MICRO&PARA LEC

Profs. Fuentes & Vicencio

OUTLINE Incomplete Morphology

Cocci in chains
I BACTERIAL CELL AND ITS ULTRASTRUCTURE
II INFECTIOUS AGENTS
III STERILIZATION AND DISINFECTION
IV INFECTION AND EPIDEMIOLOGY Bacilli in singly

I. BACTERIA AND ITS ULTRASTRUCTURE

CELL TYPES Cocci in clusters

 There are two (2) types:

Eukaryotic Prokaryotic
Bigger than bacteria or Lacks:
prokaryotic cells - nuclear membrane GRAM STAIN
- nucleus  Steps follow the abbreviation VIAS
- mitochondria
- endoplasmic reticulum  For us to see an organism under a microscope, and
determine whether they are gram positive or gram
IMPORTANT MICROBIAL GROUPS negative (with the aid of a microscope), we need to
perform gram staining.
 There are five (5) groups:

Important Microbial Groups Composition Gram + Gram -

Prions Crystal Violet
 Neither a prokaryote nor a eukaryote
 Violet
Virus  Neither a prokaryote nor a eukaryote
 Primary stain
 Smallest infectious particle Gram’s Iodine
 Can either have DNA or RNA  Brown
 Cannot be seen using the ordinary  Mordant (it increases the
microscope affinity of the primary stain
Bacteria  Prokaryote or crystal violet to the cell
Fungi  Eukaryote wall of the organism)
Parasites  Eukaryote Alcohol/Acetone
 Clear
BACTERIAL MORPHOLOGY  Decolorizer
 Refers to the shape and arrangement of bacteria  The differentiating step
 Step where errors usually
Shape Arrangement occur if not washed properly
Coccus/Cocci a. Singly – coccus Safranin
(circular) b. Pair – diplococcus  Red
c. Tetrad (four)
d. Chains – e.g. streptococcus
e. Clusters – e.g. staphylococcus (causes General Rules in Gram Staining
pimples)  All cocci are Gram Positive EXCEPT:
Bacillus/ a. Single a. Neisseria
Bacilli (rod- b. Pair b. Moraxella
shaped) c. Chain c. Veilonella
Spiral/ Not specified  All bacilli are Gram Negative EXCEPT:
Spirochetes a. Mycobacterium Less common bacilli:
Pleomorphic Not specified b. Corynebacterium g. Erysipelothrix
(can alter c. Bacillus h. Listeria
their shape) d. Clostridium i. Nocaria
e. Actinomyces j. -bacterium (Bifido-,
Incomplete Morphology f. Streptomyces Propioni-, Eu-, Arcano-)
 Identify first the shape, then the arrangement of the
bacteria

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Grams’ Reaction Gram Positive Gram Negative
 This step is important because it is the first step in  Thick peptidoglycan  Thin peptidoglycan
identifying an organism.  With inner  With inner
 What is the gram reaction and shape of the following membrane membrane
basic types of bacteria?  With cytoplasm  With cytoplasm
a. Streptococcus – gram positive; cocci  Without an outer  With outer
b. Staphylococcus – gram positive; coci membrane membrane
c. Neisseria – gram negative; cocci and sometimes
appear as diplococci
d. Bacillus – gram positive; bacilli BACTERIAL ENVELOPE
 Escherichia – gram negative; bacilli  All the concentric surface layers of the bacterial cell

1. Capsule
Complete Morphology
 Slime
 Identify the gram reaction, then the shape and
arrangement of the organism.  Glycocalyx
 Bacteria enclosed in a capsule are harder to kill and
cause more dangerous illnesses
Complete Morphology
Gram positive cocci in chains  Some Killers Have Pretty Nice Capsules
a. Streptococcus pneumoniae
b. Klebsiella pneumoniae
c. Haemophilus influenzae
d. Cryptococcus neoformans
Gram negative bacilli in singly
Gram +/- Chemical Function
Composition
Both Polysaccharide gel  Pathogenicity/
Gram positive cocci in clusters Virulence
factor
 Protect
against
phagocytosis
Gram positive bacilli in chains until
opsonized
 Immunogenic

2. Outer Membrane
 “Major permeability barrier”
CELL WALL DIFFERENCE OF GRAM +/- BACTERIA Gram +/- Chemical Function
 Refer to the illustration below: Composition
Gram - Phospholipid/proteins Hydrophobic
such as: membrane:
 Lipopolysacc  LPS =
haride endotoxin
 Lipid A  Lipid A = toxic
 Polysaccharid moiety
e  PS =
immunogenic

3. Cell Wall = Peptidoglycan

 Thin in gram negative bacteria and thick in gram
positive bactera
 Found in all free living bacteria EXCEPT Mycoplasma

Gram +/- Chemical Composition

Both Peptide
 Typically 4 amino acids
 Long
 Cross-linked to other chains
Glycan
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  Made of alternating amino sugars
Sugars found in peptidoglycan
 N-acetylglucosamine (NAG)
 N-acetylmuramic acid (NAM)

Wall-less forms of Bacteria

 Altered form of plant/bacterial cell from which the cell
wall has been partially or completely removed
 Spheroplasts (+) OM
 Protoplasts

5. Cytoplasmic membrane

Gram +/- Chemical Function

Composition
Both Phospholipid bilayer  Where energy
with many embedded metabolism
proteins occurs
 Hydrophobic
cell “sack”
 Selective
permeability
4. Cell Wall (Acid fast bacteria)  Active
 All organisms are non-acid fast EXCEPT: transport
a. Cryptosporidium sp.
b. Legionella micdadei 6. Pilus Fimbria
c. Isospora sp.  Common
d. Mycobacterium (tuberculosis)
e. Nocardia sp. Gram +/- Chemical Function
Composition
Gram +/- Chemical Function Primarily Glycoprotein (pilin)  Sex
Composition Gram -  Virulence
Acid fast Mycolic acids (which  Acid fastness  Adherence to
only are responsible for the  Resistance to cell surfaces,
acid fastness of these drying and including
bacteria chemicals attachment to
other bacteria
5. Periplasmic Space during
conjugation
Gram +/- Chemical Function
Composition
Gram - Storage space  Stores
between the inner and degradative
outer membranes enzymes
which break
down large
molecules (B-
lactamases)
 Aids regulation
of osmolarity

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7. Flagellum  40s
Upon losing their
Gram +/- Chemical Function surface area, they
Composition become 80s
Both Protein (flagellin) Motility
4. Granules
8. Axial Filaments  Corynebacterium – metachromatic granules (Babes’
Ernst Granules)
Gram +/- Chemical Function  Mycobacterium – Much Granules
Composition
 Yersinia petis – Volutin Granules
Spirochet Protein Motility
es
Gram +/- Chemical Function
Composition
Both  Glycogen Storage
 Lipids
 Polyphosphat
e

5. Endospores
 Examples include:
a. Bacillus
INTERNAL BACTERIAL STRUCTURE b. Clostridium
Gram +/- Chemical Function
1. Nucleoid Region Composition
 Also called nuclear body/chromatin body/nuclear region Gram +  Keratin coat Resistance to heat,
 Calcium chemicals and
Gram +/- Chemical Function dipicolinate dehydration
Composition
Both  DNA Genetic material (all PHYSIOLOGY, GROWTH & NUTRITION
 RNA essential genes)  For an organism to grow, they have nutritional
 Proteins requirements.

2. Plasmids 1. Source of Carbon

 Non-essential genetic material  Photo- (prefix) – utilizes light
 Chemo- (prefix) – utilizes chemical reaction
Gram +/- Chemical Function
Composition A. Heterotrophs/Organotrophs
Both DNA  Conjugation  They have the ability to utilize organic compounds such
 Drug as sugar
resistance  Photoheterotrophs/organotrophs – uses light as their
 Toxin source of energy to utilize organic compounds
production  Chemoheterotrophs/organotrophs – uses chemical
reaction as their source of energy to utilize organic
3. Ribosomes compounds
 S stands for Svedberg unit
 Theodor Svedberg is a Nobel Prize winner and inventor B. Autotrophs/Lithotrophs
of the ultracentrifuge  They utilize inorganic compounds such as carbon
dioxide
Gram +/- Chemical Function  Photoautorophs/litotrophs – uses light as their source of
Composition energy to utilize inorganic compounds
Both Prokaryotes have: CHON Synthesis  Chemoautorophs/litotrophs – uses chemical reaction as
 30s (protein synthesis) their source of energy to utilize inorganic compounds
 50s
Upon losing their 2. Oxygen Requirement
surface area, they
become 70s A. Obligate Aerobes
 Organisms that require oxygen for growth
Eukaryotes have:  Examples include PNB MC
 60s a. Pseudomonas Aerginosa

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 b. Nocardia sp.  If upon timing the autoclave for 15 minutes and no color
c. Bacillus sp. change in Geobacillus Stearothermophilis sample is
d. Mycobacterium sp. observed (still purple/violet), there is no bacterial
e. Corynebacterium sp. growth. However, if it changes to yellow, there is
growth.
B. Obligate Anaerobes  Autoclave tape – indicates that the autoclave has
 Organisms that are killed by the presence of oxygen reached 121 °C
 Examples include ABC FEP:
a. Actinomyces sp.
b. Bacteroides sp.
c. Clostridium sp.
d. Fusobacterium sp.
e. Eubacterium sp.
f. Prevotella sp.  Thermus acquaticus – discovered in thermal hot springs
in Yellowstone National Park; utilized in PCR testing
C. Facultative Anaerobes
 Organisms that can grow in the presence or absence of 4. pH
oxygen
A. Acidophile
D. Microaerophiles  0-5.5 pH
 Anaerobes that require very little amount of oxygen  Acidic
 With the suffix -bacter
a. Campylobacter sp. B. Neutrophile
b. Helicobacter sp.  5.5-8 pH
 Most clinically significant bacteria grows here
E. Aerotolerant Bacteria
 Can tolerate oxygen C. Alkalinophiles
 Examples include:  8.5-11.5 pH
a. Lactobacillus sp.  Alkaline
b. Propionibacterium sp.
BACTERIAL GROWTH
2. Carbon dioxide

A. Capnophiles
 Grow under high concentration of carbon dioxide

3. Temperature

A. Psychrophiles
 0-20 °C (cold temperatures)
 Listeria monocytogenes – responsible for the disease
Listeriosis (acquired through consumption of
contaminated food)

B. Mesophiles
 20-45 °C (moderate temperatures) 1. Lag Phase
 All human pathogens are mesophiles  Population of bacteria stays the same
C. Thermophiles 2. Exponential Phase
 45-80 °C (warm temperatures)  Also called log phase
 Hyperthermophiles – thrives in extremely hot  Population of bacteria grows exponentially
environment  Phase where bacteria is best used, because they are
 Geobacillus Stearothermophilis – formerly called actively dividing
Bacillus Stearothermophilis; an aerobic bacterium that
produces heat resistant spores; discovered in spores; 3. Stationary Phase
used in autoclave.  Population of bacteria stagnates
 Autoclave – a machine similar to a pressure cooker,
where there is a steam under pressure inside; once it 4. Death Phase
reaches 121 °C, time it for 15 minutes to kill different  Bacteria begins to die off
bacteria.
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  Population of bacteria decreases 2. Reticulate Bodies
 Reproductive form
KOCH’S POSTULATES  Multiply by binary fission, and changes back to EB
 The microorganism must be found in abundance in all  Host cell lyses, releasing EBs
organisms suffering from the disease, but should not be  Cycle is repeated
found in healthy organisms. (Before, this is considered
true, but now, we know that there are nonpathogenic 3. Viruses
microorganisms that normally live in the body).
 Is a small infectious agent that can replicate only inside
 The microorganism must be isolated from a diseased the living cells of an organisms
organism and grown in pure culture. (Not all
microorganisms are easily grown in culture media).  They are not cells but require cells for multiplication
 The cultured microorganism should cause disease  Obligate intracellular parasites
when introduced into a healthy organism. (Not all the  Cannot produce their own ATP
time due to the presence of immunity).  Uses the machinery of the host cell
 The microorganism must be reisolated from the
inoculated, diseased experimental host and identified Characteristics of Viruses
as being identical to the original specific causative Smallest  1.20-300 nm
agent. infectious units  Can only be magnified through
electron microscopes, which can
-------------------------------END OF WEEK 1------------------------------- magnify organisms on a higher
degree compared to ordinary
I. INFECTIOUS AGENTS microscopes, about 10 million
times
INFECTIOUS AGENTS  Parvovirus – smallest
 Transmissible diseases or communicable diseases  Poxyvirus – largest
comprise clinically evident illness resulting from the Do not grow on Instead, they can be cultivated via:
infection, presence and growth of pathogenic biologic artificial medium  Cell culture
agents in an individual host organism
 Chick embryo
1. Rickettsia  Animals
 Small gram negative coccobacilli Contain only They either have DNA or RNA
one kind of  DNA – e.g. Herpes virus
 Obligate intracellular parasites – meaning, they cannot nucleic acid
reproduce outside the cell  RNA – e.g. HIV virus
 Mistaken as virus Not sensitive to Never use antibiotic when dealing with vital
antibiotics infection, use antiviral.
 Have an organelle and biosynthetic machineries
 Hard to cultivate; they are fastidious, meaning, they are Viral Structure
picky and require specific requirements in order to
Viral Nucleic Is characteristic for that taxonomic group
multiply
Acid  Double stranded DNA (dsDNA)
 Reproduced by binary fission (divides into 2)
 Single stranded DNA (ssDNA)
 Transmitted by arthropod bite (arthropods are
invertebrates such as insects, ticks, fleas, flies)  Double stranded RNA (dsRNA)
 Associated with diseases of wild animals and ticks  Single stranded RNA (ssRNA)
Viral Caspid  Protein coat that protects the
 Human accidental hosts
nucleic acid
2. Chlamydiae  Possess binding site for
 Requires living cell for multiplication attachment
 They cannot produce ATP (that’s why they need living  Resistant to destruction by lipid
cells to multiply) solvent like ether
 Energy parasites Viral Envelope A. Nucelocapsid
 Very small  Combination of capsid and
nucleic acid
 Seen in infected cells as inclusion bodies B. Envelope
 Exists in two forms  Acquired during the final stage of
multiplication by budding
1. Elementary Bodies (EB)
 Virus coded proteins and
 Infectious form glycoproteins are inserted (part
 Is engulfed by the host cell and is enclosed in a vacuole that attaches to human cells)
 EB recognizes to become reticulate bodies (becomes a  Easily disrupted by lipid solvents
reticulate after) Virus shape or  The capsid is also responsible for
symmetry the ultimate shape of the virus,
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 except poxyvirus synthesized, they will now assemble to
 All animal viruses are either form a complete viral particle called
icosahedral or helical virions.
5. Release Final step
Virus Shape or Symmetry  Naked virus is released by lysis of
 The capsid is also responsible for the ultimate shape of the host cell.
the virus, except poxyvirus.  Enveloped virus is released by
 All animal viruses are either icosahedral or helical. The capsid by budding where
protein and glycoproteins coded
Virus Shape or Symmetry by virus have replaced the
Icosahedral normally present in the host cells.
 An icosahedron is a solid 20
triangular faces
4. Fungi
 Equilateral triangle
 Mycology is the scientific study of fungi.
Helical  Protein unit interact to for a coil,
 Are eukaryotic cells that lack chlorophyll
ribbon-like structure
 Member of Kingdom Fungi
 Becomes enclosed in a
membrane as it buds from host  Have cell wall and filamentous structures and produces
cell spore
 E.g. Tobacco Mosaic Virus  Condia (Conidium)
Complex  These are regular structures, but  Grow as saprophytes, meaning, it can live in decaying
the nature of symmetry is not fully matter
understood.  Can infect human
 The only animal viruses that have  Transmission is person to person (sharing bath towels)
a complex structure are the or from environment
poxyviruses.  9 classes, 100,000-200,000 species
 150-200 pathogenic species

Types of Fungi infecting Humans

Dermatophytes Infects the skin or other parts of the body
with high percentage of keratin like hair
and nails.
Subcutaneous Infects subcutaneous areas, meaning, the
deeper parts of the skin
Systemic Infects the internal organs.
Opportunistic Infects immunocompromised people.

Classes of Pathogenic Fungi

Deuteromyces  Have no recognizable form of
(Fungi sexual reproduction.
Multiplication Cycle Imperfecti)  Most pathogenic fungi belong to
 Virus multiply on the infected cells and occurs in series this group
of independent events that ends in the assembly of viral Zygomycetes  Reproduces sexually or asexually
nucleic acid, viral protein, and other viral components.
 Remember, viruses need cells to live and proliferate. Forms of Fungi
Yeast or  Are unicellular organisms that
Multiplication Cycle (Steps) creamy, pasty reproduce by budding
1. Adsorption Virus adsorbs to a specific surface fungi  Each yeast cell contains single
receptor on the host cells (adsorb, nucleus
meaning, it only sticks to the surface) Mold or Multicellular structures with branching,
2. Penetration Occurs by engulfing a naked virus or by Filamentous tubular cells
fusion of the viral envelope with the host Fungi  Hyphae – branch-like structure
cell. Only the nucleocaspid is allowed to a. Septum/Septate –
enter the cell. with crosswalls
3. Synthetic Nucleic acid is transcribed and translated b. Coenocytic – non-
Phase to proteins, which will make up structural septated or without
component of the virus as well as enzymes crosswalls
needed for the replication.  Mycelium – mass of hyphae
(Transcription and Translation of proteins;
 Conidia – spore produced by
DNA → RNA → Protein) fungi
4. Assembly When all the genetic materials are
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Comparing the structure of a mold to a tree: inactive
Hyphae – sanga
Conidia – mukhang bunga Groups of Protozoa
 Most medically important protozoa reproduce asexually
only, by binary fission or schizogony.

Groups of Protozoa
Mastigophora  Use one or more flagella for
(Flagellates) locomotion
 Includes spp., Trichimonas,
Chilomastix, Leismania,
Trypanosoma and Giardia lamblia
(a.k.a old man with eyeglasses)
 Giardia lamblia can be acquired
by drinking contaminated food
and water (causes diarrhea);
blocks the linings of the intestine
from absorbing oil
Forms of Fungi (Continuation)
Dimorphic Fungi Exists in both the yeast and mold forms  Steatorrhea – stool is now greasy
and foul smelling
Yeast Phase (Tissue Phase) Sarcodina  Use pseudopodia for locomotion
 Parasitic or pathogenic form seen (Amoeba) and for feeding
in tissue and exudates  Includes: Entomoeba,
 Obtain in culture incubated at Iodamoeba, Endolimax,
37°C Acanthamoeba, and Naegleria
Mold Phase (Mycelial Phase) Ciliatea Use cilia for locomotion. They have two
 Free living forms seen in nature (Ciliates) different nuclei:
 Obtain in culture incubated at  Larger (Macronucleus) – directs
25°C vegetative growth and cell
division
Structure of Fungi  Smaller (Micronucleus) –
Cell wall Rigid cell wall composed of chitin, glucans, participates in sexual
mannans and complex polysaccharide. reproduction
Cell membrane Contains ergosterol (unlike mammalian Includes: Balantidium
cell membrane which contain cholesterol). Sporozoa  Non motile
This is the target of antifungal drugs like  All are parasitic
Ampotericin B.  Life cycle: Schizogony,
Gametogony, Sporogony
5. Parasites  Example is a parasite that causes
 An organism that lives on or in an organism of another malaria.
species known as the host, from the body of which it  Includes: Plasmodium, Isospora,
obtains nutrient. Sarcocystis, Taxoplasma,
 E.g. Once the parasite lands on a crab, it makes its way Cryptosporidium, Cyclospora,
to a joint in the crustaceans’ exoskeleton Babesia
 Tropozoites of sporozoan are
Protozoan intracellular.
 An nonphotosynthetic
 Unicellular  Some protozoan have an elaborate life cycle during
 Eukaryotic organisms that lacks cell wall which they assume different forms and requires
 Belongs to Kingdom Protista different hosts.
 Motile using pseudopodia, cilia and flagella except  Examples:
apicomplexa group a. Trophozoite – is the actively multiplying form of
Plasmodium spp.
 Amoeba coli – non pathogenic intestinal amoeba
b. Sporozoite – infectious form
c. Merozoites – infects red blood cells
Protozoa exists as:
Trophozoites Which is the motile and non-
6. Helminths
feeding stage
Cyst Which is the non motile and the  Are not microorganisms
feeding stage; metabolically  Eggs and larvae are seen in diagnosed microscopically
in clinical samples of blood, feces and urine
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  Two (2) Phyla of Helminths:
a. Flatworms (Platyhelminthes) NUTRITIONAL GROWTH CHARACTERISTICS
b. Roundworms (Nematodes) 1. Autotrophs/Lithotrophs
 Able to utilize simple inorganic compounds
1. Flatworms (Platyhelminthes)  Carbon dioxide as carbon source, ammonium salts as
 Have flattened body nitrogen source
 Have a head and bilaterally symmetrical bodies  Include phototrophs (photosynthesis) and
 Has specialized organ system: Nervous, Excretory, chemolithotrophs (oxidation of inorganic compounds)
Reproductive
 No digestive system 2. Heterotrophs (bacteria in human body)
 Some parasitic species have no digestive tract and  Also known as organotrophs
absorb nutrients through outer covering  Unable to synthesize own metabolism
 Depend on performed organic compounds
2 Groups of Flatworms  Nutritional needs are variable
Cestodes (Tapeworm) Trematodes (Flukes)
GROWTH REQUIREMENTS
1. Physical
 Temperature
 pH
 Osmotic pressure
 Moisture & dessication

Temperature
Psychrophiles Cold loving; responsible for the spoilage of
(cold loving) refrigerated food
 True psychrophiles – optimum
growth at 15 °C
2. Roundworms (Nematodes)  Psychrotrophs – optimum growth
 Have cylindrical bodies at 20-30° C
 Bilaterally symmetrical Mesophiles Moderate temperature loving, around 20-
 Tapered at both ends 40 °C; consists of medically important
organisms
 Have complete digestive tract
Thermophiles Heat loving
 Has a well developed reproductive system Hyperthermophi Tolerate extreme temperatures; can be
 Separate male and female worm les found in hot springs
 Ascaris lumbricoides – as long as a ballpen
 Fecalysis – stool analysis 2. pH
 People, usually children, with ascaris lumbricoides  Most medically important bacteria grow at neutral or
appear to have abnormally big abdomen. Anti- slightly alkaline pH (7.2-7.6 pH)
helminthic drug must be taken properly, or this parasite  Very few bacteria grow below pH 4
will become erratic and come out of different places like  Lactobacilli grow in acidic pH
the nose, eyes, and anus.  Cholera vibrio grow in alkaline pH
 Acidophiles, neutrophiles, alkalinophiles
 Growth media includes chemical buffer to prevent acid
production
 Foods are preserved by acids produced by bacterial
fermentation

2. Osmotic Pressure
 Force a water exerts on a semipermeable membrane
surrounding the cell
7. Prions  High osmotic pressure (hypertonic) removes water
 Are very small infectious agents causing plasmolysis, which inhibits growth (i.e. salt as
 Infectious proteins preservatives)
 Proteinaceous infective particles  Low osmotic pressure (hypotonic) cause water to enter
 No nucleic acid and can cause lysis
 Associated with fatal degenerative disorders of the CNS  Bacteria are more tolerant to osmotic variations
 Produces sponge-like appearance in an infected brain because of the mechanical strength of the cell wall
(Spongiform encephalopathy)
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 THIOGLYCOLLATE BROTH
 Some bacteria can grow through a media
 Agar – solid; Broth – liquid
 Can determine an organism’s oxygen requirement

3. Moisture and Dessication

 Moisture is essential – 80% of body weight is water
 Effects of drying varies by organisms
 T. pallidum, Gonococcus are very susceptible (dies
easily)
 Tubercle bacilli, staphylococci may survive for weeks
 Bacterial spores survive several years

Lyophilization
1. Aerobic
 Freeze-dry process that protects and preserves
 Top growth
bacteria for years
 Requires full air
 Bacteria are dried in liquid nitrogen, dehydrated in high
vacuum
2. Microaerophilic
3. Moisture and Dessication  Growth just below surface
 Chemo and photoautotrophs fix carbon dioxide  Requires only minute amount of air
 Chemoheterotrophs obtain energy from organic
3. Facultative anaerobic
compounds
 Growth throughout
Growth Needs  Organisms that can grow with or without oxygen
Fastidious Relatively complex growth needs;
Bacteria nutritional needs are very specific 4. Aerotolerant anaerobic
Non-fastidious Relatively basic and straightforward growth  Some growth in oxygen
Bacteria needs  Can tolerate small amount of oxygen

BACTERIAL GROWTH CURVE 5. Anaerobic

 Lag phase  Bottom growth
 Exponential growth phase – where there are the most  Does not require oxygen
live organisms; organisms are actively dividing
 Stationary phase – has the same amount of live and
dead organisms
 Death phase

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III. STERILIZATION AND DISINFECTION  pH
 Biofilms – microorganisms living together in colonies
STERILIZATION VS. DISINFECTION (e.g. In catheters (sinusuksok sa urethra), sometimes,
nagkakaroon ng bacterial growth called biofilm, which is
Sterilization Disinfection hard to kill)
Complete destruction of all Destruction or removal of  Compatibility of disinfectants and sterilants
forms of microbial life, microbial forms, especially
including endospores (difficult disease-causing ORDER OF RESISTANCE OF MICROORGANISMS TO
to kill). microorganisms, except DISINFECTANTS/STERILANTS
endospores.
 Most resistant going to the least resistant
microorganism to disinfectant/sterilants (hardest to
DISINFECTANT VS. ANTISEPTIC easiest to kill)
 Degerming – a process that results in mechanical
removal of organism (e.g. Before performing 1. Prions
venipuncture, patients are swabbed with alcohol in the
venipuncture area)  Naked pieces of CHONS (proteins)
 When alcohol is used to clean surfaces, it is a  Very hard to kill because they are resistant to heat,
disinfectant, however, when it is used to rub the skin, it chemical, and radiation
is an antiseptic.  Cause degenerative diseases, specifically in the brain
 Examples of disease they cause include the Mad Cow
Disinfectant Antiseptic disease and Creutzfield Jakob, which can be
Physical or chemical agent Physical or chemical agent transferred to humans via contaminated fluids or bodily
that is used to destroy that is used to destroy fluids.
disease-producing disease-producing  All bodily fluids should be considered contaminated.
microorganisms on inanimate microorganisms on living
objects. tissues. 2. Spores
 Clostridium difficile contains spores
 Spores are organisms that are very hard to kill because
SEPTIC VS. ASEPTIC they are rich in proteins, lipids, and carbohydrates
 In medical terms, the prefix “-a” indicates absence
3. Mycobacteria
Septic Aseptic  Mycolic acid is a component of mycobacteria that
Indicates bacterial Absence of microorganism makes it hard to kill (such as in mycobacterium
contamination tuberculosis).
 Mycolic acid is hard to stain. Acid fast is used to stain it
BACTERIOSTATIC VS. BACTERICIDAL using Ziehl-Neelsen.
 The suffix “-static” or “-stasis” means inhibition of
growth 4. Nonlipid Viruses
 The suffix “cidal” means killing of an organism  An example is polio virus
 Microbial death – permanent loss of the ability of the
organism to reproduce under its ideal environment 5. Fungi
 An example is candida albicans
Bacteriostatic Bactericidal
Inhibition of the growth of Killing of bacteria 6. Bacteria (Vegetative Bacteria)
bacteria during the stage  Examples include MRSA and VRE
where they have the ability to  MRSA – Methicillin Resistant Staph Au
grow and multiply  VRE – Vancomycin Resistant Enterococci
FACTORS THAT INFLUENCE THE DEGREE OF KILLING 7. Lipid Viruses
 Type of organisms – the way of disinfection depends on  No description
the type of organism to be killed
 Number of organisms – the higher the number of the CONTACT TIME
organism, the harder for them to be killed  If there is a higher number of organism, longer time is
 Concentration of disinfecting agents – the more required to kill them due to factors that need to be
concentrated your agent of substance is, the more considered, which is referred to as microbial load or
powerful it is. However, alcohol is an exception. bioburden.
 Presence of organic material  Microbial load/Bioburden – total number of organisms
 Nature of surface to be disinfected – the disinfectant to present in an area
be used depends on the material of the surface
 Contact time DISINFECTION METHODS
 Temperature  Physical agent and chemical agent
BSN1E - Manuel | 11
I. Physical Agents spores are killed
 Heat, freezing and thawing, radiation, and filtration
Moist Heat: Pasteurization
1. Heat  Low temperature/short-time
 Most widely used  Used in milk and yogurt
 The longer the heat exposure and the higher the  It has the ability to disinfect but not sterilize without
temperature, the more effective it is. causing changes on the flavor of your substance
 Moist heat and dry heat  Has three (3) types:
a. Classical Pasteurization
Moist Heat: Autoclave - 62.9°C 30 mins
 Principle of steam or moist under pressure - commonly called as batch method
 To be effective, moist must be in contact with the - used to disinfect and kill milk borne pathogens
specimen b. High Temperature Short-Time (HSHT)
- 71.6°C for 15 secs
 Used when autoclaving culture media and petri
- also called flash method
dishes
c. Ultra High Temperature (UHT)
 Most effective way of killing or disinfecting - 143°C in less than a second
(temperature must be set at 180 atmospheric
pressure or psi until it reaches 121°C, which is
crucial to kill the organisms)  Dry heat requires higher temperature and a longer
period of heating
 Autoclaving has the ability to kill all organisms except
prions (even spores are killed), given that you will  Uses of dry heat include sterilization of glassware, oils,
maintain the temperature of 121°C for 15 mins jellies, and powders
(which can be extended up to 30 mins, which is done
in hospitals prior to disposal)
 Autoclave cannot be used in petroleum jelly and
mineral oil (because when these two are in contact
with a liquid, their consistency is changed)

 The photos above are similar to ovens used at home,

except they are much bigger, and glasswares are put
inside. **Bawal madikitan ng liquid kasi mababago
consistency nila at masisira yung product**
 We kill organisms via oxidation of proteins
 Heat must penetrate the object in order for it to be
disinfected.
Left: Screwed on top
Dry Heat
Middle: Differs in orientation (nakahiga) but is also screwed on
top Hot air  For it to be effective, it must reach
Right: Screw all oven 160°C to 180°C within 1.5 to 3 hrs
 Used to sterilize glasswares, gauze,
Moist Heat: Boiling dressings, equipment in molecular
 Uses the same principle as “takure” biology
Incineration  Used in animal carcasses (to kill
 For it to be a very good killing agent, it should be
able to interact with your substance for at least 15 microorganisms)
minutes  Burn the material to ashes so living
 Achieves disinfection but not sterilization because of microorganisms within the body of the
its inability to remove endospores animal won’t cause harm
Flame of  For it to be effective, we allow the
Moist Heat: Tydallization bunsen inoculating loop or needle to be red
burner hot
 Fractional sterilization – substance is placed 80 to
100°C for 30 minutes for 3 consecutive days  Burn the organisms into ashes to
 1st Day: To kill and remove vegetative spores prevent them from transferring
 2nd Day: To destroy the new crops of vegetative
2. Freezing and Thawing
spores
 3rd Day: Additional margin of safety to ensure that all  Not reliable, however, it helps

BSN1E - Manuel | 12
  Only intended for its specific use (e.g. only for Examples
bacteriology) Membrane  Water filtration
 Freezing – retards metabolic metabolism (it slows down filter (left  Sa isang syringe, iaaspirate or i-va-
the growth and multiplication of organisms as well as photo) vacuum mo yung liquid mo. Kapag na-
their chemical reaction vacuum po siya, i-pu-push mo siya,
 Not a good disinfectant (yung paglabas-pasok sa once pushed, depending on its filter
freezer increases the likelihood of microbial growth) size, yun yung capacity para dumaan
 Storage for culture media and antibiotics yung liquid and maiiwan yung mga
solutes. Because it is so small, it also
3. Radiation has the capacity to filter bacteria and
fungi
 UV
 Popular brand is called Millipore
 Produces pyrimidine dimers on DNA
Filtration  High Efficiency Particulate Air
 Low penetrating power limits use HEPA or
 Uses different type of wavelength, to be specific,  Air filtration
HEPA Filter  Used in biosafety cabinet (BSC)
around 250 to 170 nm, which is the stat of wavelength (right
that is able to damage microbial cells photo)  Has the ability to filter
 Has the ability to change or disrupt the hydrogen bonds microorganisms leaving the air
which causes changes in the DNA and can possibly expelled in the environment
cause cancer
 Example for ionizing:
a. PET Scan (Positron Emission Tomography) – a
person is injected with a radioactive material and put
inside a donut-like machine. Kapag nagkaroon ng ilaw
or blocking depende sa setting, it is possible that there
is cancer; heat sensitive
b. CT Scan (Computed Tomography)
II. Chemical Agents
Ionizing Non-ionizing  Agents that damage the cell membrane
 y-rays, x-rays and  Not harmful  QUATS and Phenol
accelerated because they have
elecrons low wavelength and 1. Quaternary Ammonium Compounds (QUATS)
a. Direct effect low energy  Examples include Zephiran and Cephachol, which are
b. Energy directly effective against gram positive organisms. Once
changes damaged, the cell membrane of an organism will lose
macromolecules its ions and the organism itself will be destroyed
c. Kills spores  Other examples include detergents, which are used in
 Can cause chemical the disinfection of countertops and benches
changes to the DNA
 Used for sterilization 2. Phenol
of surgical supplies  Disruption of the cell membrane of an organism, leading
and food to the denaturation of proteins

Examples
Lysol or No description
Cresol
Chlorhexidi  Used as a topical agent
ne  Used for surgical handwasing or
gluconate whole body disinfection
 Effective against gram positive
organisms
4. Filtration Hexochloro  Effective against gram positive
phene organisms
 Bacteria and larger microorganisms are easily removed
from liquids  Effective if 3% hexochlorophene is
used within 15 to 30 seconds contact
 Effective pore size: 0.22 microns time
 Removal of viruses requires ultrafiltration, which is Chloroxylen  Used for surgical handwashing or
feasible only for highly specialized materials ol personal handwashing
Trclosan  Used before in soaps, toothpaste, and
other cosmetic products

BSN1E - Manuel | 13
  Effective against gram positive, gram is not commonly used today as it
negative, as well as viruses causes irritability to the mucus
 Discontinued in the aforementioned membrane of people
products due to microorganisms Glutaraldeh  Compared to formaldehyde, it is less
mutating and developing resistance yde irritating and more effective
(except in toothpastes, since  Only effective in alkaline environment
according to the FDA, it is effective  2% glutaraldehyde is considered as a
against gum disease) germicidal and should be in contact
with a surface for 10 mins for it to be
AGENTS THAT DENATURE PROTEINS effective
 Examples include acids, alkalies, acetone, and organic  Sporicidal – 3 to 10 hrs contact for it to
solvent be effective (in killing spores)
 Denature proteins by disrupting the metabolism of the
cell LABORATORY ROLE IN INFECTION CONTROL
 Health care-associated infections (HAIs) – infections
AGENTS THAT MODIFY FUNCTIONAL GROUPS OF that originate in health care facilities
PROTEINS AND NUCLEIC ACIDS  Infection control – all activities related to the prevention
 Examples include heavy metals, oxidizing agents, dyes, and reduction of the cases of the spread of infection in
and alkylating agents the environment and people
 Nucleic acids include DNA and RNA  No eating and drinking inside the laboratory
 The laboratory is a dangerous place
Heavy Metals
 Disinfectants with heavy metals are considered as Hazards
bacteriostatic.  Examples include chemical, biological, physical, and
 They have the ability to damage the DNA and RNA by safety hazards
inhibiting the replication of the organism.  Regulated by the Occupational Safety and Health
Administration (OSHA) – protects workers from all types
Heavy Metals of hazards
1% Silver  Used before as a propylactic
Nitrate treatment for opthalmia neonatorum, Universal or Standard Precautions
which is an eye infection  Protect personnel from blood-borne infections
(conjunctivitis) caused by Neisseria  In 1996, the guidelines were updated
Gonorrhoea
 Require that blood and body fluids from all patients be
 Pinapatak sa mata ng baby to prevent considered infectious and capable of transmitting
opthalmia neonatorum disease.
Mercuric No description
 Blood and all body fluids, including secretions and
Chloride
excretions except sweat, regardless of whether visible
Betadine  Inactivates proteins and nucleic acids blood is present, is considered infectious.
(Brand) of a substance
 Is an iodine Standard Precautions
 Iodine has two (2) forms: tincture and Hand washing Must be done before and after touching a
iodophor. Betadine is an iodophor. patient, even with gloves, regardless of
 It causes slow release of free iodine whether the gloves is soiled or not
wherein that iodine will react to the Wearing of face Protection from potential splashes of
cell wall and cytoplasm of the mask, face blood or body fluids
organism to denature the enzymes. shield, and eye
 In blood culture, prior to getting blood, protection
such as in blood donation, swabbing Wearing of All buttons should be closed; is long-
with alcohol and betadine is done laboratory coat sleeved to protect the skin and clothing
Chlorine  Used to disinfect drinking water and from specimens; one lab coat per area
swimming pools (use different lab coat for different lab
Sodium  Present in soaps classes)
Hypochlorit Sharps disposal Where needles and syringes are
e disposed
Formaldehy  An aldehyde and ketone used as an
de embalming agent (preservation of Transmission-Based Precaution
specimens)  Prior to getting a sample or coming inside the laboratory
 Also called formalin, used at 37°C or the patient’s room, you must check if there is a post,
which could be regarding contact precaution, droplet
 Also used before in the disinfection of precaution, or airborne precaution
biosafety cabinets (BSC), however, it
BSN1E - Manuel | 14
1. Airborne Precaution  One holder discard – single usage of holder in closed
 Organisms can stay in the air for a certain time system venipuncture
 Everyone must:  Eye wash station and emergency shower should be
1. Clean their hands, including before entering and strategically assigned (should be easily accessible)
when leaving the room.
2. Put on a fit-tested N-95 or higher level respirator Definition of Terms
before room entry. Biological Any microbiological entity, cellular or non-
3. Remove respirator after exiting the room and closing Agent cellular naturally occurring or engineered,
the door. capable of replication or transferring genetic
4. Door to room must remain closed. material that may be able to provoke infection,
 For infectious organisms that remain airborne and allergy, toxicity or other adverse effects in
infectious over long distances humans, animals or plants
 Examples:
a. Mycobacterium Tuberculosis Examples include bacteria, fungi, viruses,
b. Varicella viroids, endo- and ectoparasites (nasa loob at
c. Rubeola labas ng katawan)
Biological Any material comprised of, containing, or that
2. Contact Precautions Material may contain biological agents and/or their
harmful products such as toxins and allergens
 Used to stop the spread of infectious agents that may
Biohazard Potential source of harm caused by biological
be transmitted through direct or indirect contact with the
materials
patient or the patient’s environment,
Laboratory Institutional and personal security measures
 Indirect – via fomites; fomites are inanimate objects that Biosafety designed to prevent the loss, theft, misuse,
can harbor organisms for an amount of time diversion, or intentional release of pathogens
 Everyone must: and toxins
1. Clean their hands, including before entering and
when leaving the room.
BIOSAFETY VS. BIOSECURITY
 Providers and staff must also:
 Biosafety – protecting people from bad bugs
1. Put on gloves before room entry. Discard gloves
before room exit.  Biosecurity – protecting bad bugs from bad people
2. Put on gown before room entry. Discard gown before
room exit. Do not wear the same gown and gloves for Bioesecurity or Biosafety Issue?
the care of more than one person. Capping of Needles Biosafety Issue
3. Use dedicated or disposable equipment. Clean and
disinfect reusable equipment before use on another (Proper way is to fish out)
person (such as a stethoscope).
 Examples:
a. Clostridium difficile One of your laboratory Biosecurity Issue
b. Vancomycin-Resistant Enterococci (VRE) members is a part of a
c. Methicillin-Resistant Staphylococcus Aureus (MRSA) terrorist group
3. Droplet Precautions
 Used to stop the spread of infectious agents that can be
transmitted by close respiratory contact or by exposure
of mucous membranes to respiratory secretions
 Used during the COVID-19 pandemic
 Everyone must: If marami kang trabaho pero Determine
1. Clean their hands, including before entering and mag-isa ka lang
when leaving the room. (2 Happy Birthday songs, 20 (Kapag pagod ka na, baka
seconds) mapagpalit mo yung
2. Make sure their eyes, nose and mouth are fully specimens ng patients)
covered before room entry.
3. Remove face protection before room exit.
 Examples include:
a. Neisseria meningitidis Staff with huge debt Determine
b. Bordetella
c. Influenza (When you go to the
laboratory, you should be
focused on your work. Always
Engineering Controls
remember that you are
 Controls that isolate or remove the hazard from the dealing with lives. Your work
workplace is very important)
BSN1E - Manuel | 15
 Coronavirus Protection Kit Biosafety Issue cabinet)
 Environment air is filtered/protected
(Observe laboratory rules)  Air coming inside the sash goes through the HEPA
filter, after which, the air coming outside the hood is
Double gloving – use of two now filtered
(2) gloves

Biosafety
 Engineering controls – use of biosafety cabinet (BSC),
directional airflow, and anterooms; to protect worker
and environment from the release of organisms
 Good laboratory practices – wearing of PPE and
handwashing; use alcohol if hadnwashing is not
applicable, however, handwashing is always preferred 2. Biological Safety Cabinet Class II
 Handwashing does not kill all bacteria due to rubbing  Airflow system: 70% air recirculation, 30% air exhaust
 With vertical laminar flow – exhaust and recirculated air
Biosecurity
passes through HEPA filter
 Only the eligible ones should be allowed to enter the
 Commonly used in the microbiology or bacteriology lab
laboratory
 Sa hood, may exhaust sa ilalim, i-sa-suck niya yung air,
 Examples include:
and then, ififilter niya, para yung papasok na air or
a. Doors with locks magcicirculate doon sa hood ay sterile, meaning it
b. Password/PIN protects now the organism or specimens, after which,
c. Card readers when it reaches the environment, it will also filter the air
d. Biometric
 Both the specimen and the environment is protected
e. Cameras
f. Information Security

Applied in Biosafety and Biosecurity

 Examples include:
a. Access control
b. Personnel
management/reliability
c. Inventory of biological
hazards
PERSONAL PROTECTIVE EQUIPMENT (PPE) 3. Biological Safety Cabinet Class III
 Specialized clothing or equipment that is worn by an  Self-contained ventilated system for highly infectious
employee for protection microorganisms or materials
 Include gloves, laboratory coats, masks, respirators,  Provides the highest level of personal protection
face shields, and safety glasses  Very expensive and only used for certain organisms
 Blood and body fluids must not be able to penetrate the  ULPA filter is used
PPE material  The hands are inserted inside the gloves, which
 Double gloving is also important provides safety against the organism.
 The organism is also protected due to the filter and
BIOLOGICAL SAFETY CABINET (BSC) presence of negative pressure inside.
 Located in the bacteriology section  The operator, product, and environment is protected.
 Microbiology – study of microbes
 Bacteriology – study of bacteria
 Ventilated enclosure offering protection to the user, the
product and the environment from aerosols arising from
the handling of potentially hazardous microorganisms
 Continuous airflow is discharged to the atmosphere via
a HEPA filter
 With three (3) classes: BSC I, BSC II, BSC III.

1. Biological Safety Cabinet Class I

 Exhaust fan to move inward air through the open front
 Exhaust air through HEPA filter (1 filter only)
 Possibility of product/culture contamination (open
BSN1E - Manuel | 16
 Summary
BSC I Environment air is protected.
BSC II Environment air and specimen is protected.
BSC III Environment air, specimen, and operator is
protected.

BIOSAFETY LEVELS
 Combination of laboratory practices and procedures,
safety equipment (primary barriers) and laboratory
facilities (secondary barriers)
3. Biosafety Level III
1. Biosafety Level I  Indigenous or exotic infectious agents
 Agents that are not known to cause disease  Potential for aerosol transmission
consistently in healthy adults  All practices performed in Biosafety Level 2 should also
 Agents that pose a minimal threat to laboratory be applied here.
personnel and environment  Before entering and exiting, a shower outside the door
 Authorized employees are only allowed to enter should be used.
 PPE should be used: lab gown, gloves, face shields  Examples of microorganisms include:
and eye protections (if there is a chance of splashes) a. Mycobacterium tuberculosis
 Example includes water testing laboratory b. St. Louis Encephalitis virus
c. Coxiella burnetti
 Examples of microorganisms include:
d. Brucella melitensis
a. Bacillus subtillis
b. Naegleria gruberi

4. Biosafety Level IV
2. Biosafety Level II
 Agents that are dangerous and exotic
 Infectious agents that require BSL-2 containment
 Agents that have a high risk of causing life-threatening
 Agents that pose a moderate risk for the employees
infections
and the environment
 Agents that can be transmitted by aerosol or have
 All PPE must be worn
unknown risk of transmission
 There is an immediate trash bin with a biohazard sign.
 Organisms with no available treatment or vaccine
However, they should have proper labeling (color
coding): green, black, and yellow (if infectious).  Before entering, there is an access control: camera, ID,
fingerprint scanning
 Commonly used in laboratories
 Before entering, one should remove their clothes and
 BSC II is placed far from the door in order to prevent
shower, after which, a hazmat suit should be worn.
the disruption of its airflow.
Shower again before exiting.
 Examples of microorganisms include:
 Examples of organisms include:
a. Salmonella
a. Marburg
b. Toxoplasma
b. Congo-Crimean Hemorrhagic
c. HBV
c. Ebola virus
d. HIV
 There are agents that are considered Biosafety Level 2 CLASSIFICATION OF INFECTIOUS MICROORGANISMS BY
and Biosafety Level 3. RISK GROUP
 If you are only checking for the presence of an  These are organisms that have the ability to cause
organism, use Biosafety Level 2. However, if there is diseases in humans
manipulation, if you have cultures, or there is
aerosolization risk, use Biosafety Level 3.
1. Risk Group 1
 COVID-19 is also an example
 Agents not associated with disease in healthy adult
humans (NIH)
 No or low individual and community risk
 A microorganism unlikely to cause human or animal
disease (WHO)
BSN1E - Manuel | 17
2. Risk Group 2 checking under the microscope
 Agents associated with human disease that is rarely Postanalytic  Result delivery
serious and for which preventive or therapeutic Activity  Reviewing of results
interventions are often available (NIH)  Actions stated in the result
 Moderate individual risk; low community risk
 A pathogen that can cause human or animal disease QUALITY CONTROL AND QUALITY ASSURANCE IN
but is unlikely to be a serious hazard to laboratory MICROBIOLOGY
workers, the community, livestock or the environment.  Incubator – should be around 35 to 37°C
Laboratory exposures may cause serious infection, but  Refrigerator – should also yield the correct temperature
effective treatment and preventive measures are
available and the risk of spread of infection is limited  Water bath
(WHO)  Thermometer – bought from the National Institute of
Standards and Technology (NIST), formerly called the
3. Risk Group 3 Natioanl Bureau of Standards (NBS)
 Agents associated with serious or lethal human disease  Gram stain reagent – must yield a color; purple/violet
for which preventive or therapeutic interventions may be for gram positive and red/pink for gram negative
available  Catalase reagent – hydrogen peroxide is used (in the
 High individual risk but low community risk presence of a caralyst, it will yield water and hydrogen)
 A pathogen that usually causes serious human or
animal disease but does not ordinarily spread from one
infected individual to another. Effective treatment and
preventive measures are available (WHO)

4. Risk Group 4
 Agents likely to cause serious or lethal human disease
for which preventive or therapeutic interventions are not
usually available
 High individual risk and high community risk
 A pathogen that usually causes serious human or
animal disease and can be readily transmitted from one
individual to another, directly or indirectly. Effective
treatment and preventive measures are not usually  Gaspak jar – for organisms that require higher
available percentage of carbon dioxide called capnophilic; carbon
dioxide is released through the pouch-like material
QUALITY CONTROL (QC) inside; quality control is done each use
 Measures designed to ensure the medical reliability of
laboratory data
 Checking of media and reagents to determine whether
expected results are obtained
 Documenting that the instrument meets all
 To make sure that all materials and equipment used are
in good shape

Stages of Activities that Affect Laboratory Testing Activity

Outcomes

Stages
 Autoclave – 121°C for 15 minutes; spore testing is done
Preanalytic  Order transcription (paggawa ng weekly, however, temperature is checked every load or
Activity request) every time it is used
 Specimen collection a. Automatic – automatic na maglalagay ng tubig
 Specimen identification b. Manual – ikaw yung maglalagay ng tubig
 Specimen transport c. Semiautomatic – ikaw pa rin ang maglalagay ng tubig
 Make sure to use to correct tube pero may gas range
depending on the specimen (e.g.
for venipuncture-cbc platelet, a
purple/violet top tube is used)
Analytic Activity  All activities done after receiving
the specimen until testing is
done
 Examples include urinalysis and
BSN1E - Manuel | 18
 IV. INFECTION AND EPIDEMIOLOGY

NORMAL OR INDIGENOUS FLORA

 Are microorganisms that are normally found on both
external and internal surfaces of the body of a normal
healthy individual
 External – skin; first line of defense (intact skin);
 If skin is not intact, microorganisms will easily enter into
the circulation and invade internal organs and may
 Antibiotic disk – checked weekly cause damage to them
 There are many microorganisms present in the skin, but
Yung bilog (yung puti) ay antibiotic disk. As observed in not all are pathogenic (disease-causing). Some of them
the photo below, there are zones of inhibition (yung big nourish the skin and serve as a protection due to their
circles; kapag may ganito, meaning, may reaction ang capability of competing with other pathogenic bacteria.
bacteria sa antibiotic). Kapag nagkaroon ng zone of  Internal – e.g. mucus membrane, blood, internal organs
inhibition (yung nakapaligid sa antibiotic disk), is the  Microorganisms are also present in the internal
antibiotic considered effective? We do not know yet. We surfaces of the body, however, not all are pathogenic.
should wait for the results. Check for SIR: Some are there because they have physiologic function
a. Sensitive – meaning, effective ang antibiotic sa in order to maintain the function of a specific organ.
bacteria  For example, some microorganisms that are found in
b. Intermediate – ibig sabihin, medyo effective ang the digestive tract help in food absorption and digestion
antibiotic, 50/50  When the population of the normal flora increases, they
c. Resistant – there are some organisms that are may be infectious. Thus, it is important to inhibit this by
already resistant to antibiotics observing safety protocols.
This is called AST (Antimicrobial Susceptibility Testing).
Vernier caliper is used to test the zones of inhibition as
well as the antibiotic disk. If not available, use a ruler
and measure in millimeters. If there is no zone of
inhibition, the measurement is 6mm.

 Centrifuge – checked every six (6) months; rpm or TYPES OF ORGANISMS THAT INTERACT WITH A HOST
revolutions per minute is checked 1. Parasites
 Are organisms that live at the expense of the host
a. Protozoa
b. Worms (e.g. Helminths)
c. Insects – serves as a vector (carrier of microbes)

2. Symbionts
 Are two (2) different types of organisms that can live
together, each deriving benefits from the other
 Parasitism – relationship between two (2) species in
which one benefits at the expense of the other
 Microscope – checked 4x a year or as often as needed
and whenever it is cleaned and adjusted 3. Commensals
 Biosafety Cabinet – checked annually for the airflow  Are organisms that have neutral relationship to the host
 Electronic Beam Balance – checked annually for  Neither organism nor the host is harmed
accuracy  Commensalism – a symbiotic relationship where neither
parties are harmed but one of them are benefiting from
-------------------------------END OF WEEK 3------------------------------- the other
 Entamoeba gingivalis – normal flora of the mouth
BSN1E - Manuel | 19
  Escherichia coli (E. Coli) – normally found in the large SITES NORMALLY STERILE IN HEALTH
intestine; may cause disease if found in large numbers 1. Blood
in other parts of the body (e.g. causing UTI in the  Should be free from any pathogen; normally sterile
urinary tract)  If unsterile, there is an infection
 Must be considered as sterile in order for a person to be
Two (2) Types of Commensals considered healthy
Resident Consists of relatively fixed types of
flora microorganism regularly found in a given area 2. Body fluids such as the CSF, pleural fluid, urine
at a given age  CSF (cerebrospinal fluid)
Transient Consists of non-pathogenic or potentially
flora pathogenic microorganisms that inhabit the 3. Tissues
skin mucous membrane for hours, days or  Urinary bladder, uterus, fallopian tubes, middle ear,
weeks paranasal sinuses, and other internal organs
5. Opportunists NORMAL FLORA OF THE DIFFERENT SITES
 Are microorganisms that cause disease when proper 1. Skin
opportunity arises  The flora is most abundant in moist areas
 Clostridium difficile – a gram positive bacteria that a. Aerobic and anaerobic diptheroid
normally resides in the human digestive tract. If a b. Non-hemolytic aerobic and anaerobic staphylococci
patient who is taking an antibiotic to which such c. Staphylococcus epidermidis, Peptococcus spp.
bacteria is resistant, they will proliferate and become d. Alpha-hemolytic streptococci and enterococci
pathogenic (causes pseudomembranous colitis) (Streptococcus viridans, Enterococcus faecalis)
e. Gram negative coliform bacilli and Acinetobacter
CONDITIONS THAT DETERMINE THE NATURE OF FLORA f. Fungi and yeast (Pityrosporum ovale, Pityrosporum
1. Local physiologic and ecologic conditions, which differs orbiculare, Torulopsis glabrata, Candida albicans)
from site to site and sometimes vary with age g. Nonpathogenic mycobacteria
Local Physiologic and Ecologic Condtions Factors that Eliminate Non-Resident Microorganisms from
Amount and types of No description the Skin
nutrients available  Fatty acids in sebaceous secretions – produced by the
pH Most medically important bacteria sebaceous glands
thrive at a pH level of 7.0-7.35; When
pH increases, such bacteria are hard  Presence of lysozyme – responsible for the degradation
to cultivate and may even die of bacterial cell (process of phagocytosis)
especially in acidic environments.  The keratin that keeps the skin surface dry
Oxidation-reduction No description
potentials 2. The Mouth and the Respiratory Tract

Resistance to No description A. Mouth

antimicrobial  The mouth is a warm, moist environment that has
substance such as abundant nutrients. It is densely populated with
bile and lysozyme microorganisms.
Temperature Most medically important bacteria  Periodontitis – formation of plaques in the teeth and
thrive at body temperature, around 35 gingival area (photo on the left)
to 37°C.  When bacteria present in the mouth multiplies in greater
Moisture Most bacteria thrive in moist numbers, they may cause oral cavity problems.
environment (e.g. moist areas of the  Glucose – primary energy source of bacteria
body such as the face, back, inguinal  Streptococcus mutans – causative agent of tooth decay
area and axillary region).
 Tongue and buccal mucosa
a. Facultative bacteria such as the viridans streptococci
2. Various microbial interactions, which include:
(S. salivarius, S. sanguis, S. mitis, S. mutans, S. milleri)
 Competition for nutrients are predominant microorganisms)
 Inhibition by the metabolic products of other organism b. Other bacteria are Neisseria spp., Branhamella and
such as hydrogen peroxide, volatile, fatty acids, occasionally Candida albicans
productive of antibiotics and bacteriocins

3. Bacterial adherence
 The presence of pili or fimbriae (hair-like projections)
enables bacteria to colonize a given site
 Where a bacteria attach to its host cell in order for them
to penetrate inside the tissue/cell

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  Gingival crevices and tonsillar crypts – anaerobic flora C. Small Intestine
predominates these sites:  Has scanty resident flora except in the lower ileum
a. Bacteroides which may be inhabited by Streptococci, Lactobaccili,
b. Treponemes and yeasts (Candida)
c. Fusobacteria
d. Clostridia D. Colon
g. Actinomyces  96 to 99% of species in the colon are obligate
h. Peptostreptococcus anaerobes (do not require oxygen for their survival and
die in the presence of it)
 Facultative anaerobes – prefers oxygen for survival but
is able to survive in either presence of oxygen or carbon
dioxide
 Bacteroides
 Clostridium
 Anaerobic streptococci
B. Nasopharynx  Facultative anaerobes comprise 1 to 4 of the flora
 Inhabited by oral microorganusms a. Escherichia coli – leading cause of UTI
 Transient carriage of: b. Proteus and other Enterobacteriaceae
a. Streptococcus pneumoniae – may cause pneumonia c. Enterococci
if present in the lungs d. Pseudomonas
b. Haemophilus spp. e. Lactobacilli
c. Neisseria meningitidis – may cause meningitis if f. Candida
present in the brain  Enteric bacilli in the stool is normal

3. The Conjunctival Sac 5. Genito-Urinary Tract

 Microorganisms are very scanty  Sterile above the distal 1 centimeter of the urethra
 Held in check by the flow of tears, which contain  The urine is sterile once in the urinary bladder and
lysozyme becomes unsterile the moment it passes through the
 Organisms found: urethra due to the presence of bacteria and cells like
a. Corynebacterium xerosis (diptheroids) epithelial cells
b. Moraxella species  Suprapubic aspiration – procedure where a syringe is
c. Staphylococci used to puncture the bladder to be able to collect sterile
d. Non-hemolytic streptococci urine for infection analysis
 Conjunctivitis – sore eyes; have bacterial, viral, and  Vagina
parasitic origin; source of transmission for bacterial type ◦ Is the only site in the female reproductive tract that
is through direct contact (rubbing your eyes, touching sustains a normal flora
other people) ◦ Before puberty or before the post menopausal
 Do not rub your eyes when irritated; wash it. stage, the bacteria present are coming from the
skin
◦ Lactobacilli, aciduric streptococci and yeasts
(present during puberty)
◦ Lactobacilli (specifically Lactobacilli acidophilus) is
responsible for the low pH of the vagina
◦ If it is not acidic, bacterial growth may take place
and cause infections such as:
a. Bacterial vaginosis
4. The Digestive Tract b. Gonococcal vulvovaginitis
Question: Paano nakakarating yung mga normal flora of certain areas of the body sa
A. Esophagus other areas?
Answer: One of the many reasons ay kapag immunocompromised ang isang tao,
 Have transient mouth flora madaling lumilipat ang mga normal flora na ito sa ibang parte ng katawan

B. Stomach Question: Bakit kailangan mag-urinate after having sexual intercourse? Paano
nagkakaroon ng UTI kapag hindi nag-urinate?
 Rapidly becomes sterile after meals; upon the digestion Answer:
of food, gastric juices which are acidic in nature are - The female urethra is shorter than the male urethra, and is therefore more susceptible
to infections such as UTI, for example, kapag nagkaroon ng contact ang rectum at
released, which microorganisms cannot survive vagina kasi lilipat ang mga bacteria.
 Hydrochloric acid – responsible for the breakdown of - If prior to the sexual intercourse at hindi kayo nag-wash, pwedeng magkaroon ng
introduction ng bacteria to the vagina, for example, galing sa mouth. Kailangan umihi
food; has a pH level of 1. para malinis ang urethra (at iba pang dinadaanan ng ihi) para hygienic (since ito ay
acidic before passing through the urethra).

BSN1E - Manuel | 21
BENEFITS DERIVED FROM NORMAL FLORA 4. The organism should be reisolated and shown to the same as
 The normal flora synthesize and excrete vitamins the original.
 The normal flora that prevents colonization by
pathogens DEFINITION OF TERMS IN EPIDEMIOLOGY
◦ Bifidobacteria and breastfeeding inhibit colonization
by enteric pathogens Definition of Terms
◦ Vaginal flora, particularly Lactbacillus, provides Disease Is the undesirable host-parasite relationship
protection against gonococcal vulvovaginitis resulting in interruption in the normal
◦ Prolonged oral antibiotic resistant organisms will functioning of a body structure; outcome of
have an opportunity to increase in number and an infection
produce disease Infection Is the invasion of the body by pathogenic
 Bifidobacteria – can lower the pH level of the microorganisms; may cause disease
gastrointestinal tract, and therefore inhibiting the Contamination The presence of microorganisms on the
survival of bacterial exterior surfaces of the body, water, food,
 Breastfeeding – milk contains antibodies, specifically milk or biological substances
Immunoglobulin A that help fight off enteric pathogens Pollution Indicates the presence of undesirable
 Gonococcal vulvovaginitis – an example of a sexually substances in water, air or soil;
transmitted disease (STD); Gonorrhea is the male environmental concerns
version; “tulo” in Filipino caused by Neisseria Commensals Are microorganisms that routinely colonize
gonorrhoeae body surfaces without doing harm
 Priming of the immune system Pathogens Are microorganisms that damage human
◦ Normal flora stimulates the production of cross- host either by direct evasion and injury or by
reactive antibodies (e.g. Kapag bagong panganak the production of harmful toxic products
ang mga animals, mababa yung immune system Pathogenicity Is the ability to produce disease
nila at sterile sila, and wala pa silang antibodies. Virulence Is the degree or measure of pathogenicity
Yung mga normal flora na meron sila pwedeng
mag act as antigens at mag-induce ng creation of Virulence factor – unique characteristics of
antibodies) a bacteria that makes them pathogenic (e.g.
◦ Antibody-mediated immune response (the immune having a capsule, spikes)
system recognizes the normal flora as an antigen,
therefore, inducing the production of antibodies) TYPES OF INFECTION
◦ Natural antibodies
Types of Infection
Antibiotic misuse or prolonged oral antibiotic intake causes Local infection Is confined to a limited area; the area
bacteria that are resistant to it to proliferate and cause infections. involved determines severity of infection
a. Candida albicans – normal flora; may cause diarrhea and Generalized Is widespread; microorganisms are found
other superficial infections infection even in the smallest capillaries of the body
b. Staphylococcus aureus – normal flora; may cause food Fulminating Results in death
poisoning and necrotizing enterocolitis (tissue death in colon) infection
c. Clostridium difficile – most common cause of antibiotic Exogenous Is one in which the source of
resistance infection; may cause pseudomembranous colitis infection microorganisms is outside the body
Endogenous Is one in which the source of infection is
KOCH’S POSTULATES infection from within the body
 Koch is a famous bacteriologist who discovered Specific Is caused by a known microorganism
mycobacterium tuberculosis. He proposed four (4) infection
 postulates regarding the nature of pathogens. Non-specific Is caused by an unknown microorganism
infection
1. The suspected pathogenic organism should be present in all Latent infection Generally a mild infection and usually there
cases of the disease and absent from healthy animals. are no detectable clinical symptoms
2. The suspected organism should be grown in pure culture. Synonyms: quiescent, dormant, subtypical
 Not all pathogens can be cultivated in the laboratory. infection
 Mycobacterium leprae – a gram positive bacilli Nosocomial Is hospital acquired infection
responsible for leprosy (ketong) infection
 Treponema pallidum, an STD responsible for syphilis Community Is obtained in the community during the
acquired course of our daily lives
 In some cases, an animal can be used to cultivate such infection
pathogens, but not all the time
Single infection Involves one microorganism
 Neisseria gonorrheae – can be grown through selected Mixed infection Caused by two organisms; one or more
culture media diseases may be produced
3. Cells from a pure culture of the suspected organism should Multiple Involves several microorganisms
cause disease in a healthy animal. infection
Acute infection Is a severe infection lasting for a short
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 period of time (about 6 months) Pyemia Is the presence of pus-producing bacteria in
Chronic Lasts for a long period of time (years) the blood stream
infection Viremia Is the presence of viruses in the blood
stream
EPIDEMIOLOGY OF DISEASES Sapremia Is the presence of saprophytes in the blood
 Depends on the total number of cases in a particular stream
period and in a particular location Toxemia Is the presence of toxins in the blood
stream
Epidemiology of Disease
Epidemic Involves a large number of individuals in a KINDS OF CARRIERS
short period of time  According to the method of transmission
 According to relation to disease
Examples:
a. The 1961 cholera epidemic in Manila, According to the Method of Transmission
Republic of the Philippines Fecal carrier Transmits through feces
b. Severe Acute Respiratory Syndrome Urinary carrier Transmits through urine
(SARS) in 2003 that first spread in China Respiratory Transmits through respiratory discharges
then into the Philippines carrier
c. Dengue epidemic in the Philippines in
2019 (many deaths are declared)
Pandemic Is an epidemic that spreads worldwide According to Relation to Disease
disease Incubatory An apparently healthy individual who is
Examples: carrier infected but it has not yet developed
a. Spanish flu (1918-1919) – first pandemic symptoms (bacteria is still starting to adjust
in the history; influenza virus to the individual’s body)
b. H1N1 or swine flu (2009-2010) Active carrier An individual who has an overt clinical case
c. Coronavirus 2019 (COVID19) of disease (with manifestations of disease)
Endemic Is constantly present in the community in Convalescent An individual who has recovered from the
disease low numbers carrier infectious disease but continues to harbor
large numbers of the pathogen (recovery
Examples: period)
a. Zika virus endemic in Philippines Chronic carrier Harbors the pathogen beyond the period of
b. Endemic foci of schistosomiasis recovery
infections in the Philippines (Visayas and
Mindanao) Chronic active carrier – for a long period of
c. Malaria – a vector-borne disease; most when the pathogen is present in the body
prominent in Palawan and are actively multiplying
Sporadic Occurs occasionally in a population Chronic inactive carrier – pathogen is
disease present in the body but not are not actively
Examples: multiplying
a. Sporadic outbreaks of surra in the Intermittent Transmits infection every now and then
Philippines in 1989 – caused by carrier
Trypanosoma evansi; common in carabaos, Health carrier An individual that harbors a pathogen for
horses, and cattles months or years and never become sick
b. Henipavirus in 2014 – common among Vehicle or Is an inanimate object, which transmits
bats; may cause severe acute respiratory Fomite disease when contaminated, such as food,
disease; high mortality rate among horses water, milk or beddings
Exotic disease Is strange or alien in the community Vector Is an insect or other invertebrate which
Epizootic Is an epidemic in lower animals transmits the infection. Has two (2) types:
disease mechanical and biological
Enzootic Is endemic in lower animals Mechanical Act as living fomites by picking up
disease vectors pathogens on their bodies and carrying
Zoonotic Primarily infects lower animals them from one place to another
disease Biological Transmit disease and also play role in the
vector life cycle of the pathogen
TYPES OF BLOOD STREAM INFECTIONS Isolation Is the separation of the sick from others
during the period of communicability
Types of Blood Stream Infections Quarantine Is the limitation of the freedom of movement
Bacteremia Is the bacterial invasion of the blood stream of such individuals who have been exposed
that is brief and harmless to a communicable disease for a period of
Septicemia Is the persistence of multiplying bacteria in time equal to the longest usual incubation
the blood stream producing serious disease period of the disease

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 Segregation Is the separation of a group of individuals to Direct Contact
facilitate the control of a communicable Food, water MOD – fecal-oral route
disease and milk borne Example: Typhoid fever, cholera, and
dysentery, diarrhea
PORTALS OF ENTRY
 Conjunctiva (eyes) Mycobacterium bovis – acquired from
 Nose unpasteurized milk
Animal borne Zoonotic, human to animal excreta
 Mouth
 Face Leptospirosis – a zoonotic infection usually
 Placenta acquired by humans from the excreta of rat;
 Urethra caused by Leptospira Interrogans
 Vagina (spirochete)
Arthropod Vectors: flies, mosquitoes, ticks, fleas, lice
METHODS OF TRANSMISSION OF DISEASES (Insect) borne
A. Direct Contact Fomites Non-living objects
Examples: cups, towels, beddings,
Direct Contact handkerchiefs and surgical instruments
Respiratory a. Bortadella pertussis – causative agent of
droplets whooping cough C. Miscellaneous Methods
b. Mycobacterium tuberculosis – causative  Parenteral transmission – refers to the deposition of the
agent of tuberculosis pathogen directly into a blood vessel, tissue blow the
c. COVID-19 skin, mucous membranes (e.g. Hepatitis B, AIDS and
Airborne There are some microorganisms that can protozoans that cause malaria)
transmission withstand drying
a. Mycobacterium tuberculosis FACTORS AFFECTING COMMUNICABILITY OF BACTERIA
Skin to skin Through skin abrasion or laceration  Ability of the organism to:
contact 1. Survive outside the host
Kissing a. Epstein-Barr virus – may cause infectious 2. Survive in an immune host
mononucleosis 3. Establish the carrier state
b. Herpes simplex virus type 1 – oral cavity 4. Survive in an intermediate host or vector
c. Herpes simplex virus type 2 – genitalia 5. Survive in a reservoir host
Sexual contact a. Gonorrhea – caused by Neisseria
gonorrhea STAGES OF AN INFECTIOUS DISEASE
b. HIV – caused by HIV virus 1. Incubation Period
c. Hepatitis B – caused by Hepatitis B virus  Period of time extending from the introduction of
d. Syphilis – caused by Treponema microorganisms to the host up to the time there are
pallidum signs and symptoms of the disease
Vertical Mother to baby
transmission a. Transplacental transmission – Gernman 2. Period of Illness
measles or rubella virus  Period during which there are signs and symptoms of
b. Perinatal transmission – STD’s are the disease
transmitted from mother to infant
 Gonorrhea – targets the female Outcomes
reproductive system Acute Severe, lasts for a few days; sudden
 Syphilis Chronic Last for a long period of time
 Hepatitis B Carrier state No description
 HIV infection may develop

Opthalmia neonatorum – condition where 3. Convalescent Period

an infant has acquired gonorrhea from the  Period of recovery – elimination of the organisms; repair
mother of the damage done
Prophylaxis – injected into an infant to
prevent them from acquiring disease BACTERIAL BASIC MECHANISM OF CAUSING A DISEASE
Autoinoculatio This involves the transfer of infection from Invasion of Tissues or Surfaces
n one body site of infection to one another of A. Colonization of Epithelial surfaces
the same individual.  Pili or adhesion molecules called adhesins
Example: Warts may spread from fingers to  Bacteria produces a certain protein called adhesins
the face or torso which will facilitate the invasion of tissues or surfaces
(attaches to the mucous surface membrane and
B. Indirect Contact destroys tissues)

BSN1E - Manuel | 24
  Examples: PRODUCTION OF POTENT TOXINS
a. Vibrio cholerae
b. Bordatella pertussis Exotoxin Endotoxin
c. Corynebacterium diptheriae Type of Excreted by living Integral part of the
specie gram +/- bacteria microbial cell wall of
B. Penetration of Epithelial Cells gram negative
 Invasins – trigger the host cell to take them in; special bacteria
type of adhesin Protein Polypeptides Lipid A
 Examples of bacteria that can survive and multiply structure
inside phagocytes are: Heat stability Heat-labile Heat-stable
a. Mycobacterium tuberculosis Antigenicity Highly antigenic (able Do not stimulate the
b. Listeria monocytogenes to initiate immune formation of antitoxin
c. Shigella spp. response, and hence
are used as an
 Intracellular multiplication – when microorganisms
ingredient toxoids)
multiply inside a cell
Toxoid Converted to toxoid Not converted to
C. Evading the Body Defenses toxoids
Toxicity Highly toxic Weakly toxic
 Evading phagocytosis Pyrogen Non-pyrogenic Pyrogenic
 Phagocytosis – major host defense against invading production
pathogens (cell-eating) (ability to
 Some pathogens like Streptococcus pneumoniae cause fever)
produce slippery mucoid capsules that protect them
from phagocytosis DAMAGE CAUSED BY HOST RESPONSES
 Other capsulated organisms:  Hypersensitivity – exaggerated immune response to
a. Neisseria meningitidis (bacteria) components of pathogen; acute (effects manifest in a
b. Hemophilus influenzae (bacteria) matter of hours) or delayed type (months)
c. Cryptococcus neoformans (fungi)  Streptococcus pyogenes – causative agent of sore
 Other pathogens that defend themselves against throat; also damages heart tissues
phagocytosis by producing specialized surface proteins: a. Rheumatic fever
a. Streptococcus pygogenes – causative agent of strep b. Rheumatic heart disease
throat produces surface protein called M protein, which c. Acute glomerulonephritis (damages kidneys)
also has an anti-phagocytic effect

VIRULENCE MAY BE ATTRIBUTED TO:

 Surface molecules – which act by either:
a. Promoting adherence by means of pili or fimbriae
b. Promoting resistance to phagocytosis through its
capsule or slime layer
 Extracellular enzymes – being produced by a certain
bacteria in order to increase their pathogenicity
a. Collagenase – destruction of collagen framework of
muscle (e.g. clostridium perfringes causes necrotizing
fasciitis)
b. Streptokinase and staphylokinase – dissolving of clot
c. Coagulase – formation of clot
d. Leukocidins – ability to destroy white blood cells
e. Proteases – hydrolyzes immunoglobulins
f. DNAses – destroy DNA
 Sidephores – iron binding proteins; pathogens require
iron for multiplication
◦ Iron is well-distributed in the human body. It
contains transport proteins such as ferritin,
transferrin, and lactoferrin.
◦ Iron (from the human body) binds into siderophores
and nourishes pathogens in order for them to
multiply.

BSN1E - Manuel | 25