Infectious Diseases Notes

Module 1, Topic 1
●​ Why is the study of microbiology essential for the health professional?
●​ Why are microorganisms important in the environment?
Cell Wall Structure:
-​ Peptidoglycan = repeating units of a disaccharide molecule containing two glucose
derivatives; NAG and NAM.
1.​ Gram-Pos: main component is a thick layer of peptidoglycan. The disaccharide
molecules are cross-linked to form a complex rigid network. Attached to the
peptidoglycan are other complex polysaccharides called teichoic acids. These have a
strong negative charge, influences the passage of materials in and out of the cell and
contributes to the antigenic specificity of the cell wall.
2.​ Gram-Neg: thin layer of peptidoglycan covered by an outer membrane containing
lipopolysaccharides, lipoprotein, and phospholipids. Outer membrane provides a barrier
to the entry of various substances into the cells and also prevents the actions of certain
enzymes that break down bacterial cell walls. Lipid A is an endotoxin produced by Gram
neg bacteria.
Virulence Factors:
Motility:
●​ Most common way of movement is flagella; thin rigid filaments.
●​ Flagella consist of protein subunits arranged in a complex structure.
●​ They are attached to the cell membrane and wall of the bacterium by a structure called a
basal body.
●​ Movement of the bacterium is achieved via rotation of the flagella with a propeller-like
motion.

Glycocalyx

●​ Sticky polysaccharide layer (slime layer or capsule).

●​ Protects from drying, assists in attachment to host cells.
●​ Slime Layer: Loose, helps biofilm formation on medical devices.
●​ Capsule: Firm, organized; prevents phagocytosis and enhances virulence.

Endospores

●​ Formed by Gram-positive bacilli under unfavorable conditions.

●​ Highly resistant (heat, germicides); sterilization requires 121°C for 15 mins.
●​ Essential for hygiene in hospitals and food preservation.

Growth and Reproduction of Bacteria

Environmental Factors
 1.​ Water & Osmotic Pressure:
○​ Requires isotonic environment for optimal growth.
○​ Hypotonic: Causes cell swelling and lysis.
○​ Hypertonic: Shrinks the cell, slowing growth.
2.​ Oxygen:
○​ Aerobes: Require oxygen.
○​ Obligate Aerobes: Grow only with oxygen.
○​ Anaerobes: Grow without oxygen (e.g., obligate anaerobes killed by free
radicals).
○​ Facultative Anaerobes: Adapt to both aerobic and anaerobic conditions.
3.​ Temperature:
○​ Mesophiles: Moderate temps (optimum 37°C).
○​ Psychrophiles: Cold-loving (-10–20°C).
○​ Thermophiles: Heat-loving (45–80°C).

Nutritional Requirements

●​ Carbon: Essential for cellular growth; heterotrophic bacteria rely on organic carbon.
●​ Other elements: Nitrogen, phosphorus, sulfur, trace minerals.
●​ Lab growth: Requires optimal culture media.

Bacterial Reproduction

●​ Binary fission: Produces identical daughter cells.

●​ Generation time: Typically 20–30 mins under favorable conditions.
●​ Rapid reproduction explains how minor infections can quickly escalate.

Virus Classification

●​ Classified into groups or families based on:

○​ Type of nucleic acid (ssRNA, dsRNA, ssDNA, dsDNA).
○​ Shape and structure.
○​ Method of replication.
●​ Each virus contains one type of nucleic acid, coding for:
○​ Structural proteins.
○​ Limited enzymes.
○​ Regulatory genes.
Viral Capsids

●​ Limited number of protein molecules with functions:

○​ Antigenic properties to stimulate host antibodies.
○​ Facilitate attachment and entry into host cells.
●​ Some viruses have envelopes:
○​ Glycoproteins ("spikes") aid in attachment to host cells.
○​ Enveloped viruses are more sensitive to environmental factors compared to
naked viruses.

Host Specificity and Tissue Tropism

●​ Viruses are selective in host range and tissue specificity.

●​ Plant viruses infect plants, bacterial viruses infect bacteria, and animal viruses infect
animals.
●​ Some viruses (e.g., SARS-CoV-2, Influenza A) can cross species barriers.

Viral Replication Steps

1.​ Adsorption: Virion attaches to host cell receptors.

2.​ Penetration: Entire virion enters host cell via direct penetration, membrane fusion, or
phagocytosis.
3.​ Uncoating: Capsid and envelope dismantled; nucleic acid released.
4.​ Synthesis: Viral nucleic acids and proteins synthesized using host machinery.
5.​ Assembly: Viral components assembled in the nucleus (DNA viruses) or cytoplasm
(RNA viruses).
 6.​ Release:
○​ Naked viruses cause cell lysis.
○​ Enveloped viruses bud off from host cell membrane.

Viral Life Cycle

●​ Cycle duration: Several hours.

●​ Outcomes:
○​ Immediate host cell lysis and death.
○​ Continuous virion release without immediate host cell death.

Viral Pathogenesis

●​ Low pathogenicity favored for evolutionary survival.

●​ Asymptomatic or mild infections enable virus replication and spread.

Immune Response to Viral Infection

●​ Host defenses include:

○​ Interferons: Cytokines preventing viral replication.
○​ Cytotoxic T lymphocytes: Destroy infected cells.
○​ B lymphocytes and antibodies: Neutralize free viral particles.
○​ Memory cells: Provide immunity against re-infection.
●​ Symptoms caused by immune response:
○​ Swollen lymph nodes, malaise, headache, myalgia.
●​ Recovery depends on immune system maturity and efficiency.

Viral Families (Examples)

DNA Viruses:

●​ Parvoviridae: ssDNA, naked, 18–26 nm.

●​ Herpesviridae: dsDNA, enveloped, 150–200 nm.

RNA Viruses:

●​ Picornaviridae: ssRNA, naked, 20–30 nm.

●​ Orthomyxoviridae: ssRNA, enveloped, 80–120 nm.

Acute Lytic Infection

●​ Characterized by diseases with well-defined symptoms (e.g., common cold, mumps,

influenza).
●​ Steps in infection:
○​ Virus attaches to a target cell, enters, and takes over host machinery to replicate.
 ○​ New virions cause cell lysis and death, spreading to neighboring cells and
producing symptoms.
●​ Host immune response:
○​ Eliminates the virus.
○​ Produces antibodies and immunological memory, leading to long-lasting
immunity for many diseases.
●​ Some viruses mutate, altering their outer envelope or capsid (e.g., influenza), enabling
reinfection with new strains.
●​ Over 100 different viruses cause cold symptoms; immunity develops only against the
specific infecting virus.

Subclinical Infections

●​ Infections with no recognizable symptoms; may show:

○​ General malaise, slight fever, or lymphadenopathy.
●​ Recovery often occurs without awareness of the infection.
●​ Immune response:
○​ Produces antibodies and a cellular response.
○​ High antibody levels (antibody titre) indicate immunity.
●​ Many viral infections are self-limiting, with the immune system clearing the virus
completely.

Persistent Viral Infections

●​ Some viruses remain in the host for long periods, resulting in different outcomes:

Latent Viral Infections

●​ Virus remains dormant in host cells, reactivating later to cause disease recurrence.
○​ Common with herpesviruses and HIV.
○​ Initial disease followed by apparent recovery, but some viral particles persist.
○​ Often hides in non-target cells to evade the immune system.
○​ Reactivated by compromised immunity (e.g., shingles from VZV, cold sores from
HSV).
●​ Slow infections may lead to new, distinct symptoms years later.

Chronic Viral Infections (Carrier State)

●​ Virus persists in the host with continuous low-level production and shedding.
○​ Carriers are asymptomatic but infectious (e.g., Hepatitis B, HIV).
○​ Outcomes of Hepatitis B:
■​ Acute infection with recovery and immunity.
■​ Fulminant infection causing death.
■​ Chronic carrier state (5–10% of adults).
Oncogenic Viruses

●​ Transform human cells into cancer cells by altering growth regulation.

●​ Mechanisms:
○​ Introduce a transforming gene into the cell.
○​ Alter expression of a pre-existing proto-oncogene.
●​ Result:
○​ Viral DNA integrates into host genome and replicates with it.
○​ Loss of contact inhibition leads to uncontrolled replication and tumor formation
(neoplasia).

Disease Examples by Infection Type

●​ Acute infection: Influenza virus, Hepatitis A virus.

●​ Latent infection: Herpes simplex virus, Varicella-zoster virus.
●​ Chronic infection: Hepatitis B virus, HIV.
●​ Slow infection: Caused by unconventional agents; symptoms appear after months or
years.

What is Microbiology and How Do We Classify Microorganisms?

●​ Microbiology: Study of microorganisms, including bacteria, viruses, fungi, protozoa, and

algae.
●​ Classification: Based on:
○​ Morphology (shape, size).
○​ Biochemical properties.
○​ Genetic characteristics.
○​ Phylogeny (evolutionary relationships).

What is an Emerging Disease and Re-emerging Disease? Give an Example.

●​ Emerging disease: A new or previously unrecognized infection.

○​ Example: COVID-19 caused by SARS-CoV-2.
●​ Re-emerging disease: A previously controlled infection resurging due to changes in
epidemiology or control measures.
○​ Example: Tuberculosis.

How Do the Structures of Gram-Negative and Gram-Positive Cell Walls

Differ?

●​ Gram-positive:
○​ Thick peptidoglycan layer.
○​ Teichoic acids present.
○​ No outer membrane.
 ●​ Gram-negative:
○​ Thin peptidoglycan layer.
○​ Outer membrane with lipopolysaccharides (LPS).
○​ Periplasmic space present.

What Structures Influence Bacterial Pathogenicity?

●​ Capsules: Prevent phagocytosis.

●​ Pili/Fimbriae: Aid in adhesion to host tissues.
●​ Endospores: Allow survival in harsh conditions.
●​ Toxins: Cause tissue damage (e.g., exotoxins, endotoxins).
●​ Flagella: Enable motility and invasion.

What is Involved in the Four Phases of Bacterial Growth?

1.​ Lag phase: Cells adapt to the environment; no division.

2.​ Log phase: Exponential growth with active division.
3.​ Stationary phase: Growth slows due to nutrient depletion or waste accumulation.
4.​ Death phase: Decline in viable cells as death rate exceeds reproduction.

How Are Medically Important Bacteria Grouped? Provide Examples.

●​ Shape: Cocci (e.g., Staphylococcus aureus), Bacilli (e.g., Escherichia coli).

●​ Gram reaction: Gram-positive (e.g., Clostridium difficile), Gram-negative (e.g.,
Salmonella).
●​ Oxygen requirement: Aerobic (e.g., Mycobacterium tuberculosis), Anaerobic (e.g.,
Bacteroides).
●​ Pathogenicity: Opportunistic (e.g., Pseudomonas aeruginosa), True pathogens (e.g.,
Streptococcus pyogenes).

What Are the General Steps of Viral Replication in an Animal Cell?

1.​ Attachment: Virus binds to host cell receptor.

2.​ Penetration: Virus enters the host cell via endocytosis or membrane fusion.
3.​ Uncoating: Viral nucleic acid is released from the capsid.
4.​ Replication: Viral genome is copied, and viral proteins are synthesized.
5.​ Assembly: New virions are assembled.
6.​ Release: Virions exit the host cell via lysis or budding.

What is a Mycoses? Provide Examples of an Associated Microbe.

●​ Mycoses: Fungal infections in humans.

○​ Superficial mycoses: Malassezia furfur (e.g., tinea versicolor).
○​ Cutaneous mycoses: Trichophyton spp. (e.g., athlete’s foot).
 ○​ Systemic mycoses: Histoplasma capsulatum (e.g., histoplasmosis).

Ebola Virus:
●​ Resulted in over 10k deaths
●​ One of the deadliest acute hemorrhagic viral diseases, mortality = 60%
●​ Transmitted through direct contact with blood or other bodily fluids from infected people.
This includes unprotected sexual contact with patients even after they’ve recovered.
●​ Can be contracted by eating bush meat
●​ Symptoms stage 1 = fever, muscle aches, weakness, headache, and sore throat.
●​ Symptoms stage 2 = vomiting, diarrhoea, rash, and malfunction of the liver and kidneys.
●​ Efforts to control spread were hampered by people’s fear and mistrust of health
authorities, and their suspicion of Western intervention.
●​ Spread = people fled to neighbouring countries.
●​ Half of the health workers who contracted the disease died.

Case Study 1: MRS-Cov

Why is it important to take a full travel history?

●​ Helps identify potential exposure to infectious diseases endemic to specific regions.

●​ Provides context for symptoms that might be linked to travel-related pathogens (e.g.,
MERS-CoV in this case).
●​ Enables timely isolation and testing to prevent disease spread.

What would need to be done about the other passengers he travelled with?

●​ Contact tracing: Identify and notify all passengers on the plane, bus, and any close
contacts in public spaces.
●​ Testing and monitoring: Screen passengers for symptoms, test for MERS-CoV, and
recommend quarantine for those exposed.
●​ Public health alerts: Issue advisories to local health authorities and the public about
possible exposures.

What precautions should healthcare workers take when caring for this
patient?

●​ Place the patient in an airborne isolation room.

●​ Use personal protective equipment (PPE): N95 masks, gloves, gowns, and eye
protection.
●​ Follow strict hand hygiene protocols.
●​ Limit the number of healthcare workers interacting with the patient.
●​ Properly disinfect and dispose of contaminated materials.
Should MERS-CoV be suspected in anybody with respiratory symptoms
who has travelled to Saudi Arabia?

●​ Yes, especially if:

○​ Symptoms include fever, cough, and shortness of breath.
○​ The travel occurred recently or involved exposure to healthcare settings in Saudi
Arabia.
○​ There is known contact with camels or confirmed MERS-CoV cases.

How does the presence of this virus in the Middle East affect preparations
for mass gatherings, such as the annual Haj pilgrimage?

●​ Enhanced screening: Health checks for pilgrims before and after travel.
●​ Public health education: Promote hygiene practices and precautions (e.g., wearing
masks, avoiding camels).
●​ Medical preparedness: Increased availability of isolation units and PPE at pilgrimage
sites.
●​ Surveillance: Monitor for respiratory symptoms during and after the event.

What are the similarities and differences regarding MERS-CoV and

SARS-CoV-2 in this scenario?

Similarities:

●​ Both are zoonotic coronaviruses causing respiratory illnesses.

●​ Spread via respiratory droplets and close contact.
●​ Require isolation and contact tracing to prevent outbreaks.

Differences:

●​ MERS-CoV:
○​ Originated in the Middle East; linked to camels as a reservoir.
○​ Lower person-to-person transmission rate.
○​ Higher mortality rate (~35%).
●​ SARS-CoV-2:
○​ Originated in Wuhan, China; linked to bats and other potential intermediaries.
○​ Higher transmissibility, leading to a global pandemic.
○​ Lower mortality rate compared to MERS-CoV.

Topic 2:
●​ Definition and Structure:
○​ Genes determine observable characteristics (phenotype) of organisms.
 ○​ A gene is a section of DNA composed of a specific nucleotide sequence.
○​ Nucleotides consist of:
■​ A nitrogenous base (adenine (A), thymine (T), guanine (G), cytosine (C)).
■​ A sugar molecule (deoxyribose).
■​ A phosphate group.
●​ DNA Structure:
○​ DNA forms a double helix with:
■​ Two strands of nucleotides held together by hydrogen bonds.
■​ Base pairing: A with T, and G with C.
○​ Complementary and antiparallel strands allow exact replication.
●​ Chromosomes and Plasmids:
○​ Genes are organized into chromosomes.
■​ Bacteria: Single circular chromosome.
■​ Eukaryotes: Multiple chromosomes within a nucleus.
○​ Plasmids in bacteria carry extra genes, e.g., antibiotic resistance.
●​ Protein Synthesis Overview:
○​ DNA directs cell division and protein synthesis.
○​ Proteins:
■​ Made of amino acids linked by peptide bonds.
■​ Essential for cellular functions like metabolism, growth, and repair.
●​ RNA and Transcription:
○​ RNA types in protein synthesis:
■​ rRNA: Forms ribosomes.
■​ mRNA: Carries genetic instructions to ribosomes.
■​ tRNA: Transfers amino acids to the growing protein chain.
○​ Transcription: DNA is copied into mRNA using RNA polymerase.
●​ Translation:
○​ mRNA directs the assembly of amino acids into proteins.
○​ Codons (3 nucleotide bases) on mRNA correspond to specific amino acids.
○​ STOP and START codons regulate translation.
●​ Gene Expression:
○​ Genes can be "expressed" (produce proteins) or "not expressed" based on
cellular needs.
○​ Expression is critical in microbial pathogenesis and antimicrobial resistance.
●​ Genotype vs. Phenotype:
○​ Genotype: Genetic makeup or information encoded in DNA.
○​ Phenotype: Observable traits or characteristics determined by gene expression.
●​ Clinical Importance:
○​ Understanding gene expression is crucial for:
■​ Recognizing antimicrobial resistance.
■​ Identifying pathogens in nosocomial infections.
■​ Linking bacterial genome changes to patient symptoms.
Horizontal Gene Transfer:
Bacterial DNA and Genetic Alteration

●​ Genetic recombination:
○​ Transfer of genes from one DNA molecule to another.
○​ Alterations similar to mutations.
○​ Crossing over: DNA from one chromosome is transferred to another, contributing
to genetic diversity.
●​ Vertical gene transfer:
○​ Genes passed from parent cell to progeny.
●​ Horizontal Gene Transfer (HGT):
○​ Transfer of genes between cells.
○​ Requires a donor and recipient cell.
○​ Occurs naturally or through genetic engineering.

Plasmids:

●​ Small, circular, double-stranded DNA molecules separate from chromosomal DNA.

●​ Exist naturally in bacterial cells.
●​ Often carry genes providing advantages (e.g., antibiotic resistance).
●​ Used to transfer DNA between bacterial cells.

Transformation in Bacteria

●​ Definition:​
Transformation involves the uptake of foreign naked DNA by a bacterial cell, altering its
properties.
●​ Applications:
○​ Used in laboratories for bacterial genome manipulation.
○​ Occurs naturally in certain bacterial species.
●​ Key Requirement:​
Bacterial cells must become "competent," meaning they are capable of readily taking up
foreign DNA.
●​ Historical Model (1940s):
○​ Experiment with Streptococcus pneumoniae:
■​ Heat-killed, pathogenic, encapsulated bacteria mixed with live,
non-pathogenic, non-encapsulated bacteria.
■​ Injected into a mouse, causing sickness and death.
■​ Result: Live encapsulated pathogenic strain was recovered.
●​ Conclusion:​
A heat-resistant factor from the killed bacteria carried the genetic information for capsule
formation, which transformed the non-pathogenic strain into a pathogenic one.
DNA Uptake:​
Live bacteria can take up DNA fragments from their environment, often from the lysis of dead
cells. This DNA is incorporated into their own genetic material.
Not Universal:​
Not all bacteria can undergo transformation. Typically, it occurs between cells of the same
genera.
Genera Capable of Transformation:

●​ Bacillus
●​ Haemophilus
●​ Streptococcus
●​ Staphylococcus​
These genera are medically significant.

Cell Wall Restrictions:​

Some bacterial cells have walls that prevent the easy entry of large DNA molecules, limiting
transformation.
Genetic Continuity:​
The transformed cell, now containing recombinant DNA, replicates and passes the newly
acquired genes on to subsequent generations.

Transduction Process in Bacteria

●​ Phage Infection:​
A bacteriophage (phage), a virus that infects bacteria, attaches to a specific receptor site
on the bacterial cell and injects its DNA into the host cell.
●​ Viral Replication:​
The phage uses the host cell's machinery to replicate its own DNA and synthesize viral
proteins. New phage particles are assembled, and the bacterial chromosome is
fragmented by phage enzymes.
●​ Lytic Cycle:​
The infected cell eventually lyses (breaks open), releasing new phage particles and
destroying the host cell.
●​ Generalized Transduction:​
During phage assembly, some bacterial DNA may be accidentally incorporated into the
phage particles instead of phage DNA. When these phages infect a new bacterial cell,
they transfer bacterial DNA from the donor to the recipient, allowing the recipient cell to
acquire new genetic traits.
●​ Phage DNA Alteration:​
The phage may carry altered DNA (with some of its own genes missing), and may not
cause lysis in the new host cell, resulting in the incorporation of donor DNA into the
recipient's genome.

Specialized Transduction
 ●​ Temperate Phages:​
Temperate phages integrate their DNA (called a prophage) into the bacterial
chromosome, entering a lysogenic cycle where the phage DNA replicates along with the
bacterial DNA.
●​ Reversion to Lytic Cycle:​
Under certain conditions, the prophage may exit the bacterial chromosome and enter the
lytic cycle, replicating new phage particles. These phages can carry bacterial DNA
fragments along with their own DNA.
●​ Specialized Transduction:​
In specialized transduction, the bacterial DNA transferred is usually from regions
adjacent to the prophage integration site. This contrasts with generalized transduction,
where random bacterial DNA is transferred. Specialized transduction can be used to
map genes on bacterial chromosomes or to select specific genes for transfer.

Conjugation

●​ Direct Cell-to-Cell Contact:​

Conjugation involves the physical contact between a donor and recipient bacterial cell. A
sex pilus forms a bridge through which DNA (typically plasmid DNA) is transferred from
the donor to the recipient.
●​ F Plasmid:​
The plasmid responsible for conjugation is called the F factor (fertility factor). Donor cells
containing the F plasmid are F+, while recipient cells lacking the plasmid are F-.
●​ F+ to F- Transfer:​
During conjugation, the F plasmid is transferred from the F+ donor to the F- recipient,
converting the recipient into an F+ cell.
●​ High Frequency of Recombination (Hfr) Cells:​
If the F factor integrates into the bacterial chromosome, it forms Hfr cells, which can
transfer not just the F plasmid but also chromosomal DNA to a recipient cell.
●​ Plasmids and Antibiotic Resistance:​
Plasmids can carry genes for virulence factors (e.g., toxins) and antibiotic resistance.
Resistance plasmids, such as those found in MRSA, allow bacteria to resist antibiotics,
making plasmid transfer a significant factor in the spread of resistance, particularly in
clinical settings.

1. What are genes?

Genes are segments of DNA (or RNA in some viruses) that encode instructions for synthesizing
proteins or RNA molecules. They are the basic units of heredity and carry the information
necessary for the growth, development, and functioning of organisms.

2. What is meant by the ‘genetic code’?

The genetic code is the set of rules that defines how the sequence of nucleotides in DNA or
RNA is translated into the sequence of amino acids in proteins. It is universal for almost all living
organisms. The code is read in sets of three nucleotides (codons), where each codon
corresponds to one specific amino acid.

3. How are proteins synthesised in bacterial cells?

In bacterial cells, protein synthesis occurs through two main processes: transcription and
translation.

●​ Transcription: The DNA is transcribed into messenger RNA (mRNA) by RNA

polymerase.
●​ Translation: The mRNA is then translated into a protein by ribosomes. The ribosomes
read the mRNA in sets of three nucleotides (codons) and match each codon with the
corresponding amino acid, linking them together to form a polypeptide chain (protein).

4. What is mutation? What types of mutation can occur in the bacterial cell?

A mutation is a change in the DNA sequence that can lead to changes in the structure or
function of the resulting protein. Mutations can occur naturally or be induced by environmental
factors (e.g., radiation, chemicals). Types of mutations include:

●​ Point mutation: A change in a single nucleotide, which may result in a different amino
acid being incorporated into a protein (missense mutation), or no change at all (silent
mutation).
●​ Frameshift mutation: Addition or deletion of nucleotides that shifts the reading frame,
often resulting in a completely altered protein.
●​ Nonsense mutation: A mutation that creates a premature stop codon, leading to a
truncated (incomplete) protein.
●​ Insertions and deletions: Addition or removal of bases that can affect the gene
structure.

5. How is the information for antibiotic resistance transferred from one

bacterial cell to another and what are the implications for the control of
infectious diseases?

Information for antibiotic resistance can be transferred through several mechanisms:

●​ Conjugation: The transfer of plasmids (small DNA molecules) containing resistance

genes from one bacterium to another via direct cell-to-cell contact.
●​ Transformation: Uptake of free DNA from the environment, often from dead bacteria,
that may contain resistance genes.
●​ Transduction: Transfer of resistance genes via bacteriophages (viruses that infect
bacteria). These mechanisms contribute to the spread of resistance, making infections
 harder to treat and increasing the need for new antibiotics. This is a major challenge in
the control of infectious diseases.

6. In which ways is recombinant DNA technology being used to benefit

humans?

Recombinant DNA technology has numerous applications:

●​ Medical applications: Production of therapeutic proteins (e.g., insulin, growth

hormones), gene therapy for genetic disorders, and vaccines (e.g., hepatitis B vaccine).
●​ Agricultural applications: Creation of genetically modified crops that are more resistant
to pests or diseases and have improved nutritional profiles.
●​ Industrial applications: Production of enzymes for various industries (e.g., detergents,
food production).

7. How does the use of nucleic acid analysis contribute to the identification
of bacteria?

Nucleic acid analysis, including techniques like PCR (Polymerase Chain Reaction), DNA
sequencing, and DNA hybridization, allows for the identification and classification of bacteria
based on their genetic material. These methods can detect specific genes or sequences unique
to particular bacterial species, providing a rapid and accurate way to diagnose infections and
study bacterial diversity.

Case Study 2.1

Which two bands are identical in this

PFGE test?

Bands 6 and 7 are identical in this PFGE result,

meaning they have the same banding pattern,
suggesting they represent the same strain or
closely related strains of MRSA.

2. What is the significance of the

result? Is it likely that the patient
acquired this infection in this
hospital?

The fact that bands 6 and 7 are identical

suggests that Joan’s MRSA strain (band 6) is
genetically the same as one circulating in the
hospital (band 7). This increases the likelihood
that Joan acquired her infection in the hospital,
especially if other patients or hospital-associated sources (such as staff or equipment) carry the same
strain. However, further investigation would be required to definitively confirm the source, including
comparing with strains from other hospitals or locations Joan may have visited.

3. Explain how this kind of test can be used to track the spread of an infection
around the hospital.

PFGE generates unique DNA fingerprints for bacterial strains. By comparing these fingerprints,
healthcare workers can track which strains are spreading within the hospital. Identical patterns across
patient samples suggest that an outbreak is due to the same strain, and comparing the genetic profiles
helps identify whether the infection is hospital-acquired or introduced from external sources. It can also
help identify cross-contamination or lapses in infection control.

4. How can this knowledge be applied to tracing SARS-CoV-2 outbreak clusters?

For SARS-CoV-2, genetic sequencing is used in a similar way to PFGE for bacteria. By sequencing the
viral genome from patient samples, researchers can track variants and mutations, identifying common
sequences and genetic similarities. This enables tracking of outbreaks, determining whether a cluster is
from a single source, and tracing the virus’ movement across different locations, helping to control
transmission.

Topic 3:

Mutualism:
●​ Two independent organisms live together to their mutual benefit
○​ Bacteria living in the large intestine (colon)
○​ Hot benefit = produces vitamin K and B, breakdown waste material
○​ Bacterial benefit = sheltered environment, continual food supply
Commensalism:
●​ Association btwn two organisms where one benefits while not causing any harm
to the other
○​ Human host + resident microbes
Parasitism:
●​ One organism benefits at the expense of the other
○​ Wide range of relationship
○​ Successful parasites maintain own life processes without damaging or
killing their host
○​ Commensal bacteria fall into this category when they cause infection
○​ True parasites = unable to live outside host always cause an infection and
produce some degree of damage.
Normal Microbiota:
●​ Normal flora microorganisms that inhabit the human body without causing
disease
●​ Humans are constantly exposed to a changing population of microorganisms
●​ Resident flora permanently reside on the skin and mucosal surfaces
●​ Transient flora colonise the skin and mucosal surfaces, potential pathogens
○​ Contaminants = transient flora carried for a brief time on hands or other
skin surfaces and can be removed by physical means such as
handwashing.
●​ Human host provides shelter and food to microbes
○​ Certain bacteria will reside in a particular area of the body; temp, moisture,
pH, oxygen
○​ Sterile sites = bloodstream / internal organs
●​ Protective properties of normal flora
○​ Create an environment which inhibits colonisation by other organisms
○​ Modify their environment to excrete chemicals with antibacterial activity.
●​ Factors that influence normal flora:
○​ Age, nutritional status, exposure to abx therapy, long hospital stay
○​ Long term antibiotic therapy: [Link] = diarrhea and
pseudomembranous colitis, C albicans = thrush (reduction of lactobacilli)
●​ Resides on:
○​ Skin - bacteria reside in or on the dead layers of skin
■​ Contaminants are transient that adhere to skin surfaces and can be
removed.
■​ Resident microbiota usually live in warm, moist areas
○​ Respiratory track - upper respiratory tract
■​ Colonised with normal flora that have pathogenic potential
○​ Gastrointestinal tract - extends from mouth to anus
■​ Oral bacteria -> URT -> stomach -> LI
○​ Genitourinary tract - lower urethra colonised with normal flora
■​ Constantly changing composition
Infection and Disease:
●​ Balance exists between a state of health and disease
●​ Pathogens can be from external environment or our own normal flora
○​ Colonise
○​ Overcome host immune defences
○​ Multiply and cause harm = symptoms
●​ Disease - harmful alteration to the physiological or metabolic state of the host
○​ Infectious disease - caused by a pathogenic microorganism or its products
●​ Pathogen - any organism capable of causing disease

Endogenous vs Exogenous Infections:

●​ Endogenous infections: occur when the source of the pathogen is the human host itself
(normal microbiota become opportunistic pathogens)
○​ Displacement to susceptible site = infection
○​ Congenital infections - occur in the fetus when the source of the pathogen is the
mother
●​ Exogenous infections: are caused by organisms from the external environment
○​ Healthcare-associated infections (HAIs) - exogenous infections acquired during a
stay in hospital
○​ Iatrogenic infection - an infection resulting from a medical procedure or treatment.
The Disease Process:
1.​ Pathogenicity and Virulence
●​ Pathogenicity - ability of an organism to produce a disease
○​ Gain entry to the host
○​ Attach to the host tissues and multiply
○​ Evade the host defenses
○​ Damage tissue and produce disease symptoms
●​ Virulence - the degree of pathogenicity of an organism
○​ Capsule
○​ Biofilm
○​ Enzymes
○​ toxins
2.​ Opportunistic infections:
●​ Infections caused by organisms that dont usually cause disease but can become
pathogenic under certain conditions
○​ Immune status of host
○​ Site infection
○​ Pathogen virulence properties
○​ Altered physiological/hormonal state
○​ Prolonged use of antibiotics
3.​ Host resistance or susceptibility
●​ Predisposed illness: diabetes, cancer, liver disease
●​ Chemotherapy for cancer patients
●​ Immunosuppressive drugs for transplant patients
●​ Immune disease, acquired or genetic
●​ Nutrition
●​ Lifestyle
●​ Age : neonates have immature immune system , elderly have decreased immune
system
●​ gender/genetic predisposition
●​ surgery/trauma provides portal of entry
●​ Physical defects
●​ Stress
●​ pregnancy

4.​ Predisposing factors:

●​ environment/living conditions
●​ Climate and natural disasters
●​ Atmospheric pollution
●​ Seasonal and secondary infections
●​ Hospitalisation​
Signs and Symptoms of Disease:
Pathological changes or damage to the host cells and tissues are characteristic of a specific
type of infections
1.​ Signs - fever, swelling, inflammation, rashes, vomiting, and diarrhoea
2.​ Symptoms - pain, headache, nausea, or a general feeling of illness
3.​ Syndrome - group of signs and symptoms which are characteristic of a particular disease