bacteria

New tools enabled the development of microbiology 

• The development of microbiology was closely linked to tools that allowed people to see microbe 

• Microscopes enabled people to see individual microbe cells 

• Agar plates allowed people to see communities of microbes (colonies) 

The first microscope 

• 1665: fungal fruiting bodies were first observed, with drawings published by english naturalist robert hooke.  

• this used a multi-lens compound microscope he developed 

• 1676: bacterial cells were first observed by the Dutch scientist Antonie van leeuwenhoek. 

• He designed and used a single lens microscope 

spontaneous genration theory

• 300BC: aristotle belived that a ‘vital force’ forma life 

• The spontaneous generation theory help that living organism could arise from non-living matter 

disproving spontaneous generation theory

• 1864: Louis Pasteur filled flasks with rich broth. He sterilised the broth by heating and created a ‘swan’s neck’ in the flasks. 

•  

• When the flask remained upright but open to the air, the broth remained sterile. 

• Tilting the flask brought the liquid broth into contact with the bend, resulted in growth in the broth. 

➢This provided strong evidence to disprove the spontaneous generation theory. 

➢ It strengthened the biogenesis theory (all life comes from preexisting life) 

biogenesis theory

• the biogenesis theory held that living organisms could only arise from pre-existing life 

the first vaccine

1798: Edward Jenner showed that inoculating a healthy person with cowpox infection material protected from smallpox. 

germ theory of disease

1835: Agostino Bassi showed that a silkworm disease was caused by a fungus. This was the first microorganism recognised as causing an infectious disease. 

handwashing

1847: Ignaz Semmelweis advocated handwashing to prevent transmission of child-bed fever between patients. 

• Two wards, one with doctors and midwifes, rates of diseases much higher to in doctors ward, due to doctors training medical students on autopsies, who would then go upstairs to deliver babies 

pasteurisation

1862: Louis Pasteur demonstrated that heating wine for a short period killed the microbes responsible for wine spoilage. This process was named pasteurisation. 

disinfectant

1867: Joseph Lister treated surgical wounds with phenol (carbolic acid), reducing post-operative infections. This was the first disinfectant.

growing bacteria

1876: Robert Koch was the first to grow bacteria in pure culture – with help from Angelina Hesse. 

• With this breakthrough, Dr Koch devised a set of 4 experimental steps known as Koch’s Postulates to show a link between a bacterium and a disease.  

• He used these to identify bacteria causing anthrax, tuberculosis, and cholera. These steps are still used today. 

What are bacteria 

• Single celled microbes, in contrast to acellular microbes (such as viruses) 

• Bacteria are prokaryotes, 

• Bacetria are everywhere, abundant in seawatera nd soil associated with plants and animals 

• Bacteria make up out microbiota (beneficial icrobes) 

• Occasionally, they can cause disease 

found in nearly every niche on the planet, may be adapted to extremes

Bacteria have both positive and negative effects on us 

Negative 

• Human disease 

• Plant and animal disease 

• Food and material spoilage 

Positive effects 

• Biochemical cycles 

• Producing O2 

• Breaking down dead organic matter 

• Nitrogen fixation and nutrient cycling 

• Agriculture and food production 

• Biotechnology 

• Bioremediation 

• Basic research 

Bacteria are prokaryotes 

• Pre-nucleus, includes bacteria and archaea 

• Eukaryotic cells are larger and more complex than prokaryotic cells 

• Doesn't have organelles, relies of surface area to volume ratio, so cannot get too big 

• Lack nucleus, instead have nucleoid 

• Divide by binary fission 

• Lack intracellar organelles 

• Rigid cell wall 

• Surface organelles (motility, attachment) 

key processes of bacteria

1. Metabolism: 

Uptake of chemicals from environment, their transformation within a cell, and elimination of wastes into the environment cell is thus and open cell system 

2. Reproduction (growth) 

Chemicals from environment are turned into new cells under direction of preexisting cells 

3. Differentiation 

Formation of new cells structure such as a spore, usually as part of a cellular life cycle 

4. Communication 

Cells communicate or interact primarily by means of chemical that are released or uptaken 

5. Movement 

Living organism are often capable of self-propulsion 

biofilm

Biofilms are structures of bacterial communities attached to surfaces. 

• Held together by polysaccharides, secreted by the bacteria. 

• Protect bacteria from toxins and predators. 

 

Medically important because: 

1.  they form on many solid surfaces, including teeth or medical devices. 

2.  Bacteria become resistant to antibiotics and immune cells 

How are bacteria classfiied 

• Classification of microorganisms places them into groups with evolutionarily-related organisms. 

• Early classification of bacteria was based on physical traits (phenotypicproperties) that could be observed or measured, including: 

• Morphology (cells, colonies) 

• Differential Staining 

• Motility 

• Metabolism 

• Habitat 

• Pathogenicity 

 

• However phenotypes are not always reliable for classification 

• Distant relatives might appear similar, while close relatives might not appear similar. 

• Phenotypes can change – depending on environment or other signals. 

• Relatedness is difficult to quantify based on phenotypes. 

phylotyping

Physical traits may change, but DNA sequence does not. 

Phylotyping is the comparison of the DNA sequences of specific genes. It is a reliable way to establish evolutionary relationships (= phylogeny). 

Genes that are useful for phylotyping must: 

• be widely distributed 

• be highly conserved 

• contain regions of variation 

• not be spread by horizontal gene transfer 

Widely used phylotyping genes include components of ribosomal RNA. 

• 16S rRNA prokaryotes 

• 18S rRNA eukaryotes 

Process of phylotyping eg with bacteria 16S small subunit rRNA 

1. 16S rRNA gene is sequenced 

2. Aligned with sequence from other organisms 

3. Alignments used to generate a phylogenetic tree 

Universal phylogenetic tree of life 

• 16S and 18S sequences reveal the evolutionary history of all cells 

• There are three domains of life: bacteria, archaea, and eukarya. 

• Bacteria and archaea are very distinct evolutionarily. 

• All cells descend from a single ancestor, LUCA (=last universal common ancestor) 

Common shapes of bacteria 

• Bacteria have a range of cell shapes, size, and ararangements 

• Variations in cell morphology enable adaptation to a range of environments. 

Common shape insclude 

• Rod  

• Coccus 

• spirilum

less common shape include:

• spirochete

• budding and appendages bacteria

• filamentous

Some like spirochete are more adapted to living in a host, while filamentous and stalk and hydra are more adapted to living in environment 

Bacteria can undergo cell division where it stays togetehr instead of completly seperating. Shape depends on how they divide: (along what plane) 

Shape can tell what adapted for 

Arrangements of rod-shaped bacteria  

(bacilli (rods) 

• Eg myccobacterium tubercolosis: 

Streptobacilli: 

Strepto=twisted; bacilli=rods 

• Eg ballcillus anthracis 

Arrangement of coccoid arrangemetns 

Cocci=spherical: 

• diplococcus: two

• streptococcus: string

• staphylococcus: 2d triangle

• tetrad: square

• sarcina: cube

Arrangement of spiral shape bacteria 

vibrio: one curve

spirllium: spirally curve

spirochete: thin

Structure of bacteria 

Bacteria consist of the following 

• A cytoplasmic membrane,  

• usually surrounded by cell wall and sometimes an addition outer layer 

• An internal cytoplasm  

• contains ribosomes, chromosomes, and enzymes 

• External structures 

• Such as capsules flagella, and pili 

inside bacteria

• Bacteria cells contain ribosomes, a nucleoid, and other components in their cytoplasm 

• Unlike eukaryotic cells bacteria do not have intracellular organelles 

• Dna all in one place, so can adapt faster than eukaryotes 

• The bacterial nucleoid contains DNA (the chromosome) organised by DNA-binding proteins but not enclosed in a nuclear membrane  

The cytoplasmic membrane 

• The cytoplasmic membrane forms the boundary between a cell and its environment. 

• It is semi-fluid, comprised of a phospholipid bilayer and embedded proteins, which may form channels. 

Its main function is to regulate movement of materials in and out of the cell by transport mechanisms.

The bacterial cell wall 

•  Doesn't really keep anything inside the cell (the cell membrane dosent that) 

• Bacterial cell wall is made outside the cytoplasmic membrane 

• It is made of multiple layers of peptidoglycan, which is extensively covalently linked and strong (like a chain link fence) 

Gram-positive cell envelope 

• Thick layer of peptidoglycal on surface that interacts with environment 

• Gives very rigid structre, determines shape of cell 

• Eg of pathogens incl. Staphylococcus aureus, Streptococcus pyogenes, Listeria monocytogenes, Bacillus anthracis, Clostridium tetani 

The gram negative cell envelope 

• Thin peptidoglycan layer 

• Have inner and outer membrane, with peptidoglycan layer between, with space between 

• Immune system aprticularly primed to recognised compoents of grma negatiive cell wall 

• Pathogens incl. Escherichia coli, Salmonella enterica, Helicobacter pylori, Vibrio cholerae, Pseudomonas aeruginosa, Yersinia pestis 

• Gram-negative bacteria also have an outer membrane, located outside of the cell wall. 

• The outer membrane is partly composed of lipopolysaccharide (LPS), also known as endotoxin. 

• Lipid A is immedialey recognised as foregn, causes septic shock due to immune system overreaction 

• It is an integral part of the cell envelope and only released from dead bacteria that are broken down. It can cause endotoxic shock (immune response to endotoxin) during bacterial infections 

preparation of gram stain

1. Spread culture over slide in thin film 

Dry in air 

2. Pass slide through flame to heat fix  

Flood slide with stain, rinse and dry 

3. Microscopy 

Place drop pf oil on slide, examine with 100x objective 

procedure of gram staining

1. Flood heat-fixed smear with crystal violet for 1 min 

Result is all cells purple 

2. Add iodine solution for 1 min 

Result is all cells remain purple 

3. Decolourise with alcohol briefly – about 20 sec 

Gram positive cells are purple, gram negative cells are colourless 

4. Counterstain with safranin for 1-2 min 

Gram positive cells are purple, grams negative cells are pink/red 

• Gram-positive cells: dark blue or purple 

• Gram-negative cells: red or pink 

• The stain also enables determination of cell shape (e.g., Gram-positive rod, Gram-negative vibrio) 

Acid-fast stain for mycobacterium species 

Some bacteria dont stain withn gram stain, sometime need different stain more specific for thebacteria 

• Mycobacterium species (eg tuberculosis and leprae)nare detected with ziehl0neelsen acid-fast stain.  

• Acid-fast bacteria retain the bright red carbolfuchsin. 

• Non acid-fast bacteria stain blue. 

acid-fast stain procedure

1. Stain with carbolfuchsin (red) 

2. Decolourise with HCl/ethanol 

3. Counter stain with methylene blue 

 

• This is important for these types of bacteria because they are important human pathogens (cause tuberculosis and leprosy respectivly) 

• Often slow growing in lab and present with other types of bacteria, so good to differentiate them 

Acid-fast cell wall 

• Dont have outer membrane, more closely related to gram positive 

• Have thin peptidoglycan layer by instead have waxy coating made of mycolic acid  

Capsules  

• Protective outer layer 

• Polysaccharide layers 

• May be thick or thin 

• May assist in attachment to surfaces or resist desiccation 

• Protect against phagocytosis (important virulence factor) 

• Therefore can prove much more deadly 

Examples incl: 

• Mycobacterium tuberculosis,  

• Mycobacterium leprae 

• Even though protect bacteria, the capsules very good for vaccines since immune system not able to digest it, but if can recognize, is coated in antibodies and phagocytes can bind to it then digest 

Pilli 

Appendages that help in attachment 

• Pili are filamentous organelles found on the surface of some bacteria. 

• Pili are mainly used to attach bacteria to surfaces or to each other. 

• Bacteria can have two kinds of pili: 

• Long conjugation pili (also called sex pili). Involved in the transfer of genetic material. 

• Short attachment pili (also called fimbriae). These contribute to the pathogenicity of some bacteria. 

flagella

Enable bacteria to swim 

• Particularly prevalent in food-bourne bacteria 

• Flagella are motility organelles expressed on the surface of bacteria. 

• They are long filaments that are rotated by a motor complex at the base of the structure. 

• Flagellated bacteria include: 

• Listeria monocytogenes, Bacillus cereus (Gram-positive) 

• Escherichia coli, Salmonella enterica, Helicobacter pylori, Vibrio cholerae, Pseudomonas aeruginosa, Yersinia pestis (Gram-negative). 

flagella arrangements

• Monotichous 

 eg vibrio choerae 

• Amphitrichous 

 eg campylobacter fetus 

• Lophotrichous 

 eg helicobacter pylori 

• Peritrichous 

 eg proteus mirabilus 

Structure of gram-negative flagellum 

• Embedded in series of rings in cell envelope 

• Hollow tube powered through ATP 

• Has a hook 

filament  

• – long outermost region surrounding a hollow core. 

Hook  

• – curved, slightly wider than filament 

Basal body –  

• anchors the flagellum to the cell wall and plasma membrane. 

chemotaxis and movement

Chemotaxis=  directed movement of cells  towards attractive things and away from repulsive things

• speed and direction of flagellar rotation results in various patterns of motility. 

• “Run” = movement in one direction for a length of time 

• “Tumble” = abrupt, random changes in direction; caused by reversal of flagellar Rotation 

Motility enables movement toward a favourable environment or away from an adverse one. If the stimulus is a chemical, this is known as chemotaxis. Movement toward an attractant results in many runs and few tumbles – runs are longer when the concentration is increasing. 

Peritrichous flagella

• Counterclockwise rotation, cell runs 

• Flagella spread apart in clockwise rotation, cell tumbles 

• Random reorientation then counterclockwise rotation makes cell run in new direction 

Polar flagella

• Reversible flagella 

• Counterclockwise roation of flagella =run 

• Clockwise roation=cell reverse 

• Unidirectional flagella 

• Clockwise roation, cell runs 

• Roation stops, reoreitnation is random 

• Cw rotation, cell runs 

Life processes carried out by bacteria require energy 

Reproduction: 

•  Synthesis of structural material for new identical daughter cells. 

Differentiation: 

•  Synthesis of new specialised cell types. 

Communication:  

• Production of signal molecules, signal transduction 

Self propulsion:  

• Flagellar biosynthesis, motility, chemotaxis 

Metabolism supplies bacterial cells with energy; is the sum of all chemical reactions that occur in a cell 

bacteria can be used for:

Can be used for: 

Sewage treatment 

• Cyanobacteria remove harmful organic matter 

Nitrogen fixation 

• Bacteria in soil makes atmospheric nitrogen assesible to plant and therefore to things that eat plant 

Beverages and food 

• Can be cultivated for food use, eg fermentation 

Drug productions 

• Virtually all antibiotics made from microbes, eg penicillin 

Bacterial metabolism 

• The major elements C, H, N, O, P, S need to be assimilated into the cell, often against a concentration gradient. 

• The imported elements then need to be converted into the molecules that make up the structural components of the cell, 

•  i.e., polymers of sugars, amino acids, and lipids, to enable cell growth. 

• This process requires energy 

Catabolic and anabolic pathways 

Pathways can be categorized as either catabolism or anabolism 

Catabolism: break larger molecules to smaller ones 

• Produces energy and precursor molecules 

Anabolism: combine smaller molecules to make more complex, larger ones 

• Produces macromolecules 

Linkage: 

• Catabolic and anabolic reactions are frequently linked by energy. Catabolic reactions provide the energy needed for anabolic reactions. 

• Sometimes energy not enough, so Adenosine triphosphate (ATP) is a small molecule used to store or release energy 

Catabolic pathways 

Catabolic pathways break down macromolecules into simple component parts, releasing energy in the process. 

• These reactions release energy and are therefore exergonic. 

• AB → A + B 

Anabolic pathways 

Anabolic pathways build macromolecules by combining simpler molecules, using energy in the process. 

• These reactions require energy and are therefore endergonic. 

• A + B → AB 

Microbial metabolism 

• Cellular respiration (oxidative phosphorylation) 

- Aerobic 

- Anaerobic 

• Fermentation (substrate level phosphorylation) 

• Photosynthesis Light Reactions (photophosphorylation) 

Oxidation-reduction (redox) reactions 

Oxidation = removal of an electron 

Reduction = addition of an electron 

Oxidation-Reduction (Redox) Reactions are always coupled. 

• Redox Reactions involve electrons being donated by an electron donor and accepted by an electron acceptor. 

• The oxidised/reduced form of an atom either side of a Redox reaction is known as a redox couple. 

Aerobic respiration 

The catabolism of glucose by aerobic respiration entails the complete oxidation of the carbon in glucose with oxigen as the terminal electron acceptor 

 

• the aerobic respiration of glucose occurs in the following stages: 

1. Glycolysis 

2. Krebs Cycle 

3. Electron Transport Chain 

4. Chemiosmosis 

NADH and FADH2 act as electron carriers, citric acid cycle continues until acetyl CoA is used up, oxidative phosphorylation produces the most energy 

Final electron acceptors for each type of respiration

Aerobic respiration, anaerobic respiration, and fermentation have different final electron acceptrs 

Anaerobic respiration otherwise has same step. 

Aerobic respiration uses oxygen, anaerobic respiration uses other biological moelcules 

fermentation

• Still undergoes glycolysis 

• One process by which pyruvic acid is subsequently metabolized in the absence of oxygen is called fermentation. 

• Fermentation results from the need to recycle NAD by passing the electrons of reduced NAD off to other molecules. 

• Two most common pathways are homolactic fermentation and alcoholic fermentation. 

• Neither captures energy in ATP; just removes electrons from reduced NAD to keep glycolysis going 

Bacteria produce a range of fermentation end products 

• Lactic acid: cheese 

• Ethyl alcohol and co2 : wine 

bacterial genetics

• Bacteria are haploid organisms – they only have one copy of eachchromosome. 

• Bacteria usually have a single, circular chromosomes. 

• Bacteria may have plasmids in addition to a chromosome. 

Bacterial dna replication 

• New strands of DNA are copied by the DNApolymerase enzyme in the 5’ → 3’ direction. 

• The process is initiated by an RNA primer. 

• The double-stranded helix opens apart to allow synthesis to take place. 

• One strand may be synthesized continuously (known as the leading strand). The lagging strand is synthesized discontinuously as Okazaki fragments. 

• As synthesis proceeds, the temporary RNA primers are removed and Okazaki fragments are joined together, resulting in a continuous new DNA strand. 

Replication proceeds bi-directionally: both directions at once 

DNA replication is semi-conservative – each new DNA molecule contains one strand from the parent 

Genetic processes 

1. Replication.  

DNA makes new DNA 

2. Transcription.  

DNA makes RNA as the first step in protein synthesis 

3. Translation.  

RNA links amino acids together to form proteins. 

Transcription and translation occur simultaneously in bacteria (as transcription occurs, mRNA is immediately translated to proteins) 

Transcription 

• Transcription is the process where RNA is copied from the DNA chromosome.  

• It begins when RNA polymerase binds to the “start” (promoter) sequence 

• Transcription proceeds in the 5’ → 3’ direction, then stops when RNA polymerase reaches the “stop” (terminator) sequence 

translation

• Translation is the synthesis of proteins from a message RNA (mRNA) template. 

• The mRNA is translated in codons, a sequence of three nucleotides. 

• Each codon specifies a specific amino acid. Individual amino acids are carried in by tRNA molecules. 

• Translation of mRNA begins at the START codon, AUG, on the mRNA. Translation ends at a STOP codon (UAA, UAG, or UGA) on the mRNA 

Bacteria readily share DNA with other bacteria 

Transformation:  

• DNA is taken up from the environment. 

Transduction:  

• Bacterial DNA is transferred via a virus that infects bacteria (phage) 

• Can sometime introduce host DNA to bacteria 

Conjugation:  

• DNA is transferred between bacteria via a conjugation pilus. 

DNA sharing between bacteria can mean antibiotic resistance, enabling bacteria to share genes allowing bacteria to hide from immune system etc 

Bacterial Growth and Cell Division 

• Bacterial growth refers to an increase in number of cells, not an increase in size. (population increase) 

• Cell division in bacteria, unlike cell division in eukaryotes, usually occurs by binary fission. 

• During binary fission, a cell duplicates its components and divides into two identical daughter cells. (asexual reproduction) 

• The daughter cells become independent when a septum (partition) grows between them, and they separate 

Binary fission 

Symmetric cell division 

Bacteria growth in liquid media 

When bacteria are added to fresh liquid media, they normally go through four distinct growth phases: 

1. Lag phase - numbers do not increase but bacteria are adapting to the medium. 

2. Log phase (logarithmic or exponential growth) – highest rate of growth. 

3. Stationary phase – cell division produces new cells at the same rate that old cells die. 

4. Decline phase – cells die more rapidly than new cells arise due to depletion of nutrients or buildup of toxic waste products 

Measuring bacteria growth 

1. Direct cell counts  

• using a specialized microscope counting chamber 

2. Turbidity measurement of bacterial growth 

• A liquid culture of bacteria has a cloudy appearance (turbidity).  

• Turbidity can be measured using a spectrophotometer. 

• Unscattered light is measured, giving readings in optical density 

3. Viable cell counting 

Colonies on a plate are counted – measuring a living, reproducing population. Dilutions ensure a countable number.

transmission 

Passage of an infectious agent to a new host 

Contact transmission 

Direct contact 

• Eg animals bites 

Indirect contact by fomites  

• (inanimate objects, buttons, rusty nail, etc) 

Droplets 

• Eg from sneezes, sitting next to someone coughing 

Airbone, faecal-oral 

• Waterborne 

• Airborne, incl dust particles 

• Foodborne 

Vector borne 

• Biological 

• Lives part of life inside animal, transfers to another 

• Organisms taken up by vector and transmitted to next host 

Mechanical  

• Eg flys pick up something from landing on rubbish etc, transmitt when land on something else 

Steps in infection process

How many pathogen needed to start disease can vary widely depending on disease 

• Must be exposed to pathogen 

• Pathogen must adhere to skin or mucosa 

• Pathogen must invade through epithelium 

Pathogen must be established: colonosation and growth oth pathogen 

• Must avoid/survive immune system 

• Pathogen can produce toxins to neutralise, kill immune cells 

-Can be local effect or systemic  

• Invasiveness 

-Pathogen invades past intial site of infection, spread to rest of body 

• Tissue damage 

-Can occur both due to pathogen or due to immune response to disease 

Time course for a ‘typical’ bacterial disease 

Incubation period 

• Where pathogen is adhere and may begin to increase in numbers a small amount 

• May not be any symptoms 

• Can sometimes be contagious during this period, pathigen can find new hosts 

prodromal phase 

• Pathogen detected by immune system 

• Produces some ‘flu-like’ vague symptoms, get sense are sick 

• Immune sysetm is activated 

• Invasive (Disease) phase 

• Symptoms become more severe, toxins being produced in high enough numbers to  

• – Acme 

• Peak of invasive phase, pathogen coutn is highest 

• – Fulminating 

• Term for when disease onset occurs very fast, acme is reached ra[idly (within hours) 

Decline phase 

• If hsot survives, pathogen numebrs decline eitehr due to treatment or immuen response 

Convalescence period 

• Repair/recovery period, fix tissue damage 

• Can sometime take a long time 

Bacterial virulence mechanism for colonization and disease 

Virulence facotrs increase bacteria's ability to infect 

Bacteria must: 

• Avoid being killed by immune system (macrophages, complements factors) 

• Uses capsule 

• Flagella (inhibits phagocyte killing 

• Produces toxins which induce symptoms (enterotoxin 

• Endotoxin:  

• Something recognised by immune system as foreign, so immune system produced symptom (eg fever) 

• Sideophores 

• Proteins taht steal iron from host 

Bacterial infections of the skin 

Very few things can infect through intact skin, but are weak spots 

• Hair follicles 

• Abrasion, cuts to skin 

epidermal layer has no blood access, prevent pathogen from entering blood 

The skin for s a protective barrier to infection 

• the skin is the largest single organ of the body. 

• Skin surface consists of a thin epidermis and a thicker, underlying layer, the dermis. 

• The epidermis lacks blood vessels and is nourished by nutrients that diffuse from the dermis. 

• The epidermis has several layers of dead epithelial cells that function as a barrier against injury and infection.  

• The epidermis is renewed every 15-30 days. 

• Dead cells is important as viruses cannot infect dead cells 

• Cells contain keratin, a water-proofing substance. 

• Complex protein, very difficult to break down for bacterial enzymes 

antimicrobial secretions of the skin

help limit pathogen growth 

• Sebaceous glands secrete sebum (lipids and organic acids) 

• Sebum helps maintain an acidic pH to discourage pathogen growth 

• The high salt concentration (from sweat glands) also inhibits many organisms. 

microflora on the skin

• The normal microflora is adapted to low pH and high salt conditions. 

• Resident bacteria exclude pathogens from colonizing but can occasionally cause infections too. 

Common components of the skin microflora 

• – Staphylococcus epidermidis 

• – Staphylococcus aureus 

• – Propionibacterium acnes 

• – Pityrosporon ovale (a fungus) 

staphylococcus aureus 

skin infection

Staphylococcus: Gram positive, non-motile cocci 

Eg  Sty 

• Lesion due to bacterial infection atthe base of an eyelash 

Folliculitis (pimple) 

• Lesion due to bacterial infection of hair follicle 

Furuncle (boil) 

• Pus-filled lesions 

Carbuncle 

• Massive pus-filled lesion 

Scalded-skin syndrome 

• Caused by exfoliatin-producing strains of Staphylococcus aureus.  

These toxins travel through the bloodstream and affect skin over much of the body.  

• The upper skin layers peel off on leaves. Most common in infants. 

furuncle

• Redness, tenderness, swelling are classical signs of inflammation. 

• Bacterial enzymes and pore-forming toxins cause tissue damage. In response, the host deposits fibrin, a tough fibre-like protein that forms a protective web. 

• The result is an abscess. 

• S. aureus remains trapped in abscess (therefore laregly stays local), limiting spread and damage. However, the bacteria are also protected from immunity and antibiotics! 

• Produces pus, mostly dead immune cells 

• Eventually some S. aureus may escape from the abscess if not treated 

• Typically need to be lanced and treated with antibiotics 

Transmission and diesease of staphylococcus aureus

• staphylococcus aureus colonises many healthy people. 

• Normally, S. aureus resides in the nasal passages. When it stays where it’s supposed to, it rarely causes a problem. 

• But S. aureus can cause opportunistic infections.  

• These occur when the microbe gets into a location where it doesn’t belong, i.e., in the blood, lungs, bones, or open wounds.  

strains of staphylococcus aureus

• the 1950’s, methicillin-resistant Staphylococcus aureus (MRSA) strains appeared and are now significant pathogens. 

• MRSA is resistant to methicillin, an antibiotic 

• the bacteria acquired a toxin that kills human immune cells 

• MRSA also acquired genes from commensal Staphylococci that made it more salt-resistant and hence more likely to be carried on the skin 

• Epidemic strains of S. aureus, on the skin, have led to increasing numbers of community-acquired MRSA infections. 

• Infections spread easily through skin-skin contact and pose a particular issue in contact sports. 

streptococcis pyogenes 

Has potential to be both skin and respiratory pathogen 

Streptococcus: Gram positive, non-motile cocci 

Causes:

Erysipelas: 

• Due to abrasions or surgery; begins as small raised lesions.  

• Caused by hemolytic streptococci.  

• Bacteria spread through the lymphatic system, form strong red lesions. 

impetigo 

• A pus-producing infection which affects the face and other parts of the body. Also caused 

• by Staphylococci. 

Necrotising fasciitis 

• Manifests as the death of large amounts of tissue due to the release of toxins.  

• Bacteria live on the dead tissue, producing more toxins. Amputation may be necessary

human respiratory system and infections

• The average human breathes in approx 500 million litres of air in a lifetime. 

• The Human Respiratory System can be infected by a range of bacterial species 

• Indirect contact: airborne transmission 

• Very little barrier between alveoli and blood (due to need for gas exchange), weakness 

• Therefore important to ensure lower respiratory tract is protected from pathogens by upper respiratory tract (much more common than lower tract infections) 

 

• Pathogens can make us more likely to sneeze/cough, in order to spread disease to new hosts 

• Pathgens can live for horus on air (depending on size) 

Upper respiratory tract 

How does upper respiratory trcat protect the lungs> 

• Coarse hairs in the nose filter large dust particles from the air. The nose is lined with numerous mucus-secreting cells and ciliated cells. 

• The pharynx and trachea also contain mucus-secreting cells and ciliated cells. 

• The mucus moistens inhaled air and traps dust and other particles which may contain microorganisms. 

 

• The cilia move in synchronised waves and propel particles and microorganisms which have become trapped in the mucus upwards and away from lungs 

• this forms the so- called ciliary escalator which keeps the mucus blanket moving at a rate of 1-3 cm/hr. 

• Long term smoking severely imoacts ciliary escaltor, liekly to get smokers cought, which is another metohd of moving oathogens up 

Normal microflora of upper respiatroy tracts 

The normal microflora of the upper respiratory tract of healthy individuals contains pathogenic and non-pathogenic bacteria: 

• Haemophilus influenzae 

• Klebsiella pneumoniae 

• Neisseria meningitidis 

• Staphylococcus aureus 

• Staphylococcus epidermis 

• Streptococcus pneumoniae 

• Streptococcus pyogenes 

Streptococcus pharyngitis (strep throat) 

• an upper respiratory disease caused by the group A Streptococcus species Streptococcus pyogenes. 

• Gram-positive cocci, nonsporulating, anaerobic, aerotolerant, homofermentative 

• S. pyogenes also causes other diseases, e.g., impetigo and necrotising fasciitis of the skin; otitis media of the inner ear.  

• Strep throat is characterized by local inflammation and fever. Enlargement of the tonsils and the lymph nodes in the neck can also occur 

Streptococcus pharyngitis (strep throat) method

• Most isolates produce streptolysins, toxins that lyse red blood cells. 

•  On blood agar plates, this is seen as clear zones (a process known as β-haemolysis). 

• Some strains of S. pyogenes carry a lysogenic phage that encodes an endotoxin known as erythrogenic toxin.  

• This toxin produces a pink rash and damages small blood vessels and instigates a fever.  

• These symptoms are known collectively as scarlet fever. 

• S. pyogenes also produces a capsule. 

Streptococcus pharyngitis (strep throat) symptom

• Inflammation of the throat 

• Tonsils swell and can develop pus-filled lesions 

• Lymph nodes in the neck swell 

• Onset can be accompanied by chills, headache, nausea, and vomiting 

• Absence of cough or nasal discharge 

scarlet fever symptoms

• Pinkish red skin rash 

• Tongue has a spotted-strawberry appearance and loses its upper membrane and becomes enlarged 

• High fever 

Diagnosis of strep throat 

In addition to clinical symptoms and signs, diagnosis is based on Rapid Antigen Detection (RAD) systems. 

• A swab is taken of the patient’s throat  

• Surface antigens are extracted 

 

• S. pyogenes antigens are detected with an immunological assay using antibodies specific for S. pyogenes surface proteins. 

• Assays include Enzyme-Linked Immunosorbent Assay (ELISA), Latex-Bead Agglutination, and Fluorescent Antibody Staining. 

 

• Another diagnostic test involves in vitro cultivation of the bacteria from a throat swab.  

• Blood agar plates are examined for β- haemolysis – a clear zone on the plates that indicates streptolysin toxins. 

strep throat treatment

Penicillin and its semi-synthetic derivatives are used for treatment. 

Erythromycin can be used in individuals who have acquired penicillin allergies. 

 

Strep throat currently remains relatively susceptible to penicillin antibiotics and its derivatives 

Mycobacterium tuberculosis 

• Tuberculosis (Tb) is caused by the bacterium Mycobacterium tuberculosis. 

• Tb is one of the oldest recorded human diseases. 

• The bacteria were discovered by Robert Koch in 1882, for which he received the Nobel Prize. 

• At the time, 1 in 3 European adults died of tuberculosis (the “White Plague”)  

M.tb characteristics

• rod shaped 

• Acid-fast cell wall 

• Aflagellate 

• Long generation time (16-20 hr to double) 

• Capacity for ‘dormancy’ 

• Obligate aerobe (requires oxygen) 

• Lacks ‘classical’ virulence factors (pili, flagella, or toxins) 

Tb facts 

• About 1/4 of the world’s population – 2 billion people – are infected with tuberculosis. Most do not have any symptoms. 

• ~5-15% of infected individuals become sick or infectious at some point. In 2025, over 10 million people fell ill with TB.  

• Concurrent infection with HIV greatly increases these odds (20-30 times). 

• Untreated persons with active TB can infect 10-15 people/year. 

• TB caused an estimated 1.23 million deaths in 2025. TB is the leading infectious killer. 

• Over 95% of deaths occur in low- and middle-income countries. 

symptoms of tb

• Contracted via aerosols 

• Primary site of disease=lungs 

Symptoms: 

• Persistent cough 

• Loss of appetite 

• Weight loss 

• Fevers 

• Night sweats 

• constant tiredness 

Disseminated tuberculosis: 

• Bacteria can spread beyond the lungs in active Tb 

• Disease can spread to brain, GI tract, lymphatic, genitourinary tract, bones 

treatment of tb

Prevention: 

• live BCG vaccine 

• variolation 

Diagnosis 

• microscopic and culture examination of sputum samples 

• - Most common/standard 

• X-ray 

• -Cloudy area shows tubercule; immune response trying to contain infectious agent 

• tuberculin-skin test 

• -Tests if someone has been previously exposed (not exclusive to infection, can have had the be cured, or have been vaccinated) 

• - Positive test is red lesion at injection site 

• PCR 

• cytokine profile 

Intervention 

• surgery 

• antibiotics: isoniazid, rifampin, pyrazinamide, ethambutol, streptomycin 

Uptake of mycobacterium tuberculosis 

• When the Mtb reachs the lung in aerosol droplets, the bacteria are phagocytosed (eaten) by resident macrophages. 

• Mtb inhibits phagosome-lysosome fusion - the bacteria survive inside the macrophage. 

• Infected macrophages release cytokines, attracting other immune cells. 

• The cells fuse to form a granuloma (tubercle) that contains the bacteria. 

• Mtb can survive indefinitely in a granuloma.

Infection cycle of Mycobacterium tuberculosis 

For 90% of patients, bacterial replication stops once a granuloma has formed in the lungs. 

• This is latent tuberculosis (patient feels fine). 

In ~10% of cases, the bacteria replicate, and active tuberculosis develops. 

• People with latent TB can develop active TB later in life. 

• Immune suppression, smoking, and HIV infection increase the risk of active TB 

• Active TB is very contagious, bacteria can disseminate beyond the lungs

granuloma

the pathogen is encased in and contained by immune cells. 

Mycobacterium tuberculosis Treatment 

Starts with a combined therapy (if take one, likely to develop resistance)  

• - Isoniazid 

• - Rifampin 

• - Pyrazinamide 

• - Ethambutol or streptomycin 

• Regimen may be adjusted when drug susceptibility results are known. 

• Total treatment time = 8 weeks of 4 drugs + 16 weeks of 2 drugs = 24 weeks total 

Mycobacterium tuberculosis: The other drug problem 

TB patients often fail to take full course of prescribed medication. 

• TB course of treatment is long 

• Many pills have unpleasant side effects 

• Many patients stop taking pills when they start to feel better 

• More susceptible bacteria are killed quickly… more resistant bacteria persist and proliferate. 

Multi-drug resistant TB (MDR-TB): resistant to at least two of the optimal drugs for treating TB (“first line”). 

Extensively drug resistant TB (XDR-TB): resistant to at least four drugs for treating TB (“first and second line”). 

Solution: 

Directly Observed Therapy, Short Course (DOTS) 

• Health care worker watches patient swallow each dose of medication. 

• Improves adherence, reduces relapse and acquired drug resistance. 

• Cures TB 80% of the time. 

• DOTS is widely used in New Zealand too 

Bacterial Infections of the Gastrointestinal Tract 

• The GI tract enables us to ingest food for energy. 

• Bacteria are introduced at the same time in food and water. 

• On average, ~8 x 1010 microbes are consumed each day. 

• Our large intestine is also home to about 1014 resident bacteria. 

• These bacteria colonise shortly after birth.  

They play a key role in our health. 

• Metabolism 

• Gut development 

• Immune development 

• Protection from disease

Introduced via food and water 

Mouth 

• Many resident microbes, including teeth biofilm 

Stomach 

• Extremely acidic kills most bacteria. Few resident microbes 

Small intestine 

• Digestion aided by secretions from liver and pancreas.  

• Most digested food absorbed here. 

Large intestine 

• Many resident microflora. 

• Anaerobic, so microbes mainly ferment. 

• indigestible fibre metabolised, beneficial products made 

Streptococcus mutans and Disease of the Mouth 

eat sugar—> breaks down into glucose and fructose. glucose is fermented by bacteria, (becomes dextrans: cemenst bacteria to tooth). fructose becomes lactic acid (eats away tooth enamel)

cause tooth decay and periodontal disease if untreated