Rachelle Grace Chan

Microbiology

- It is the study of the biology of microscopic organisms such as viruses, bacteria, fungi, algae, slime
molds, and protozoa

Bacteriology

- A branch of microbiology dealing with the identification, study, and cultivation of bacteria and
with their applications in medicine, agriculture, industry, and biotechnology

Taxonomy

- An area of biologic science comprising three distinct, but highly interrelated, disciplines that
include classification, nomenclature, and identification
- Classification highlights characteristics that are common among certain groups while providing
order to the variety of living things
- The science of classification is known as taxonomy, and taxon is an alternative expression for a
classification category.

Classification

- Kingdom, Division, Class, Order, Family, Genus, Species

o 5 Kingdoms (devised by Robert Whittaker)
▪ Monera (Prokaryotae) – prokaryotes, such as bacteria and cyanobacteria
▪ Protista – includes protozoa, unicellular algae, and slime molds, all of which are
eukaryotes and single-celled
▪ Fungi – molds, mushrooms, and yeasts. These organisms are eukaryotes that
absorb simple nutrients from the soil
▪ Plantae – plants
▪ Animalia – animals
- The organization of microorganisms that share similar morphological, physiologic, and genetic
traits into specific groups or taxa
o Morphology
▪ Cocci (spherical)
▪ Bacilli (rod-shaped)
▪ Spiral (Leptospira, Borrelia, Treponema)

Prokaryotes

- “Pro” means before and “karyon” means nucleus, nut, kernel, or corn
- These are organisms that do not contain a true nucleus surrounded by nuclear membrane,
characteristic of lower forms such as bacteria
- They do not contain organelles and all functions take place in the cytoplasm or cytoplasmic
membrane (the counterpart of cytoplasm in eukaryotic cells is nucleoplasm)

Eukaryotes

- Meaning “true nucleus”

- Organisms whose cells have a true nucleus bound by a nuclear membrane within which lie the
chromosomes
- Cells of higher plants and animals, fungi, and protozoa: morphologically more complex and larger
than prokaryotes
- Contain many membrane-bound organelles in which cellular functions are performed:
endoplasmic reticulum, Golgi body, mitochondria, lysosomes, and nucleus
- More complex compared with prokaryotic cell

Gram Stain

- All cocci are G(+), except Neisseria, Veillonella, Moraxella/Branhamella

- All yeasts are G(+)
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- All spiral organisms are G(-)

- All bacilli are G(-) except Bacillus, Bifidobacillus, Mycobacteria, Actinomyces, Clostridium,
Corynebacterium, Propionibacterium, Erysipelpthrix, Rhusiopathiae, Listeria monocytogenes,
Lactobacillus, Nocardia (BBMACCPELLN)

Gram negative cell wall

- Composes of thin layer of peptidoglycan (can be found on the inner part of the cell envelope)
- Outer membrane: protein, phospholipids, lipopolysaccharides (LPS)
- For LPS:
o Lipid A – major constituent; toxic
o Core polysaccharide
o Antigenic O – specific polysaccharide for serologic identification
- LPS – found only on G(-) cell wall
- Contains endotoxin
- The periplasm is the specific area for transpeptidation (process of replicating peptidoglycan)

Acid-fast organisms

- Mycobacteria, Nocardia, coccidian

Organelles:

- Plasma/Inner Membrane
o Lipoprotein surrounding the cytoplasm
o Functions as mitochondria, Golgi apparatus, and lysosomes of eukaryotic cells
o Functions:
▪ Generate ATP
▪ Site of Photosynthesis
▪ Site of respirations
▪ Regulates osmotic pressure
▪ Transports solute
- Ribosomes – site of protein synthesis
- Nucleoid – DS DNA; where the chromosomes are located ; all bacteria have only 1 chromosome
except Vibrio cholera (has more than 1 chromosome)
- Plasmids – antibiotic resistance structure; exists independently of chromosome; DS DNA;
sometimes disappear during cell division and they can transform bacteria to become pathogenic
o Large – responsible for the production of beta lactamase against beta lactam of penicillin
and oxacillin
o Small – resistant to tetracyclines, chloramphenicol, and gentamicin
- Inclusion bodies – food reserve; lessens the osmotic pressure
o Glycogen
o Carboxysome – cyanobacteria (produce blue pigment), nitrifying bacteria, thiobacilli
o Gas vesicle (bacteria that are usually found beneath earth surface) – Halobacteria,
Cyanobacteria, Thiothrix
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o Cyanopophysin
o Poly-B-hydroxybutyrate
o Metachromatic granules/volutin/polyphosphate granule
▪ Corynebacterium diphtheriae – Babes Ernst
▪ Mycobacterium tuberculosis – Much’s Granules
▪ Yersinia pestis – Bipolar Bodies
▪ Actinomyces – Sulfur granules

Appendages

- Glycocalyx
o Outward complex of polysaccharides
o Attachment of bacteria to the cell
o Resist phagocytosis/desiccation
- Pili/Fimbriae
o Hairlike structure
o Neisseria gonorrhaea – without flagellum but with pili
o Common pili – virulence factor/attachment
o Sex pili – conjugation process
- Flagellum
o Organ for locomotion
o Taxis – the movement of the bacteria toward or away from a particular stimulus
o Protein component: flagellin
o Types of flagella arrangements in bacteria
▪ Monotrichous – A single flagellum extending from one end of the bacteria
▪ Amphitrichous – A single flagellum (or multiple flagella) can extend from both
ends of the cell
▪ Lophotrichous – Several flagella (tuft) can extend from one end or both ends of
the cell
▪ Peritrichous – Multiple flagella may be randomly distributed over the entire
bacterial cell

Bacterial Nutrition and Growth

- Oxygen requirements
o Aerobic bacteria
▪ Use oxygen and grow well in room air
▪ Obligate aerobic – Bordetella, Brucella, Pseudomonas, Haemophilus
o Anaerobic bacteria
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▪ Obligate anaerobic – an organism that strictly does not require the presence of
oxygen; die in the presence of oxygen (Bacteroides, Clostridium)
▪ Facultative anaerobe – organisms that do not require oxygen but grows better in
the presence of oxygen; E. coli
o Microaerophilic – organisms that require 2-10% oxygen for growth
o Aerotolerant anaerobe – anaerobe that grows well in the presence of oxygen
o Enzymes that inhibits the toxic effect of oxygen – superoxide dismutase (SOD) and
catalase
- Carbon dioxide requirements
o 0.03% CO2- needed by aerobic bacteria
o Capnophilic bacteria- requires 5-10% CO2
- Nutritional requirements
o As to carbon source
▪ Autotroph- they use CO2 as the sole source of carbon
▪ Heterotroph- they use reduced, preformed, organic molecule from other bacteria
o As to energy source
▪ Phototroph- organisms that use light
▪ Chemotroph- organisms that use the energy produced by the oxidation of organic
or inorganic compounds
o As to electron source
▪ Lithotroph- they reduced inorganic molecules
▪ Organotroph- they require organic substances (CHO, CHON, Lipids) for growth
and multiplication; all bacteria that inhabit the human body fall into this group
o Most of G(+) are chemoheteroorganotrophs
o Most of G(-) are photoautolithotrophs
o Saprophytes- require dead organic substances
o Parasites- require organic substances from living tissues
- Temperature requirement
o 35-37degC-is the optimum temperature for most bacteria
o Psychrophilic/Cryophilic- grows well at 0ᵒC to a maximum of 15ᵒC; example: Listeria
monocytogenes & Yersinia enterocolitica
o Mesophilic- 20-45ᵒC, most of the pathogenic bacteria grow at this temperature; example:
Escherichia coli
o Thermophilic- 50ᵒC-60ᵒC; Bacillus stearothermophilus (indicator of autoclave) and
Thermus aquatic
o Hypothermophilic- 80-113ᵒC; example: Sulfolobus, Pyrococcus, Pyrodictium
o Extremophilic- prokaryotes that are able to live at unusual conditions like absence of
oxygen, increased temperature and below earth’s surface
o Thermal death time- time required to kill the bacteria at constant temperature
o Thermal death point- temperature required to kill the bacteria at constant time; example:
pasteurization: 63ᵒC (15 minutes)
- pH requirement
o Acidophilic- 0-5.5 (Lactobacillus acidophilus)
o Neutrophilic- 5.5-8.0
o Alkalinophilic- 8.5-11.5 (ex. Bile salt); Vibrio and Bacillus alcalophilus
- As to moisture requirement
o Bacteria loves moist environment
- As to pressure requirement
o Barophilic- organisms that grow rapidly in the presence of high pressure 600 to 1100atm
pressure
- As to high salt concentration requirement
o Requires increased concentration of sodium chloride (6.5% NaCl); Staphylococcus aureus
and Vibrio cholerae
- As to growth factor requirement
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o Purine, pyrimidine and amino acids

Bacterial Growth

- Lag phase/Period of Rejuvenescence

o No doubling cell
o Biosynthesis
o Adapt or adjusting to new environment
o Resistant to antibiotics
- Log phase/Exponential
o Doubling cells
o Biochemical process
o Susceptible to antibiotics
- Plateau/Stationary
o Balance between cell division and dying organisms
o Evidence: drying of culture medium
- Death/Period of Decline
o Death
o Cessation of bacterial growth
o Toxic waste

Physical Method

- Application of heat
o Has 2 types
▪ Moist heat
• Boiling – coagulates protein/denatures; 100C for 10-15mins; kills
vegetative form and non-sporulating bacteria only
• Autoclave – steam under pressure; cannot kill Hep A virus; 121C for
15mins, 15psi for materials in lab; 132C for 30-60mins, 15psi for medical
waste; biological indicators: Bacillus stearothermophilus and Clostridium
PA 3679
• Fractional sterilization/Intermittent sterilization/Tyndallization – Arnolds
sterilizer (100C for 30mins for 3 consecutive days)
• Inspissation – for materials with high protein content; 70-80C for 2hrs for
3 consecutive days; LJ (Löwenstein-Jensen) medium for Mycobacterium
tuberculosis
• Pasteurization – partial sterilization (2months); example: vaccines
o LTH (Low Temperature Holding) – 63C for 30mins (milk, dairy,
alcohol)
o HTST (High Temperature Short Time) – 72C in 15mins
o UHT (Ultra High Temperature) – 140C for 3secs.
▪ Dry Heat
• Denatures protein
• Biological indicator: Bacillus subtilis variation Niger
• Types:
o Flaming
o Oven – for glassware; 160-170C in 1.5-2hrs
o Incineration – 300-400C for materials in lab; 879-980C for
medical wastes
o Cremation – infectious disease/highly contagious
- Filtration
o Vaccines, radioisotopes, toxic chemicals
o Types:
▪ Depth filters – fibrous/granular material (ex: asbestos)
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▪ Membrane filters (circular filters) – cellulose acetate/polycarbonate (0.1mm

thick); examples: antibiotics, oil production
• Liquid filtration
• Air filtration – ex: HEPA (High Efficiency Particulate Air) filter
• Critical sterilizing – parenteral equipment, IV drugs (0.22um)
• 0.45um – filtration of fungi, molds, and protozoa
- Low/Cold Temperature
o Bacteriostatic – inhibits growth of bacteria
o 0-7C – ref temperature
o Example: Listeria monocytogenes lives best at 4C, Syphilis (Treponema pallidum) – killed
at 2-8C for 72hrs
- Desiccation/Lyophilization
o Through drying or dehydration
o Bacteria that can resist desiccation:
▪ Neisseria gonorrhea (pili) – 1hr
▪ Mycobacterium tuberculosis (Much’s granules) – 2 months
▪ Bacillus, Clostridium (spores) – 10years
- Osmotic Pressure
o Increase osmotic pressure = death of bacteria
o Salt and glucose
o Plasmolysis – the protoplasm shrinks away from the rigid cell wall
- Radiation
o Biological indicator: Bacillus pumilus
o Types:
▪ Ionizing radiation – for syringe, needle (ex: y-ray of 1500-2500 radiation), x-ray,
sunlight
▪ Non-ionizing radiation – operating room, laboratory (ex: UV light of 10-400nm)

Chemical Method

- Antisepsis – applied topically to skin (antiseptic)

- Disinfection – usually applied to inanimate objects (disinfectant)

Disease

- A specific illness of disorder characterized by a recognizable set of signs and symptoms

attributable to hereditary infection, diet, or environment
- Classification of infectious diseases:
o Communicable disease – spread from one host to another, directly or indirectly
o Contagious disease – spread easily from one person to another
o Non-communicable disease – not spread from one host to another
- As to occurrence:
o Sporadic disease – occurs occasionally
o Endemic disease – constantly present in a particular location or population
o Epidemic disease – many people acquire the disease in a particular location or population
o Pandemic disease – an epidemic that spans the world (worldwide epidemics)
- Effects of infectious disease
o Symptoms – subjective feelings not obvious to an observer (pain, malaise)
o Signs – objective changes that can be measures (fever, redness, swelling, paralysis)
o Syndrome – a group of signs and symptoms that are associated with a disease (ex: AIDS)
- Phases of Infectious diseases
o Incubation period – the time between the exposure to a pathogenic organism and the
onset of symptoms of a disease
o Prodromal period – first signs and symptoms of disease
o Clinical/illness period – peak of characteristic signs and symptoms of infection of disease
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o Decline period – signs and symptoms begin to subside as host condition improves; the
condition of host deteriorates to death
o Convalescent period/period of recovery – full recovery of surviving host
- True pathogens – are able to invade the tissue of healthy individuals through some inherent ability
(power) of their own
- Opportunistic pathogens – organisms that normally do not cause disease in their natural habitat
in a healthy person; they may cause disease f the host is weakened or if they enter a different
part of the body. Example: Neisseria meningitides – normal flora of the respiratory tract but can
cause meningitis; Escherichia coli – normal flora of the GIT but causes UTI

Factors influencing Virulence

- Toxic factor
o Toxigenicity – ability to produce toxic substances
o Toxins – are poisonous substances produced by pathogenic microorganisms
- Enzyme factor
o Hyaluronidase, coagulase, leucocidin, collagenase, streptokinase, hemolysin, lecithinase
- Cellular structure
o Capsule – resists phagocytosis

Transient flora – inhabit but do not multiply

Resident flora – inhabit and multiply

Virulence – degree of pathogenicity

Virulent – pertaining to a very pathogenic or rapidly progressive condition

Infectious agent factors

- Adherence – pili (fimbriae); surface polysaccharides

- Proliferation
o Secretory antibody, lactoferrin, lysozyme – prevents proliferation
- Tissue damage
- Exotoxins
o Secreted or excreted by living bacteria
o Toxicity is due to simple protein
o Found outside the cell
o Heat labile; inactive at 60c
o From g(+); some from g(-)
o They can be cytotoxins, neurotoxins, enterotoxins
o Usually produces no fever
o Highly toxic/antigenic
- Endotoxins
o Secreted or excreted by dead bacteria
o Toxicity is due to Lipid A (from LPS)
o Found on outer membrane
o Heat stable (121C)
o From g(-)
o Stimulates the fever center
o Low toxic/antigenic
o Synthesized directly by chromosomal genes

Epidemiology

- Study of occurrence, distribution, and causes of disease and injury

- Carrier – a person or animal who harbors and spreads a microorganism that causes disease but
who does not become ill
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o Casual/acute/transient carrier – harbors the microorganism temporarily for a few days or

weeks
o Chronic carrier – remains infected for a relatively long time, sometimes throughout life
(Typhoid bacillus)
o Convalescent carrier – an individual who has recovered from infection but continues to
harbor large numbers of the pathogen
o Active carrier – an individual who has an over clinical case of the disease

Endemic – when an organism of diseases constantly present in a population; it is indigenous to a

geographic area or population

Epidemic – when a disease affects significantly large number of people at the same time in a geographic
area; influenza is a classic example of an epidemic

Pandemic – epidemic over a large area affecting tens of millions of people

Incidence period – the time between exposure to a pathogen and the onset of symptoms; difficult to
determine because individuals often have difficulty pinpointing the date or time of exposure – an
individual may be infectious during this period

Morbidity rate – the rate at which an illness occurs; a measure of the infectiousness of an organism; is the
number of cases of a disease in a specified population during a defined time interval

Mortality rate – is the number of deaths due to a disease in a population

Antimicrobials (Antibiotics)

- Bacteriostatic – inhibits other microorganism

- Bactericidal – destroy/kill the organisms
- Narrow spectrum – effective against a limited number of pathogens
- Broad spectrum – destroy different kinds of organisms
- Classification:
o Natural drugs – produced by bacteria or fungi
o Semisynthetic drugs – these are chemically modified natural drugs with added extra
chemical groups
o Synthetic drugs – chemically produced drugs
- Minimal Inhibitory Concentration MIC) – lowest concentration of drugs that inhibit the
microorganism
- Minimal Bactericidal Concentration (MBC) – lowest concentration of drugs that kills the
microorganisms
- Therapeutic Index (TI)
o Is the ratio of the toxic dose to the therapeutic dose
o Increase in TI = more effective
- Characteristics of a good antibiotic
o Must kill or inhibit the microorganism
o Must have selective toxicity
o Must be non-allergenic
o Must be stable
o Must remain in the specific body tissue
o Must kill the pathogen before mutation can happen
- Action of antimicrobials
o Inhibiting cell wall synthesis
o Inhibiting protein synthesis
o Inhibiting nucleic acid synthesis
o Destroying the cell membrane
o Inhibiting essential metabolites
- Cell wall inhibitors
o Bacitracin
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o Cephalosporin
o Ampicillin
o Imipenem
o Penicillin
- Vancomycin – inhibits translocation and elongation of peptidoglycan; a glycopeptide; a cup-
shaped molecule; structurally similar to teicoplanin drug
- Isoniazid – acts only on growing cells; can be either be bactericidal or bacteriostatic
- Penicillin – against D-alanyl-D-alanine (peptidoglycan)
- Penicillin G – destroyed by stomach acids (parenterally)
- Penicillin V – not destroyed by acid (orally)
- Penicillinase-resistant penicillin – methicillin, nafcillin, oxacillin
- Cephalosporins – cephalothins, cefoxitin, ceftriaxone, cephalexin, cefixime, cefoperazone
- Ampicillin – effective against g(+) and g(-); not destroyed by acid
- Carbenicillin – effective against Pseudomonas and Proteus; not destroyed by acid
- Tetracycline – liver and kidney damage; yellowing of teeth of children
- Chloramphenicol – depression of bone marrow (aplastic anemia); leukopenia (toxic side effect)
- Aminoglycosides – cyclohexane ring (deafness); loss of balance (toxic)
- Macrolide antibiotics – erythromycin, clindamycin, azithromycin
- Protein Synthesis Inhibitors
o 30S ribosome inhibitor
▪ Misreading of mRNA; interferes with aminoacyl-tRNA
▪ Tetracycline – bacteriostatic
▪ Aminoglycosides – bactericidal
o 50S ribosome inhibitor
▪ Inhibition of peptidyl transferase; inhibits peptide chain elongation
▪ Binds to 23S rRNA
▪ Chloramphenicol – bacteriostatic
▪ Macrolide
▪ Erythromycin – bacteriostatic/cidal
▪ Clindamycin – bacteriostatic/cidal
▪ Lincomycin
- Nucleic Acid synthesis inhibitors
o Rifampicin
o Mitomycin
o Metronidazole – disruption of DNA; anaerobic bacteria
o Novobiocin
o Nitrofurantoin
o Quinolones and fluroquinolones
o Ciprofloxacin
o Nalidixic acid
o Norfloxacin
o Levofloxacin – interfere with DNA gyrase and replication; enteric bacteria (E. coli);
bactericidal
- Essential metabolite inhibitors – inhibits enzyme activity
o Folic acid inhibitor
▪ Sulfonamides – high therapeutic index
▪ Trimethoprim – blocks tetrahydrofolate synthesis
▪ Trimethoprim-sulfamethoxazole (SXM)
▪ Co-trimoxazole
▪ Dapsone
▪ Isoniazid
- Others
o Anti-TB drugs – rifampicin, isoniazid, pyrazinamide, ethambutol, streptomycin
- Cell membrane inhibitors
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o Polymyxin B – g(-); P. aeruginosa

o Polymyxin E (Colistin) – ointment
- Anti-fungal agents
o Polyenes (Amphotericin B)
o AZOLE (clotrimazole, ketoconazole, fluconazole)