Mid Term Revision Flashcards
ILOs
- Have knowledge of the human microbiome project
- Have knowledge of the normal healthy human microbiota.
- Discuss the potential role of the human microbiota in health and impact of disappearance of some microbiota in health and disease.
- Evidence of microbiome causality of disease
- Potential of synthetic microbiomes in medicine
- Potential of metabolic approaches to microbiome manipulations and therapies
- Understand the difference between disease and infection
- Understand what constitutes an infection
- Be able to discuss the concept of virulence and virulence factors
- Have an appreciation of polymicrobial diseases
- Have an appreciation of disease mechanisms – entry, establishment, evasion, damage
- Have an understanding of the clinical significance of the anatomy of disease causing microorganisms
- Understand classical approaches employed in the clinical microbiology laboratory
- Be aware of current advancements in approaches to clinical microbiology
- Be able to describe an example of a Gram negative pathogen
- Be able to describe an example of a Gram positive pathogen
- Understand the concept of zoonoses and emerging infections
Antigenic Drift
Point mutations in the genes encoding the virus glycoprotein envelope
Reduces antibody binding affinity
(hemagglutinin and or neuraminidase genes)
Antigenic Shift
Genetic reassortment of genome segments between human and animal viruses. These combine to form a new subtype
The human gut microbiome
- protects against disease by crowding out pathogenic organisms
- The co evoluton hypothesis
What do gut microbes do?
- Immune system regulation
- Removal of toxins
- Crowd out pathogens
- Improve intestine function
- Gut-brain links in communication
- Important as liver- metabolites in gut
- Considered a vital organ
The Human Microbiome Project
Highly parallel DNA sequencers + high throughput mass spectrometers enable characterisation of whole microbial communities :
- genomes
- proteins
- metabolic products
Human Microbiome Analysis
16S rRNA - component of the 30S subunit (prokaryotic ribosomes)
This is a highly conserved region with variable regions - it can be used to identify and distinguish between bacteria (taxonomic groups)
OR
culture independent sequencing techniques (for less common types of organisms)
VBNC
Viable non culturable (vast majority)
Genome sequencing allows analysis
The core human microbiome
the set of genes present in the human gut
The variable human microbiome
the set of genes present in a smaller subset of humans
Variables:
- host genotype
- physiological status (including: innate and adaptive immune systems)
- host pathobiology (disease)
- host lifestyle (inc, diet)
- host environment
The gut microbiome
- The most heavily colonised organ is the GI tract
- Contains approx 70% of all microbes in the body
- Strict anaerobes predominate over facultative aerobes and anaerobes
- Dominated by 2 phyla: Bacteriodetes (bacteriodes) and Firmicutes (clostridium)
- The human gut contains 500-1000 species
Evidence of microbiome in disease
- Intestinal microbiota is distinct in irritable bowel syndrome - host genetics play a part
- Association with microbiota and obesity in mice and humans
Helicobacter pylori
- 1st formally recognised bacterial carcinogen
- 4th cause of cancer related death globally
- Contains a urease enzyme that converts urea to ammonia which is alkaline, neutralises some of the stomach acid around it
- Microaerophilic, spiral shaped, gram negative bacteria
- Approx 50% human population is infected
- Induces gastritis, peptic ulcers, gastric cancer and mucosa-associated lymphoid tissue lymphoma
- Susceptibility is multifactorial (environment, genes, immune status, other microbiology)
- Difficult to eradicate
Crohns Disease
- Adhesive and invasive form of ecoli (AIEC) in CD patients
- Intracellular invasion by AIEC is associated with active CD and intestinal pathology
- The receptor that facilitates AIEC binding in epithelial cells is unregulated in CD
- Host genetics: Defects in innate immunity (eg. mucosal barrier, autophagy, phagocytosis)
- Microscopically (loss of barrier, inflammatory cytokines, lesions and fibrotic scarring)
- Microbiota (AIEC, dysbiosis, carcinogenic microbiota)
Obesity related shift in microbiota
A shift in the relative abundance of bacteriodetes and firmicutes has been observed in obese humans - more Firmicutes
Obesity associated microbiome has more capacity for energy harvest in mammalian cells
Human Microbiome Project Therapeutics
Potential strategies for therapeutic microbiome manipulation:
- Antibiotics
- Bacteriophage
- Probiotics
- Prebiotics
- Synbiotics
- Nutritional therapy
- Microbiota restoration
Example Microbiota Therapies 1
Lactobacillus jensii
Vaginal commensal Lactobacillus jensenii engineered to produce antiviral protein cyanovirin-N: colonisation by recombinant bacteria inhibits host infection by SHIV in simian model
Example Microbiota Therapies 2
Lactococcus lactis
Lactococcus lactis genetically modified to produce anti inflammatory cytokine interleukin-10 (IL10): administration in mice with colitis shown to reduce inflammation during gut transit
Example Microbiota Therapies 3
E.coli
Probiotic E coli engineered to synthesise N-acyl-phosphatidylethanolamines (NAPEs): host mediated conversion of NAPEs to N-acylethanolamides (NAEs) prevents obesity in mice (through inc. satiety)
Metabolic Therapies
- Bacterial gut metagenome produces primary and secondary metabolites
- Secondary metabolites are called ‘specialised metabolites’
- Specialised metabolites can produce molecules that have effects in the body, e.g. GABA produced by bacteria can have neurological effects
Metabolic Therapies - Lactobacillus rhamnosus
- Lactobacillus rhamnosus produces GABA
- Probiotic treatment increases GABA receptor expression in the hippocampus
- This reduces anxiety and depression behaviours in the mouse model
Disease definition
conditions that impair normal tissue function
Disease and infection are not synonymous
Infection definition
When a pathogen invades and begins growing within a host
Disease and infection are not synonymous
What is a ‘true pathogen’?
An infectious agent that causes disease in virtually any susceptible host
What is an opportunistic pathogen?
Opportunistic pathogens are potentially infectious agents that rarely cause disease in individuals with healthy immune systems
Pathogenicity definition
The capacity of a microbe to cause damage in a (susceptible) host
It is a discontinuous variable, that is, there is or is not pathogenicity
It is a microbial variable that can only be expressed in a susceptible host: it is dependent on host variables.
EEMSD - pathogenicity!
Encounter - Entry - Multiplication - Spread - Damage
Damage:
Tissue Pathology
Loss of organ function
Growth in normally sterile sites
Virulence definition
The amount of damage a pathogen is able to cause in a host
Virulence is a continuous variable, that is, it is defined
by the amount of damage or disease that is manifest
Discontinous vs. Continuous variables
Virulence: continous variable + experimentally determined
Pathogenicity: discontinous variable + host dependent
How is virulence measured?
LD50 (lethal dose) or ID50 (infectious dose)
- LD50: the amount of a toxic agent that is sufficient to kill 50% of a population within a certain time
- ID50: the infective dose that will cause 50% of exposed individuals to become ill
What could influence the ID50 and LD50 values of a pathogen?
- route of infection - e.g. cutaneous anthrax vs. inhalation anthrax (latter is systemic - ‘cardinal’s cap’)
- host immune status
- genetic makeup of host
Virulence Factor definition
Molecules produced by bacteria, viruses, fungi, and protozoa that add to their effectiveness
Koch’s molecular postulates
- “The gene under investigation should be associated with pathogenic members of a genus or pathogenic strains of a species.” The gene should be found in all pathogenic strains of the genus or species but be absent from non-pathogenic strains
- “The gene, which causes virulence, must be expressed during infection.“
- “Specific inactivation of the gene(s) associated with the suspected virulence trait should lead to a measurable loss in pathogenicity or virulence.”
- “Reversion or allelic replacement of the mutated gene should lead to restoration of pathogenicity.”
Classic virulence factors
Toxins
Limitations of the virulence factor concept
Pathogenicity conferred by virulence factors is difficult to apply to many microbes whose pathogenicity is limited mostly to immunocompromised hosts
e.g. C. albicans and Aspergillus fumigatus
Biofilm definition
A syntrophic consortium of microorganisms
Cells stick to each other and often also to a surface
Adherent cells become embedded within a slimy extracellular matrix
Matrix is composed of extracellular polymeric substances (EPS)
In a biofilm, the physical nature of this entity protects the
bacteria
Requirements for disease
1. Point of entry
2. Establishment
3. Avoiding host defence mechanisms
4. Damaging the host
UTIs
Most common hospital infection is UTI
Normally a change in pH in urinary tract (normally acidic) causes UTI
Portals of entry - mucous membranes
- Mucous membranes need to be protected:
- Washing with secretions, e.g. tears, saliva, mucous and urine
- Filter hairs in nasal passages prevents entry of large particles.
- Cilia in respiratory tract push mucous and microbes upward.
- Non-specific innate Mechanisms:
* Mechanical Factors e.g. keratinised surface of skin (tough so acts as an
effective barrier against entry)