Block 4 - Pathogens Flashcards
Discuss the initial difficulties of classifying microbes.
Classifying microbes initially challenging due to size, they were first classified by shape. Advances in biochemistry, metabolism and microscopy enabled the detection of the presence of;
- Spore formation
- Aerobic conditions
- Cell staining results
- Motility
Discuss gram-staining in bacteria.
Bacteria can be classified as:
* Gram-negative
* Gram-positive
* Variable
The Gram stain procedure differentiates bacteria into Gram-positive (purple) and Gram-negative (pink/red) based on cell wall structure, using crystal violet, iodine, decolorization, and safranin.
Gram-positive bacteria are bacteria that give a positive result in the gram stain test.
Gram-negative bacteria are bacteria that give a negative result in the gram stain test.
“Variable bacteria,” specifically “gram-variable bacteria,” refers to bacteria that do not consistently stain as either Gram-positive or Gram-negative during the Gram staining process, showing a mixed pattern of pink and purple cell.
Discuss which types of bacteria are gram-negative.
o Bacillota, mycoplasmatota and actinmyocetota are all gram-negative.
Bacillota (Firmicutes) – bacillales, clostrida and lactobacillales.
Mycoplasmatota (mycoplasma).
Actinmyocetota (actinobacteria) – actinomycetaceae and bifidobacteriaceae.
Describe which types of bacteria are gram-positive.
o Pseudomonadota are all gram-positive.
Alphaproteobaceria – rhizobiales and rickettsiales.
Betaproteobacteria – neisseriales.
Gammaproteobacteria – enterobacteriales.
Epsilon-proteobacteria – camplyobacterales.
Define the term microbiota.
Microbiome is often used in the literature to mean the population of microorganisms at a specific location however the term should now be microbiota.
Describe how the different microbiotas can be anaylsed.
The most widely used method is to perform amplicon sequencing of the 16S rRNA gene for bacteria and the ITS for fungi. Microbiota studies are based on ecological principles which are used to ;
- Describe individual samples (alpha diversity)
- Compare samples (beta diversity)
Additional ‘omics’ technologies can be applied to the same sample to understand the ecosystem further.
Describe alpha diversity.
Alpha diversity is a measure of how diverse a sample is based on:
* How many species there are (richness)
* How abundant each species are (evenness)
Within a sampled environment.
Describe beta diversity.
Beta diversity is a measure of how different (or similar) two samples are to each other.
Discuss dysbiosis.
An imbalance in the bacterial composition in a given ecological niche. Typically seen as:
Loss of beneficial bacteria.
Overgrowth of potentially pathogenic bacteria.
Loss of overall bacteria diversity.
Often associated with negative consequences.
Outline factors potentially affecting the microbiota.
Genetics
Air pollution
Antimicrobials
Medications
Diet
Stress
Chemicals
Pathogens
Early life experience
Describe the human microbiota.
Originally estimated ratio of bacteria to human cells was 10:1. Sender, Fuchs and Milo now estimate number of bacteria in a 70 kg “reference man” to be 3.8x10^13, human cells in a 70 kg “reference man” are estimated to be 3.0x10^13. Bacteria to human cell ratio is approximately 1:1, total bacterial mass is approximately 0.2 kg.
Describe the human microbiota project.
Funded by the NIH 2007-2016, HMP1 300 healthy individuals.
Up to 3 points.
Nasal passages, oral cavity, skin, gastrointestinal tract and urogenital tract.
16S rRNA sequencing to identify core healthy microbiome, metagenomic whole genome shotgun sequencing for functions and pathways.
Describe the integrative human microbiome projects (HMP2).
Three studies on dynamic changes in the microbiome and host:
- Pregnancy and preterm birth
- Inflammatory bowel disease
- Stressors that affect individuals with prediabetes
Describe the gut microbiota.
The most well characterised human microbiota.
Bacteria in the gut can:
Help rejuvenate host tissue
Inhibit inflammation
Metabolic complex carbohydrates
Synthesises of vitamins
Impact of obesity
Discuss the skin microbiota and acne.
Skin microbiota consist of anaerobic, aerobic and facultative bacteria.
Approximately 10^4 – 10^5 bacteria/sebaceous gland. Beneficial roles of the skin microbiota include:
* Promoting epithelial tight cell junction expression
* Immunomodulation
* Secretion of antimicrobial peptides
Increased hormonal activity during puberty stimulates oil production in the sebaceous gland. Cutibacterium acnes degrades sebum triglycerides and results in inflammation.
Describe viruses.
Viruses are not ‘alive’ but are obligate intracellular parasites that infect all forms of life. They are unable to replicate outside of host cells.
Outline the steps in the viral life cycle.
1) Recognition
2) Attachment
3) Fusion / Penetration
4) Uncoating
5) Transcription
6) Protein Synthesis
7) Replication
8) Assembly / Envelopment
9) Lysis and release / Budding and release
Define the latent and eclipse periods in viral infection.
The latent period is the time before an increase in intracellular virus.
The eclipse period is the time before an increase in extracellular virus.
[see supporting diagram]
Describe the general patterns of infection.
- Acute infection -> a short duration, high severity infection.
- Persistent infection -> a very long duration, high severity infection.
- Latent, reactivating infection -> a short duration, varying severity reoccurring infection.
- Slow virus infection -> a short but relapsing high severity infection.
[see supporting diagram]
Discuss herpes simplex & VZV latency.
1) Primary infection.
Herpes simplex = mild pharyngitis fever.
Varicella = chicken pox.
Virus transit up peripheral nerve, latent virus in sensory neuron in dorsal root ganglion of the spinal cord.
2) Recurrence.
Herpes simplex = cold sore.
Varicella = zoster (shingles).
Age and X-irradiation (act via depressed CMI), local injury or infection (e.g. sinusitis) activates the virus in the neuron.
Outline the determinants of viral disease.
- Target tissue
Portal of entry
Access of virus to target tissue
Tissue tropism of virus
Permissiveness of cells for replication - Viral pathogen (strain)
- Immune status
Competence of the immune system
Prior immunity to the virus - Cytoplasmic ability of the virus
- Immunopathology
- Virus inoculum
- General health of the individual
- Genetic make-up of individual
- Age
Outline the factors in viral epidemiology.
o Critical community size
o Mechanisms of virus transmission
Respiratory or salivary spread.
Formities (e.g. tissues, clothes).
Sexual contact.
Zoonoses (animals, insects [arboviruses]).
Blood transfusions, organ transplant, needle sharing (common in drug abusers).
o Geographical/Season
Presence of cofactors or reactors in environment.
Habitat and season for arthropod vectors.
School/Universities session; close proximity.
Climatic conditions.
Outline the 3 main controls of virus diseases.
1) Public health care
2) Vaccination
3) Chemotherapy
Outline the difficulties of designing an anti-viral drug.
1) Few biochemical pathways unique to viruses.
2) Therapeutic index often very low.
3) Selection of drug resistant mutants.
4) Many viruses which cause similar diseases have very different modes of replication and may not be sensitive to some drugs.
5) By the time symptoms appear often chemotherapy is too late to make much difference to clinical course of disease.
Describe the properties of viruses in taxonomic constructions.
Properties of genome
Type of nucleic acid = DNA or RNA
Strandedness = single or double stranded
Linear or circular
Sense = positive - naked RNA infectious, negative – naked RNA non-infectious and needs an enzyme to copy RNA
Nuclear of segments
Nucleotide sequence
Outline the overall symptoms of influenza.
Central -> headache
Nasopharynx -> runny or stuffy nose, sore throats, aches
Systemic -> fever (usually high)
Muscular -> extreme tiredness
Respiratory -> coughing
Joints -> aches
Gastric -> vomiting
Discuss in depth influenza A and its features.
Type A influenza viruses which are responsible for human pandemics are spheroidal particles, about a tenth of a micrometer across. The virus has an internal nucleocapsid, containing the viral genome, and matrix protein, a lipid bilayer and external surface proteins.
The genome consists of eight single-stranded RNA segments that code for 10 proteins; PB2, PB1, PA, HA (hemagglutinin), NP (nucleoprotein), NA (neuraminidase), M1 (matrix protein), M2 (ion-channel protein) and two nonstructural proteins, NS1 and NS2.
Subtypes of the type A virus are classified according to structural variants for the two surface proteins; hemagglutinin (15 variants, H1 to H15) and neuraminidase (9 variants, N1 to N9).
An ion-channel protein (M2), embedded in the lipid bilayer, is a target for the antiviral drugs amantadine and rimantadine, which inhibit the protein’s function.
Describe viral replication in living cells.
Viruses can only replicate in living cells. Influenza infection and replication is a multi-step process: firstly the virus has to bind to enter the cell, then deliver its genome to a site where it can produce new copies of viral proteins and RNA, assemble these components into new viral particles and finally exit the host cell.
Describe how influenza A can mutate.
The influenza A virus can mutate in two different ways; antigenic drift – in which existing antigens are subtly altered - and antigenic shift – in which two or more strains combine.
Antigenic drift causes slight flu mutations year on year, from which humans have partial but not complete immunity.
Describe the effects of viral mutation.
Flu viruses mutate over time causing small changes to proteins on their surface called antigens. If the immune system has met a particular strain of the virus before, it is likely to have some immunity; but if the antigens are new to the immune system, it will be weakened.
Describe swine acting as a vector for influenza virus.
Swine serve as ‘mixing vessels’ for the genes of avian, porcine and human forms of the influenza virus. In the host pig, the avian and mammalian viruses can share (reassort) their genes and so create new strains of the flu. Swine have probably played an important role in the history of human influenza epidemics.
Discuss the anti-viral drug Oseltamivir.
Oseltamivir is an antiviral drug that slows the spread of influenza virus between cells in the body by stopping the virus from chemically cutting ties with its host cell.
Median time to symptom alleviation is reduced by 0.5-1 day.
The drug is sold under the trade name Tamiflu and is taken orally in capsules or as a suspension.
It has been used to treat and prevent influenza A and influenza B infection is over 50 million people since 1999.
Discuss the anti-viral drug Zanamivir.
Zanamivir is a neuraminidase inhibitor used in the treatment and prophylaxis or influenzavirus. It is currently marketed by GlaxoSmithKline under the trade name Relenza.
Zanamivir works by binding to the active site of neuraminidase, rendering the influenza virus unable to escape its host cell and infect others.
Zanamivir reduces the time to symptom resolution by 1.5 days if therapy is started within 48 hours of the onset of symptoms.
Discuss inflammation in relation to viral infection.
Common symptoms of the flu such as fever, headaches and fatigue are the result of the huge amounts of proinflammatory cytokines and chemokines (such as interferon or tumour necrosis factor) produced from influenza-infected cells.
Influenza does cause tissue damage, so symptoms are not entirely due to the inflammatory response.
This massive immune response might produce a life-threatening cytokine storm. This effect has been proposed to be the cause of the unusual lethality of both the H5N1 avian influenza, and the 1918 pandemic strain.
Outline the strategies for dealing with an epidemic.
1) Mitigation, focuses on slowing but not necessarily stopping epidemic spread reducing peak healthcare demand while protecting those most at risk of severe disease from infection.
2) Suppression, which aims to reverse epidemic growth, reducing case numbers to low levels and maintaining that situation indefinitely.
Summarise the non-pharmaceutical interventions to viral epidemics.
o CI
Case isolation in the home.
Symptomatic cases stay at home for 7 days, reducing non-household contacts by 75% for this period. Household contacts remain unchanged. Assume 70% of household comply with the policy.
o HQ
Voluntary house quarantine.
Following identification of a symptomatic case in the household, all household members remain at home for 14 days. Household contact rates double during this quarantine period, contacts in the community reduce by 75%. Assume 50% of household comply with the policy.
o SDO
Social distancing of those over 70 years of age.
Reduce contacts by 50% in workplaces, increase household contacts by 25% and reduce other contacts by 75%. Assume 75% compliance with the policy.
o SD
Social distancing of entire population.
All households reduce contact outside household, school or workplace by 75%. School contact rates unchanged, workplace contact rates reduced by 25%. Household contact rates assumed to increase by 25%.
o PC
Closure of schools and universities.
Closure of all schools, 25% of universities remain open. Household contact rates for student families by 50% during closure. Contacts in the community increase by 25% during closure.
Describe the structures and features of coronavirus.
Coronavirus form enveloped and spherical particles of 100-160 nm in diameter. Contain a positive sense, single stranded RNA genome of 27-32 kb.
The 5’ terminal 2/3 of the genome encodes a polyprotein, pp1ab which is further cleaved into 16 non-structural proteins involved in genome replication and transcription.
The 3’ terminal 1/3 of the genome encodes structural proteins including envelope glycoprotein spike, envelope, membrane and nucleocapsid.
Spike protein binds to receptor on cell surface.
ACE2 – human angiotensin-converting enzyme 2 is the receptor for coronavirus.
Describe what is meant by the reproduction number.
The reproduction number (R) is the average number of secondary infections produced by a single infected person.
An R value of 1 means that on average every person who is infected will infect 1 other person, meaning that total number of infections is stable.
If R is greater than 1 the epidemic is growing, if R is less than 1 the epidemic is shrinking.
Describe what is meant by the growth rate.
The growth rate reflects how quickly the numbers of infections are changing day by day.
It is an approximation of the percentage change in the number of infections per day.
If the growth rate is greater than 0 then the epidemic is growing, if the growth rate is less than 0 then the epidemic is shrinking.
The size of the growth rate indicates the speed of change.
