Microbiology 2

What is Mycology?

Study of fungi

(They are aerobic or facultatively anaerobic chemoheterotrophs)

What makes Fungi different to Bacteria

• Fungi has sterols present in membrane

• the sterols are used for sexual and asexual reproduction

Thallus? Hyphae?

• Thallus = the whole body of the fungus

• The thallus is made of long thread-like structures called hyphae

Functions of hyphae

• Vegetative hyphae → grow into the surface/food, absorb nutrients (the “feeding” part)

• Reproductive (aerial) hyphae → grow upwards, produce spores (the “spreading/reproduction” part)

Asexual Reproduction

Methods:

1. Fragmentation of hyphae → pieces of hyphae grow into new fungi

2. Spores → tiny “seeds” that grow into new fungi

Types of asexual spores

Types of asexual spores:

1. Conidiospore, Arthrospore, Blastospore → not in a sac (just free spores)

2. Sporangiospore → inside a sac (sporangium) at the end of a stalk called a sporangiophore

Sexual Reproduction

1. A haploid nucleus (+ strain) from one fungus enters the cytoplasm of a haploid nucleus (- strain) from another fungus

• Only the cytoplasm fuse at this stage, nuclei remain separate for now

 

2. The + and - nuclei fuse to form a diploid nucleus (zygote nucleus)

 

3. The diploid nucleus undergoes meiosis to produce haploid sexual spores

Dimorphism

• Some fungi can grow as unicellular (yeast) or as Mold

• For most, the temp can tell us which one

• 37C for yeast and 25C for Mold

Lichens

A partnership (symbiosis) between:

1. A fungus (provides structure, protection, holds water)

2. Algae (provides food by photosynthesis)

Good and Bad Algae

Good algae

• Convert CO2 to O2

• Are food

• Can be symbiotic

 

Bad algae

• Algal bloom= use O2 off other algae

• Toxins and pests

Protozoa

• Trophozoite → the active feeding and growing form

• Cyst → a dormant, resistant form that helps survive harsh conditions

Excavate

…are flagellated unicellular organisms

(Unusual as they have no mitochondria and reproduce by fission)

Phylum Amoebozoa

• Protozoa (unicellular, eukaryotic organisms)

• Move by pseudopodia (“false feet”) → temporary extensions of the cytoplasm

• Feed by phagocytosis → engulfing food particles with pseudopodia

• Much larger than bacteria

Phylum Apicomplexans

• Obligate intracellular parasites → must live inside host cells to surviv

• Have special organelles at the apex that help them penetrate host cells

• No movement structures

• Two-host life cycle:

  • Mosquito = definitive host (sexual reproduction happens here)

  • Human = intermediate host (asexual reproduction happens here)

Life Cycle of Plasmodium vivax

1. Mosquito bite (infection begins)

• Female Anopheles mosquito bites human → injects sporozoites

2. Liver stage

• Sporozoites travel in blood → enter liver cells

• Multiply asexually → release merozoites into blood

3. Blood stage (causes malaria symptoms)

• Merozoites enter red blood cells (RBCs)

• Inside RBCs → grow into trophozoites (“ring stage”)

• Multiply → RBC bursts → releases more merozoites → infect more RBCs

4. Sexual stage in humans

• Some parasites in RBCs develop into male and female gametocytes (sexual forms)

• These stay in the blood, waiting for the next mosquito bite

5. Back to mosquito (sexual reproduction)

• Mosquito bites infected human → takes in gametocytes

• In mosquito gut → gametocytes fuse → form zygote → develops into sporozoites

• Sporozoites migrate to mosquito’s salivary glands

6. Cycle restarts

• Mosquito bites another human → injects sporozoites again

Toxoplasma gondii

• Transmission: Mainly from cats (in cat feces), or from undercooked meat

• Disease: Toxoplasmosis

  • Usually mild in healthy people

  • Dangerous in pregnancy → can cross placenta and cause fetal infections (brain/eye damage, miscarriage)

Cryptosporidium

• Transmission: Fecal–oral route (especially contaminated water)

• Disease: Cryptosporidiosis

  • Watery diarrhea, stomach cramps

  • Very severe in immunocompromised patients (e.g., AIDS)

Helminths

WORMS

• Reduced digestive system → many absorb nutrients directly from host

• Reduced nervous system → don’t need to sense much, host provides environment

• Reduced locomotion → little need to move; host carries them

• Complex reproduction → produce lots of eggs to ensure transmission

Groups of Helminths

1. Flatworms (Platyhelminthes)

   • Trematodes (flukes) → flat, leaf-shaped; suckers for attachment

   • Cestodes (tapeworms) → long, segmented; no digestive system, absorb nutrients

2. Roundworms (Nematodes)

   • Cylindrical, complete digestive system (mouth → anus)

   • Many are parasites of humans and animal

Trematodes (Flukes)

Example: Lung Fluke (Paragonimus spp.)

• Transmission: Eating undercooked freshwater crabs or crayfish with cysts.

• Life cycle:

  • Eggs → water → hatch → infect snails (intermediate host).

  • From snail → infect crabs/crayfish.

  • Humans eat undercooked crab → larvae migrate from intestine → lungs.

• Symptoms: Chronic cough, bloody sputum, chest pain (mimics TB).

• Hosts: Snail = intermediate; Human = definitive.

Cestodes (Tapeworms)

Example: Beef Tapeworm (Taenia saginata)

• Transmission: Eating undercooked beef with cysts (larvae).

• Life cycle:

  • Eggs in human feces contaminate grass → cows eat eggs.

  • Larvae form cysts in cow muscle.

  • Humans eat undercooked beef → adult worm develops in intestine.

• Symptoms: Often mild; abdominal discomfort, weight loss, visible proglottids in stool.

• Hosts: Cow = intermediate; Human = definitive.

Nematodes (Roundworms)

a) Pinworm (Enterobius vermicularis)

a) Pinworm (Enterobius vermicularis)

• Transmission: Fecal-oral (ingestion of eggs, especially in children).

• Life cycle: Eggs hatch in intestine → adults live in colon → females lay eggs around anus at night.

• Symptoms: Intense perianal itching, especially at night.

• Host: Human only (direct cycle).

Nematodes (Roundworms)

b) Ascaris lumbricoides (giant intestinal roundworm)

b) Ascaris lumbricoides (giant intestinal roundworm)

• Transmission: Ingesting eggs in contaminated food/water.

• Life cycle: Eggs hatch in intestine → larvae migrate through blood → lungs → coughed up and swallowed → mature in intestine.

• Symptoms: Abdominal pain, intestinal blockage, coughing (lung migration).

• Host: Human only.

Nematodes (Roundworms)

c) Hookworm (Ancylostoma, Necator)

c) Hookworm (Ancylostoma, Necator)

• Transmission: Larvae penetrate skin (often bare feet, soil contaminated with feces).

• Life cycle: Larvae enter bloodstream → lungs → coughed up and swallowed → intestine.

• Symptoms: Anemia (they suck blood), fatigue, malnutrition.

• Host: Human only.

Arthropods as Vectors

• Arthropods = animals with:

  • Segmented bodies

  • Hard exoskeleton (outside skeleton)

  • Jointed legs

• Vector = an arthropod that carries and transmits disease-causing microorganisms (pathogens) from one host to another.

Microbial classification and biological basis

• Taxonomy: Classification based on observable traits (phenotype), e.g., shape, staining, biochemical tests.

• Phylogeny: Classification based on evolutionary history (genotype), e.g., DNA, RNA, protein sequences.

• Both help understand what an organism is like and how it evolved.

Classification of Organisms

• Organisms are grouped into taxa (Domain → Kingdom → Phylum → … → Genus → Species).

• Binomial nomenclature: Genus (capitalized) + species (lowercase), italicized, e.g., Escherichia coli.

• Classification reflects both similar traits and evolutionary relationships.

The tools used for classification of various organisms.

• Morphology: Shape, flagella, endospores

• Staining: Gram-positive/negative, acid-fast

• Biochemical tests: Sugar fermentation, enzyme activity, selective media

• Serology: Antibodies detection (ELISA, slide agglutination)

• Phage typing: Bacteriophage sensitivity

• Molecular methods: rRNA sequencing, PCR, DNA fingerprinting

• Prokaryotic groupings include Bacteria and Archaea, each with subgroups and example species.

Archaea Classification

• Methanogens: produce methane from CO2

• Extreme halophiles: require high salt

• Thermoacidophiles: live in high temperature and acidic environments, use sulfur

Types of bacteria (special bacteria)

• Giant bacteria: unusually large bacterial cells

• Intracellular bacteria: live inside host cells (e.g., Rickettsia, Chlamydia)

• Gliding bacteria: move without flagella

• Other examples: spore-forming bacteria (Bacillus, Clostridium), wall-less bacteria (Mycoplasma)

Non-proteobacteria

• Cyanobacteria: oxygenic photosynthesis, some fix nitrogen

• Phototrophic bacteria: purple and green bacteria, anoxygenic photosynthesis

• Gram-positive bacteria: cocci, endospore-forming rods, non-spore-forming rods, irregular rods, Mycobacteria

• Spirochaetes: Treponema, Borrelia, Leptospira

• Chlamydias: obligate intracellular parasites

• Mycoplasmas: no cell wall

Proteobacteria

• Gram-negative, physiologically diverse

• Subdivisions:

  • α: Rickettsia, Bartonella, Brucella, Rhizobium

  • β: Burkholderia, Bordetella, Neisseria

  • γ: Pseudomonas, Legionella, Vibrio, Enterobacteriales (E. coli, Salmonella)

  • δ: Bdellovibrio, Desulfovibrio

  • ε: Campylobacter, Helicobacter

Sterilisation

Removal of all microorganisms

Commercial sterilisation

Removal of microorganisms in food which may cause diseases

Disinfection

Removal of common microorganism from surfaces

Pasteurisation

• Definition: Controlled heating to kill pathogens and spoilage microbes, but not all microbes

• Example: Milk (heated at 72°C for 15 sec)

• Purpose: Safe to drink, but still contains some microbes → NOT sterilisation

Filtration

• Definition: Physical removal of microbes by passing liquid or air through a filter with tiny pores

• Example: Sterilising heat-sensitive liquids (antibiotics, vaccines)

• Note: Can remove bacteria, but viruses may pass through unless ultra-filters are used

Refrigeration

• Definition: Cooling slows down microbial metabolism and growth

• Example: Food storage at 4°C

• Effect: Slows growth, doesn’t kill

Lyophilisation (Freeze-drying)

• Definition: Combination of freezing and drying to preserve microbes or food

• Process: Frozen → water removed by vacuum

• Effect: Keeps cultures/food stable for years. Microbes are dormant, not dead

• Example: Preservation of bacterial cultures, coffee

Desiccation (Drying)

• Definition: Removal of water → microbes cannot grow or reproduce

• Effect: Many survive and grow again when water is added

• Example: Dried fruits, jerky

Osmotic Pressure

• Definition: High salt or sugar concentration draws water out of microbial cells

• Effect: Prevents growth, but not always lethal

• Example: Salted fish, honey, jams

Methods of Moist Heat Control

1. Boiling (100 °C)

• Kills most bacteria, fungi, protozoa, and viruses

• But does not reliably kill endospores

• Example: Disinfecting baby bottle

 

2. Autoclave (Steam under Pressure)

• 121 °C, 15 psi, 15 minutes

• Steam under pressure reaches higher temperatures than boiling

• Sterilises → kills all microbes, including endospores

• Used for: surgical instruments, lab media, dressings, waste

Dry Heat Sterilisation

• Kills microbes by oxidation (burning) instead of protein denaturation (like moist heat).

 

Methods:

• Flaming, passing instruments (like inoculating loop) through a flame

• Incineration, burning waste materials (medical dressings, carcasses)

• Hot-air sterilisation (oven), 170 °C for 2 hours → sterilises glassware, metal instruments

Static

The growth of the micrograms has be stopped for now

Cidal

Microorganism has been killed and wont become alive again

MIC – Minimum Inhibitory Concentration

The lowest concentration of a drug that inhibits visible growth of a microorganism

MIC – Methods

1. Disc Diffusion

• Paper discs with antibiotic are placed on agar inoculated with bacteria

• Antibiotic diffuses outward → creates a zone of inhibition (clear area)

• Larger zone = more effective drug

• Qualitative: Sensitive, Intermediate, or Resistant

 

2. E-test (Epsilometer test)

• Plastic strip with a gradient of antibiotic concentration placed on agar with bacteria

• Elliptical zone of inhibition forms

• The point where the zone edge meets the strip = the MIC value (in µg/mL)

• More precise than disc diffusion

 

3. Broth Dilution Test

• Bacteria are grown in liquid broth with different concentrations of antibiotic

• The lowest concentration with no visible growth = MIC

• Can also determine MBC (Minimum Bactericidal Concentration) if plated afterwards

Antimicrobial drugs

Treatment of microorganisms within infected host is chemotherapy

• These drugs must be selectively toxic (not to kill the host)

• Narrow spectrum affects a specific type of microbe

• Broad spectrum is active against many different types of microbes

Site and mode of action

• Inhibition of cell wall synthesis

• Interference with synthesis of peptidoglycan by preventing elongation of the polymer

• Interference with protein synthesis by binding to ribosomes and preventing attachment of t-RNA and therefore arresting translation

• Injury to plasma membrane

• Inhibition of nucleic acid synthesis

• Interference with metabolic function

• Antiviral drugs

• Antiprotozoal drugs

• Anthelminthics

Effects of antimicrobial agent use

• Destruction of the microbe (cidal effect)

• Stops microbes growth (static effect)

• Rise of antibiotic resistance

• Occurrence of superinfections

Combination

• Synergism= enhanced effect

• Antagonism= interfere with the others action

• No effect

Antibiotic resistance

• Acquisition= the microbes have the gene to protect themselves

• Mutation= they have under gone a change which activate the gene

Mechanisms of antibiotic resistance

1. Organism lacks structure an antibiotic inhibits.

2. Organism impermeable to an antibiotic

3. Organism inactivates an antibiotic

4. Organism modifies a target structure of an antibiotic

5. Organism alters a biological pathway an antibiotic blocks

6. Organism actively pumps out the incoming antibiotic

Define

Colonisation

Pathology

Etiology

Pathogenesis

Infection

Disease

• Colonisation: occupation of specific niches of the host by harmless or symbiotic microorganisms (normal flora)

• Pathology: the study of disease

• Etiology: the cause of a disease

• Pathogenesis: the development of disease

• Infection: invasion of the body by pathogens (disease may or may not be the result. the invading microbe may exist in equilibrium with the host defence systems and the host becomes a carrier (typhoid Mary)

• Disease: an abnormal state in which the body is not performing normal functions

Define

Commensalism

Mutualism

Parasitism

Opportunistic Infection

• Commensalism: one organism benefits and the other is unaffected

• Mutualism: both organisms benefit

• Parasitism: one organism benefits to the detriment of the other

• Opportunistic infection: changes in the normal flora by deodorants, caustic soaps, antibiotics or change in the health status can lead to opportunistic infections

Define

Synergism

Antagonism

• Synergism: two microbes work together to make a disease worse

• Antagonism: normal microbiota protect us by blocking harmful microbes

Koch's postulates:

1. Isolate same agent of disease from every infected tissue

2. Purify in culture

3. Re-create the disease in a healthy animal using purified agent

4. Demonstrate that re-created disease is due to the same agent

Exceptions to Koch's Postulates

• Organisms that do not grow well or at all on artificial medium organisms

• Some disease symptoms can be caused by several different

Modes of Transmission

Communicable diseases

• Transmitted from person

• TB, Hep B and C

 

Contagious diseases

• Highly infectious, fast spreading from person to person

• Chicken pox, measles, flu

 

Non-communicable diseases

• Accidentally introduced into host

• Tetanus

Define

Local Infection

Systemic Infection

Focal Infection

• Local infection= small area of the body

• Systemic= most of the body is affected by spreading organism

• Focal infection= spread via lymph or blood system to other parts of the body.

Define

Bacteraemia

Veremia

Septicaemia

Toxaemia

• Bacteraemia is presence of bacteria in blood

• Viremia is presence of virus in blood

• Septicaemia is multiplication of bacteria in blood

• Toxaemia is presence of toxin (like tetanus) in blood

SARS-CoV: A classic zoonosis

1.  Inter-species contact:

Chinese wholesale animal markets house >100 species simultaneously

 

2. Cross-species transmission

• Many species are susceptible

• civets, ferret badgers, monkeys, rodents, cats, pigs

 

3. Sustained transmission

• Civet-to-civet and human-to-human transmission documented

 

4. Adaptation

• Spike protein binds to host cell receptors and determines host specificity

• Rapid evolution following initial infections in civets and people
  SARS-CoV from initial outbreak (2002) showed greater affinity for human receptors than civet viruses or later (2004) mild human cases

Disease development

Incubation period

• Time between invasion of the host and onset of symptoms

 

Prodromal period

• Onset of mild general symptoms

 

Period of illness

• Acute phase of disease with maximum symptom display

 

Decline period

• Easing of the symptoms (secondary infection risk)

 

Convalescence

• Period to full recovery

EPIDEMIOLOGY

• The study of where, when and how often specific diseases occur and how they are transmitted in host populations

• Fathered by John Show in 1848-1849, he monitored epidemic of cholera in London

Descriptive epidemiology, (collection of data)

• Retrospective - collecting information of past cases

• Prospective - studying healthy individuals who are likely targets of next outbreak and then following the cases as they become subjects of disease

Analytical epidemiology

Analysing collected data to determine the probable cause

• Case control - comparing data from affected and non-affected individuals during disease period/outbreak to determine predisposing factors such as age, sex, genotype or location (backwards)

• Cohort - comparing matched groups of individuals, with and without disease history (forwards)

Experimental epidemiology

• Hypothesis followed by testing the hypothesis by differential treatment of matched groups, say with particular drug and placebo

• Case reporting is very important in every study

• Mortality - incidents of death due to a particular disease

• Morbidity - incidence of disease in the population

Define

Pathogenicity

Virulence

Portals of Entry

• Pathogenicity= the ability to cause disease by overcoming host defences

• Virulence= degree of pathogenicity

• Portals of entry= entry point of pathogen into the host mucus membrane, skin, parenteral or subcutaneous deposition (via vector)

Mucous Membrane

• The most common entry for microbes are the reparatory and gastro intestinal mucosa

• Then the genitio urinary tract and the conjunctiva

Cutaneous: Skin

• Cuts or abrasions

• Hair follicles

• Sweat glands

• Invaders such as hookworm larvae can bore through intact skin

• Some fungi can utilise keratin as a food source and infect the skin

Parenteral

(below the tissue)

Bites, injections, cuts

Preferred portal of entry

• To cause disease, the microorganism has to enter a host in a specific way, otherwise it becomes subject to host defences

• Eg Salmonella typhi will cause disease when ingested but not when enters through skin

• Streptococci can cause pneumonia when inhaled, but no disease occurs if they are ingested

Infectious dose

The greater the number of invading cells, the greater is the chance of disease

• ID50= Infected 50%

• LD50= Kills 50%

Pathogenicity Determinants

Adherence

Adherence

• Ability to attach to host tissues

• Adhesins may be non-specific structures on the cell wall such as glycoproteins, lipoproteins and LPS or specifically encoded structures such as fimbriae

 

• The receptors on the host cells are usually sugars, these are NOT present for the benefit of the microbes

• Some adhesin, receptor reactions are so specific that microbes can only attach and penetrate a particular type of cells only

• Eg Neisseria gonorrhoeae fimbriae can only attach to columnar epithelial cells.

Pathogenicity Determinants

Capsules

Capsules

• Glycocalyx layer surrounding the cell wall forms a capsule

• It resists phagocytosis by macrophages, by preventing adherence

• Host defence then must produce antibodies to the capsule antigen which in turn opsonise the capsule and allow phagocytosis

• Production of capsules is a known virulence factor

• Capsules are not always related to virulence, can be utilised by bacteria to form biofilms

Degradative enzymes

• Leucocidins: destroy leucocytes

• Haemolysins: destroy red blood cells

• Coagulases: clot fibrinogen in blood , avoid phagocytosis (hide)

• Kinases: break down fibrin, dissolve blood clots which would isolate infection (spread)

• Hyaluronidase: hydrolyses connective tissue

• Collagenase; breaks down collagen, causes major tissue damage

• Necrotising factors; lecithinase, proteases, siderophores etc

Invasion into host cells

• Attachment of bacterial cells induces production of proteins called invasins (invasols)

• Alter host cell membrane

Exotoxins

• Living bacteria

• Damage and kill cells directly Cytotoxins (diphtheria and erythrogenic)

Neurotoxins

• Botulinum toxin is produces Clostridium botulinum

• Blocks release of neurotransmitter acetylcholine and prevents muscle contraction (flaccid paralysis)

• Tetanus toxin is produced by Clostridium tetani

• Blocks Glycine release and muscle relaxation (lockjaw)

Enterotoxins

• Intestinal system

• Poopy water

Endotoxins

• Endotoxins are part of cell wall of gram neg bacteria

• Causes pyrogenic response and septic (or endotoxic shock)

Plasmids and lysogenic bacteriophage

Can carry virulence factors, genes encoding toxins fimbriae, degradative enzymes

Cell damage of host cell by viruses - cytopathic effect

Some effects that viral infection has on the host cells are very specific to the infecting virus

• Arrest of cell cycle

• Formation of inclusion bodies

• Formation of syncytium-fused cells (fused cells)

Flagella

• Long filamentous appendage that move bacteria

• Monotrichouse= single at one pole of the cell

• Amphitricha's= single at both poles of the cell

• Lophotrichouse= two or more at one pole of the cell

• Peritrichous= distributed all over the cell

 

Axial Filaments (endoflagella)

Fimbriae and Pili

• Fimbriae is used for attachment to host tissue

• Pili is involved in motility and transfers plasmid DNA between bacteria