts when they elongate but remain attached to each other
c. C. albicans has mycelial form at 37°C and produce pseudohyphae at 20°C
C. Mycelia are fluffy surface masses of hyphae
a. Aerial Mycelium – portion above the surface of medium
i. Reproductive Mycelium – portion of aerical mycelium that develop reproductive spores
b. Vegetative Mycelium – portion that grows into the substrate, absorbs food for growth

NOTES BY LACABA, Justine Val Jade B.

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FUNGAL REPRODUCTION

I. BASIC PRINCPLES
A. fungal spores are formed either asexually or by an asexual process
a. conidia are asexual spores of filamentous fungi (molds) or mushroom
b. sexual process involves nuclear fusion with subsequent meiosis
B. reproduction differs according to fungal classifications
a. ascomycetes and basidiomycetes belong under dikarya
i. life cycle has 3 main stages: haploid, dikaryonic, and diploid
ii. sexual reproduction involves plasmogamy, karyogamy, meiosis ± mitosis → form spores
1. sexual spores are made from diploid forms
iii. asexual reproduction involves only mitosis of haploids → form conidia
1. asexual spores are made from haploid forms

II. SEXUAL SPORES

A. Zygospores – single large spores with thick walls
B. Ascospores – formed in a sac called ascus
C. Basidiospores – formed on tip of pedestals called basidium

III. ASEXUAL SPORES (CONIDIA)

A. Conidiospores
a. formed on specialized hypha, freed by abstrictions
B. Sporangiospores
a. Sporangioconidia
i. formed on specialized hypha in round containers on a stalk called sporangium
ii. exhibited by Rhizopus and Mucor
1. in Rhizopus, when 2 hyphae mates, zygospore is formed
2. zygospores undergo meiosis froming haploid sporangium
C. Thallospores – spores that are NOT formed on a conidiophore
a. Arthroconidia
i. arise from fragmentation of ends of hyphae
ii. exhibited by Coccidioides immitis
b. Blastoconidia
i. round spores formed by budding process of yeasts
1. one cell to one spore basis in Blastomyces dermatitidis
2. multispore basis in Paracoccidioides barzliensis
ii. pseudohyphae: buds don’t detach, form sausage chains instead
1. exhibited by Candida albicans (forms when yeast are exposed to 20°C)
c. Chlamydoconidia
i. rounded, thick-walled, resistant structures in hyphae
ii. nutrients shunted from adjacent cells to one cell
iii. exhibited by Candida albicans (diagnostic terminal chlamydospores)

TABLE 4.1 Morphologic Classification of Conidia

Classification Description
Conidia According to Size
Microconidia small and single celled, requires a microscope
Macroconidia large, multicellular, divided either/both transverse & longitudinal wall
Conidia According to Shape
Fusiform spindle-shaped
Clavate club-shaped
Muriform
Conidia According to Arrangement
Sessile and Lateral develop directly on the side of the hypha, no conidiophore or stem
En Grappe clustered
Pedunculated develop from the end of a short conidiophore

FUNGAL CLASSIFICATION

I. PSEUDOMYCETES
A. false fungi that actually are bacteria that form filamentous structures
B. Schizomycetes
a. produce diseases clinically similar to fungal disease like madura foot & lumpy jaw
b. belong to actinomycetes
C. Myxomycetes
a. nonpathogenic slime molds

II. EUMYCETES
A. Non-septate Fungi
a. Phycomycetes
i. sexual spores: zygospores (related to Zygomycota, also non-septate)
ii. asexual spores: chlamydospores (except Rhizopus which make sporangiospores)
b. Zygomycetes

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B. Septate Fungi (Eumycota)

a. Ascomycetes
i. sexual spores: ascospores
ii. asexual spores: conidiospores
b. Basidiomycetes
i. sexual spores: basidiospores
ii. asexual spores: none
c. Deuteromycetes (Fungi Imperfecti) – cannot undergo sexual reproduction
i. sexual spores: none
ii. asexual spores: conidiospores, arthrospores, blastospores, chlamydospores

MYCOTIC PATHOGENESIS

I. BASIC PRINCIPLES
A. two types of host response: granulomatous or non-granulomatous
B. some can be detected by using skin tests for delayed hypersensitivity reaction
C. reduced cell-mediated immunity predisposes to disseminated disease
D. Fungal Disease may be due to: allergies, toxicosis, or infection

II. OVERVIEW OF FUNGAL DISEASES

A. Fungal Allergies
a. hypersensitivity to spores or volatile fungal metabolites
b. plays a role in:
i. sick building syndrome, allergies, farmer’s lung, silo worker’s disease
ii. Aspergillus fumigatus – cause IgE-mediated allergic bronchopulmonary aspergillosis
B. Mycotoxicoses
a. result from ingestion of fungal-contaminated foods; psychotropic or toxic mushrooms
b. plays a role in:
i. Aspergillus flavus – cause hepatocellular carcinoma due to aflatoxin
ii. ergot alkaloids – cause St. Anthony’s fire
iii. Psilocybe mushrooms – psychotropic
iv. Amanita mushrooms – cause liver necrosis due to amanitin and phylloidin
C. Mycoses (Fungal Infection)
a. mycoses range from superficial to overwhelming systemic infections
b. can be classified as superficial, cutaenoys, subcutaneous, and systemic (see Table 4.2)
TABLE 4.2 Classification of Mycoses
Superficial Cutaneous Subcutaneous Systemic Opportunistic
Tinea versicolor Dermatophytes Sporotrichosis Blastomycosis Candidiasis
Tinea nigra Lobomycosis Paracoccidioidomycosis Cryptococcosis
Black Peidra Rhinoentomorphomycosis Coccidioidomycosis Aspergillosis
White Piedra Rhinosporidiosis Histoplasmosis Mucormycosis
Maduromycosis Penicilliosis
Chromoblastomycosis Pneumocystis
Phaeohyphomycosis

DIAGNOSTIC MYCOLOGY

I. DIRECT MICROSCOPIC EXAMINATION

A. uses specimens such as sputum, lung biopsy, skin scrapings
B. depends on findings of characteristic asexual spores, hyphae, or yeast
C. Rapid Microscopic Methods
a. KOH Mount – use skin scapings, enhance visibility of unaffected fungus
b. India Ink Mount – insensitive; nigrosin stain of CSF highlights the capsule of Cryptococcus
c. Giemsa or Wright’s Stain – use thick blood/bone marrow, detect intracellular Histoplasma
d. Calcofluor White Stain – gives fungus fluorescent white appearance on black background
D. Histologic Staining – special stains for those not seen in H&E stain
a. Gomori Methenamine-Silver Stain – fungi are dark gray to black
b. Periodic Acid-Schidd (PAS) Stain – fungi are hot pink to red
c. Gridley Fungus Stain – fungi are purplish rose with yellow background
d. Calcofluor White Stain – same as above
e. Immunofluorescent Stain – available to some gunfal pathogens

II. FUNGAL CULTURE

A. use of special media: enriched media with antibiotics
B. Saboraud’s Dextrose Agar
a. facilitates appearance of slow-growing fungi by inhibit growth of bacteria
b. inhibition of bacterial growth by low pH, penicillin, streptomycin, and cyclohexidine

NOTES BY LACABA, Justine Val Jade B.

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III. TESTS FOR NUCLEIC ACIDS

A. includes DNA probes and nucleic acid amplification tests (NAATs)

IV. SEROLOGIC TESTS

A. Fungal Antigen Detection
a. uses known antibodies to identify circulating fungal antigens in serum. CSF. Or urine
b. available for Histoplasma and Cryptococcus
B. Antibody Detection
a. generally requires acute and convalescent sera
b. complicated by cross-reactivity among pathogenic fungi or inability to produce antibody

NOTES BY LACABA, Justine Val Jade B.

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BASICS OF PARASITOLOGY 05

CHARACTERISTICS OF PARASITES & THEIR HOSTS

I. PARASITES
A. a symbiotic relationship where one animal lives in expense of another animal, the host
B. General Types of Parasites
a. Host Relationship
i. Facultative – can survive outside host, may exist in free-living state
ii. Obligate – can only survive in the host
b. Location
i. Endoparasite – within the host, result in infection
ii. Ectoparasite – outside the host, result in infestation
c. Life Cycle
i. Simple – only has one host
ii. Complex – has ≥1 intermediate host which then transfers to definitive host
C. commensals may become parasitic when opportunity presents itself

II. HOST
A. hosts may be one of three types:
a. Intermediate Host – host in which early larval forms develop into intermediate parasite
b. Definitive Host – host in which larva; stages infect & mature into sexually mature adult
c. Reservoir Host – any host essential for parasite survival, focus for spread to other hosts
i. Essential reservoir hosts – when eradicated, may cause eradication of parasite
B. Paratenic Hosts – only carries parasite for transfer, parasite does not undergo development

III. VECTORS
A. living transmitters of disease
B. can be classified as one of the following:
a. Mechanical Vectors – nonessential to life cycle of pathogen
b. Biological Vectors – serve as site of developmental event (also intermediate hosts)

PARASITIC ARTHROPODS

I. ARTHROPODS
A. arthropods are invertebrates with chitin exoskeleton, joint appendages & segmented body
B. arthropods of medical importance (see Table 5.1)

TABLE 5.1 Arthropods of Medical Importance

Organism Sceintific Name Disease Features
Class Insecta
Lice Pediculus humanus pruritus of scalp or trunk; nits seen on hair shaft
Lice Pediculus pubis pruritus in pubic area; nits seen on hair shaft
Flies Dermatobia hominis pruritic, painful, erythematous nodule, larva may be seen emerging from nodule
Bedbugs Cimex lectularius pruritic, erythematous wheal
Class Arachnida
Mites Sarcoptes scabeii pruritic, erythematous papules, and linear tracks
Ticks Dermacentor ascending paralysis

PARASITIC PROTOZOANS

I. PROTOZOANS
A. single-celled animals, have no multicellular stages
B. has two distinctive forms:
a. Trophozoites
i. actively motile form, don’t survive outside the body
ii. rarely withstand normal stomach acid, generally non-infectious
b. Cysts
i. sturdy resting changes, can survive at least a while in the environment
ii. can withstand stomach acid, most common infective form via fecal-oral spread

II. CLASSIFICATION OF PROTOZOANS

A. Amoebas
a. move by pseudopods created by streaming protoplasm
b. includes Entamoeba, Acanthamoeba, and Naegleria

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B. Ciliates
a. move by action of cilia
b. includes only Balantidium coli which rarely cause dysentery
C. Flagellates
a. move by the action of flagella
b. Giardia and Trichomonas have trophozoites and cysts
c. Trypanosoma and Leishmania are hemoflagellates, infect blood and tissues
i. Trypomastigotes – free living, elongated, flagellated forms with undulating membrane
1. seen extracellularly in blood in Trypanosoma
ii. Amastigotes – oval cells without flagellum
2. seen in infected tissues (Trypanosoma) or macrophages (Leishmania)
D. Apicomplexa aka Coccidia
a. intracellular protozoans with complex life cycles, gliding motility & apical complex
b. includes the following:
i. Cryptosporidium, Cyclospora, Isospora, Histoplasma
ii. Plasmodium, Babesia

PARASITIC HELMINTHS

I. NEMATODES (ROUNDOWORMS) MNEMONIC! NEMA2T3ODES

N – Necator
A. also known as roundworms, includes the following (see Table 5.2) E – Enterobius
B. transmission can occur in several ways: M – Mosquito-borne Wuchereria, Brugia
a. ingestion of eggs – Enterobius, Ascaris, Trichuris, Toxocara A2 – Ascaris, Ancylostoma,
b. ingestion of larvae in undercooked meat – Trichinella (EAT3) T3 – Trichiuris, Trichinella, Toxocara
O - Onchocerca
c. direct invasion of skin by larval forms – Necator, Ancylostoma, Strognyloides D - Dracunculus
d. larval transmission via insect bite – Wuchereria, Loa, Onchocerca E – Eye worm (Loa loa)
S – Strongyloides
TABLE 5.2 Nematodes of Medical Importance
Intestinal Nematodes Filariasis Tissue Nematodes

○ Trchiuris trichiura ○ Cutaenous Larva Migrans ○ Lymphatic Filariasis ○ Dracunculus medinensis

○ Capillaria philippinensis □ Ancylostoma braziliense □ Wuchereria bancrofti ○ Angiostrongylus cantonensis
○ Trichinella spiralis □ Ancylostoma caninum □ Brugia Malayi ○ Angiostrongylus costaricensis
○ Enterobius vermicularis ○ Visceral Larva Migrans ○ Subcutaneous Filariasis
○ Ascaris lumbrcoides □ Toxocara canis □ Onchocerca volvulus
○ Strongyloides stercoralis □ Toxocara cati □ Loa loa
○ Hookworms □ Gnathostoma spinigerum
□ Ancylostoma duodenale ○ Anisaki simplex
□ Necator americanus

II. TREMATODES (FLUKES)

A. type of flatworms (Platyhelminths) informally called flukes
B. Morphology of Adult Flukes
a. usually flat, elongated, leaf-shaped worm
b. hermaphroditic, except schistosomes
c. enveloped by noncellular integument (cuticle)
d. has attachment organs
i. oral sucker – anterior portion, surrounds mouth
ii. ventral sucker – more posterior, aka acetabulum, on ventral surface
iii. genital sucker – only found in Heterophyes heterophyes
e. digestive system: muscular esophagus, 2 intestinal ceca ending blindly
f. reproductive system
i. genital pore – region of the ventral sucker
ii. 2 testes leading to genital pore, 1 ovary
iii. uterus – largest organ filled with eggs, winds to genital pore
g. vitellaria – glandular structure, produce shell material, lateral to intestinal ceca
h. vitelline ducts – inward to ovary, where shell is formed over ovum
C. Morphology of Eggs
a. smooth, hard shell, transparent, yellow-brown
b. most have operculum (escape hatch for miracidium), absent in schistosomes
c. opercular shoulders – slight flare, line of cleavage between shell and operculum
d. spines may be present
D. Life Cycle of Trematodes
a. Definitive host is usually a vertebrate
i. metacercaria is the infective stage (cercaria for schistosomes)
ii. mode of transmission is ingestion (skin penetration for schistosomes)
iii. fluke eggs land in water, develop into early larval form that infects 1st IH
b. 1st intermediate host is usually a snail
i. released from first host as cercaria
c. 2nd intermediate host may be fish, crustacean, snails, or aquatic plants
i. except schistosomes which DO NOT have a 2nd intermediate host)
ii. released from second host as metacercaria

NOTES BY LACABA, Justine Val Jade B.

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TABLE 5.3 Trematodes of Medical Importance

Blood Flukes Liver Flukes Intestinal Flukes

○ Fasciolopsis buski
○ Schistosoma haematobium ○ Clonorchis sinensis ○ Echinostoma ilocanum
○ Schistosoma mansoni ○ Opistorchis felineus ○ Heterophyes heterophyes
○ Schistosoma japonicum ○ Opistorchis viverrine
○ Schistosoma intercalatum ○ Dicrocoelium dendriticum
○ Schistosoma mekongi ○ Fasciola hepatica
Lung Flukes
○ Fasciola gigantica
○ Paragonimus westermani

III. CESTODES (TAPEWORM)

A. type of flatworms (Platyhelminths) informally called tapeworms
B. Morphology of Adult Tapeworms
a. scolex (head) – used to adhere to small intestinal mucosa
i. four muscular, cup-shaped suckers
ii. except Diphyllobothrium latum (2 slit-like pores)
b. neck – region immediately posterior to scolex
c. proglottids – body segments, form chains called strobila
i. immature: new segments, do not contain fully developed structures
ii. mature: larger, near the middle, with reproductive organs
iii. gravid: terminal portion; usually filled with eggs in uterus
d. adults are monoecious (hermaphrodites) and oviparous
e. adults have incomplete digestive system with no circulatory system
C. Morphology of Eggs
a. non-operculated (except D. latum)
b. external shell – varies in appearance
c. embryonic membranes – protective covering for oncosphere, varies in number and thickness
d. oncosphere – 6-hooked (hexacanth) embryo
D. Life Cycle of Cestodes
a. human cestodes have complex life cycles except Hymenolepis nana
b. humans as definitive host – D. latum, T. saginata, H. diminuta
i. infective stage: larva coming from intermediate host (cysticercus, cysticercoid larva)
ii. diagnostic stage: gravid proglottids, eggs
c. humans as intermediate host – E. granulosis
i. infective stage: embryonated egg
d. humans are either definitive or intermediate host – T. solium, H. nana

TABLE 5.4 Cestodes of Medical Importance

Diphyllobothriidae Taeniidae Hymenolepididae Dipylidiidae
Taenia solium
Hymenolepis nana
Diphyllobothrium latum Taenia saginata Diphylidium caninum
Hymenolepis diminuta
Echinococcus granulosus

PARASITIC PATHOGENESIS

I. EFFECTS OF PARASITE ON THE HOST

A. Interference of vital processes - most widespread type of injury
b. through actions of secretions, excretions, and other products of the parasite
i. D. latum – cause megaloblastic anemia by damage to the jejunum
ii. F. buski – toxemia
B. Invasion/Destruction
a. E. histolytica – flask-shaped ulcers
b. Malaria – RB destruction to release merozoites
c. Ascariasis – perforation of bowel mucosa
C. Immunosuppression
D. Host-like antigens & antigenic variation
E. Secretions and excretions stimulate host resistance

I. EFFECTS OF HOST ON THE PARASITE

A. Duffy blood group – negativity confer resistance to P. vivax
B. Sickle Cell Trait, Thalassemia – resistance to P. falciparum
C. high protein diet – unfavorable to amoebas
D. carbohydrate rich diet – favorable to tapeworms
E. Immunity
a. immunity to reinfection – Leishmania
b. premunition – resistance to hyperinfection in endemic areas (Plasmodia, hookworms)
c. p7assive immunity – conferred by materal Ab vs malaria, schistosomes, filaria
F. Eosinophil – kills young Schistosomes and microfilariae
G. Cytokines
a. stimulates killing of Schistosomes by eosinophils
b. cause cachexia in Trypanosomiasis

NOTES BY LACABA, Justine Val Jade B.

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III. CHARACTERISTICS OF PARASITIC DISEASE

A. symptoms are proportional to parasitic burden
a. hence, the most common manifestation of parasitic infection is ASYMPTOMATIC
b. except Fasciola hepatica – very large, invades the liver
B. reinfection
a. may come from environment
b. may come from autoinfection – observed in Strongyloides & Enterobius
C. chronic infection may occur
a. eg Chaga’s disease (megacolon, megaesophagus, dilated CM)
D. reactivation of latent infection may occur in immunocompromising conditions
a. eg Toxoplasmosis (infective only in the immunocompromised)
E. eosinophilia
a. observed when there is either tissue destruction or larval infection
b. occurs in presence of larva (eg Ascaris where there is larval lung migration to the lungs)

DIAGNOSTIC PARASITOLOGY

I. COMMON TECHNIQUES
A. Direct Wet Film (direct feal smear)
a. uses iodine solutions: Gram’s Iodine, Lugol’s iodone, modified D’Antoni’s iodine
b. used to visualize amoebal cysts (kills trophozoites)
B. Concentration Method
a. sedimentation and floatation of fecal matter
b. separate protozoan cysts and helminthic eggs
C. Permanently Stained Slides
a. used for Entamoeba histolytica
D. Serologic Tests + Stool Exam
a. E. histolytica and E. dispar – can only be differentiated through PCR
b. also used in identification of Giardia and Cryptosporidium
E. Modified Acid Fast Bacilli (AFB) Stain
a. used for cryptosporidium, Cyclospora, and isospora
i. AFB(+) smaller than RBC → Cryptosporidium
ii. AFB(+) larger than RBC → Cyclospora, Isospora

II. SPECIAL PROCEDURES FOR RECOVERY OF LARVA & OVA (see Table 5.5)

TABLE 5.5 Special Techniques in Recovery of Larva & Ova

Technique Description Identification
Baermann Apparatus strongyloides larva
Harada Mori filter paper strip procedure hookworm, strongyloides, trhcistrongylus larva; ascaris
Agar Method evaluate larval tract strongyloides (whiplike), hookworm (snake-like)
Scotch Tape Swab swab of perianal area for ova enterobius, taenia ova
Schistosomal Hatching Test for isolation of miracidia schistosoma miracidia
Entero (String) Test duodenal sample via string strongyloides, liver fluke

III. EXAMINATION OF BLOOD & OTHER TISSUES (see Table 5.6)

TABLE 5.6 Examination of Blood & Other Tissues

Technique Specimen Identification
whiplike - Microfilariae
Blood Microscopy Fresh blood
undulating & twisting - Trypanosomes
Thick & Thin Blood Smear Fresh blood Plasmodium
Concentration Methods Fresh blood Leishmania, Trypanosomes, Microfilaria
CSF Analysis CSF Naegleria
FNAB Tissue Imprints Leishmania, Toxoplasma
Spleen, Liver, BM Leishmania
Cornea Acanthamoeba
Intestine Cryptosporidium
Biopsy & Aspiration Liver E. histolytica
Rectal Mucosa Schistosoma
Muscle Trichinella
Skin Nips Onchocerca, Mansonella
Sputum Exam Sputum Entamoeba, Ascaris, Strongyloides, Paragonimus, Cryptosporidium
Urine Microsocopy Urine Trichomonas, Schistoma, Wuchereria, Brugia, Loa, Onchocerca

NOTES BY LACABA, Justine Val Jade B.

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