Bacteria have 3 main forms- cocci:

shaped,

- rod shaped and spirilli- spiral shaped.

The gram stain is a method used to distinguish different types of bacteria. It distinguishes between two different types of

Bacteria are stained with a violet dye and iodine, rinsed in alcohol and then stained with a red dye. In Gram-positive bacteria, the peptidoglycan in the cell wall

the dye causing the stain to be

Gram-negative don't take up the dye because there is an

that resists the dye. The cells of the gram-negative only absorb the counter-dye making them appear

After the gram stain, the bacteria may be identified using a variety of techniques- culture and microscopy, biochemical and serological tests, DNA techniques

Bacterial pathogens need to: colonise (using surface structures to adhere such as fimbriae and pili), persist (need to avoid subvert or circumvent host defences in or outside cells), replicate, disseminate within cells, tissues between organs and hosts, cause disease

Extracellular pathogens include:

, Streptococcus, Yersinia and Neisseria

Intracellular pathogens include: Coxiella, Salmonella, Mycobacteria and

Motility and invasion of host cells require two-related multi-protein machines; flagella are required for

and type III secretion system is required for

Flagella- Essentially, a coordinated assembly of ring and rod

Protein structures protrude through membrane and the rotation of these cause movement: Ring o protein subunits form in there inner membrane on the cytoplasmic face, this forms a channel for the assembly of the rod via secretion of proteins from this pore. Rod-like proteins and

proteins (which integrate the new subunits to the existing structure) form a hook structure- this is the precursor to the flagella. The hook is of fixed length, capping proteins are then

and new protein subunits are added at the base of the flagella. Protein subunits form the flagella again involving capping proteins. Rotational plate at the base of hook structure provides the proton-motive force-

which provides the movement.

Type III secretion system- similar to flagella assembly but instead of secreting polymerising proteins, this system secretes

proteins into host cells. For example, the invasion of epithelial cells of the GI tract by salmonella: Needle tip structure secretes effector proteins through a bacterial

complex which forms a channel into the host cell. This injection of effector protein interferes with the cellular

pathways by mimicking host proteins and induces actin monomers to polymerise, literally altering the

The actin cytoskeleton pushes out the cell membrane of the epithelia cell to engulf the salmonella. This provides the transport mechanism for the proteins. The type of effector proteins determine the result of the injection. The type III secretion system is only viable in

bacteria. The bacteria needs to make contact with the host cells with a translocate couple to initiate the processes above

Previous example of salmonella and Listeria uses the actin cytoskeleton to move

and spread from cell to cell. Upon endocytosis of Listeria, it escapes the endosome and it begins to reorganise the actin cytoskeleton by inducing polymerisation of actin at

of the bacteria. It appears like a rocket. Using the actin cytoskeleton Listeria can propel itself through the cell, through the cell membrane and into other cells

- transfer of self-transmissible plasmid between two bacteria using pili

- DNA uptake from the environment, free DNA uptake

- DNA transfer via bacteriophage viruses

Huge variation in bacterial genomes, bacteria replicate using

so daughter cells are genetically identical to the parent cell. This means that there is no variation during vertical gene transfer in bacteria. Variation occurs due to

Core genes comprise

of the bacterial genome, the rest are accessory proteins. The vast majority of accessory proteins are acquired via

Horizontally acquired DNA that contributes to bacterial virulence are called pathogenicity

They're a major driving force in the

of bacterial pathogens. Bacterial genomes are all mixable and mutable. They also have a very rapid generation time. Lots of evolution

There are two sources of infection:

- from within the body and

from outside the body

There are bacteria residing in all the outside surfaces of our body. They are commensal but only in the area they inhabit.

Extrinsic sources include aerosol transmission e.g.

Faecal-oral transmission to infect GI tract - contaminated food and water

Sexual transmission- unsafe sex. Nosocomial transmission- infection between

Direct contact and vector borne transmission

The outcome of viral infection depends on the balance between the viral

and host

to the virus

Patterns of virus infection: • Acute infection followed by viral clearance • Acute infection but ‘accidental’ tissue infected with permanent damange • Persistent infection: latent, slow, transforming • Long incubations

Acute infection-

Acute infections are characterised with their

production and resolution. Many are unapparent or are asymptomatic

The adaptive immune response provides immunity However, the viruses continue to circulate in populations by

However, people can still die from acute viral infections – prime example

Accidental pathogenesis – poliovirus transmitted by the faecal oral route causes a localised infection of the small intestine. However, if the poliovirus reaches

it causes paralysis

Rubella causes mild rash, but in the early stage foetus, it has a strong tropism for dividing neuronal tissue causing neural defects

Persistent infection:

Chronic, low level replication of viruses in tissues that regenerate. For example,

Hepatitis B and C can be chronically carried

Latient infection: viral genomes are maintained but no virus is seen until episodes of

of the virus occurs when immunity wanes e.g. Epstein Barr

Viral persistence occurs because they can evade immune surveillance by: Downregulating

compensating for the lost MHC class

escape from CTL by mutation e.g. Hepatitis C virus

infecting tissues with reduced immune surveillance, i.e.

and skin

Latency: Herpes simplex virus

No virions or viral proteins detected, except for

(LATs) Neurons do not divide and contain hundreds of copies of the herpes simplex genome waiting for reactivation under

conditions. Frequency of reactivation varies form host to host

Viral genes can switch between latency and reactivation

The outcome of infection can vary, depending on:

Virus

– a single mutation in poliovirus makes two strains that changes their virulence completely

Virus load – the first child in the family to contract chickenpox has a

illness than following children because the second child has closer contact and thus gets infected with a higher dose

Host immune response and status

Host co-morbidity (other infections making them more susceptible)

Co-infections

Other medications

Host genetics- genetics of the host may make them immune, less or more susceptible to disease. For example, CCR5Δ32 mutation protects against HIV 1 infection etc.

Human immunodeficiency virus (HIV):

Replication cycle-

1. Fusion of the HIV cell to the

2. HIV RNA, reverse transcriptase, integrase, and other viral proteins enter the host cell.

3. Viral DNA is formed by

4. Viral DNA is transported across the

and integrates into the host DNA.

5. New viral RNA is used as genomic RNA and to make viral proteins.

6.New viral RNA and proteins move to cell surface and a new

HIV virus forms

7. The virus matures by

releasing individual HIV proteins

HIV (human immunodeficiency virus) is a

and a member of the retrovirus family.

HIV infects and destroys helper T cells of the immune system causing a marked reduction in their numbers.

Loss of

cells leads to generalised failure of the immune system and susceptibility to life threatening opportunistic infections.

gp120 – an HIV

having a molecular weight of 120 that protrudes from the outer surface of the virion. This glycoprotein binds to a CD4 receptor on a T cell to facilitate entry of viral nucleic acid and proteins into the cell.

CD4 – a large glycoprotein that is found on the surface of

T cells, regulatory T cells, monocytes, and dendritic cells. Its natural function is as a co–receptor that assists the T cell receptor (TCR) to activate its T cell following an interaction with an antigen presenting cell. CD4 is a primary receptor used by HIV–1 to gain entry into host T cells.

Co–receptor (CCR5 or CXCR4) – protein molecules on the surface of lymphocytes or monocytes that bind to the

of HIV and facilitate, usually with CD4, entry of viral nucleic acid and proteins into the cell.

Fusion of virus and cell membranes – a merging of cell and virus membranes that permits HIV proteins and nucleic acids to enter the host cell.

Preintegration complex (PIC) – It is composed of viral RNA and

(nucleocapsid, p6, Vpr, integrase, and matrix) as well as some host proteins. It functions to

genomic RNA into double stranded DNA prior to integration into the host genomic DNA.

Reverse transcriptase – an enzyme found in HIV that creates double stranded DNA using viral RNA as a template and host tRNA as primers.

Integrase – An enzyme found in

including HIV that permits the viral DNA to be integrated into the DNA of the infected cell.

Protease – an enzyme that hydrolyses or cuts proteins and is important in the final steps of HIV maturation.

are used to treat the disease after the host has been infected

is preventing disease before the causative agent is acquired. This means that the pathogen does not have the chance to initiate infection in the host

are examples of prophylactic treatment. They reduce the incidence and thus prevalence of disease because they allow immunological

to form

They can result in lifelong immunity and may even help in the eradication of a virus e.g. smallpox, potentially polio and measles

Different types of vaccine:

Live attenuated vaccine: These are live viruses that have been weakened so that they aren’t pathogenic, but can still cause antigenic response

Inactivated vaccine: These are viruses that have their genetic material

but retain their capsid and envelope so surface proteins can be recognised for antigenic responses

Fractionated subunit vaccine: The virus is digested and fractionated into small pieces, but antigenic responses can be made because the virus is still present, just in pieces

Recombinant subunit vaccine: Bacteria are used to integrate viral genomes into their own genome, they are either clones to form a live virus

or a DNA vaccine. . Or, the proteins coded for by the viral genome are expressed to make proteins that are used to make a subunit vaccine or virus like particles that can act as a vaccine

To make a live attenuated virus vaccine, you take the pathogenic virus and make it evolve to adapt to other animal cells until they aren’t infective to humans. This can be used as a live attenuated vaccine

Live attenuated- Rapid, broad and immunity is

Dose, sparing, cellular immunity, requires

may revert

Inactivated- Safe, can be made from wild type virus, frequent boosting needed and high doses needed

Eradication of smallpox was possible because there is no

and thus once eliminated from man the disease cannot be reseeded. In addition the ability to detect infected cases due to the obvious symptoms and the fact that all infected individuals become symptomatic was crucial.

Today variola major virus exists in just two laboratories in the world where it is preserved. Newer versions of vaccinia virus exist that have been developed as safer live attenuated vaccines such as MVA Ankara. These can be genetically manipulated to express other antigens and may be used in the future as vaccines against other diseases.

WHO aims to eradicate

Poliovirus is also given as an inactivated vaccine –

or a live attenuated vaccine- salbin

Viruses are intracellular obligate parasites. This means that they are hard to combat with drugs chemotherapeutically because they reside inside cells. So it is hard to find a drug that attacks just the virus, but leaves the cell intact

Also, the only stage that can be affected is the virus

but as the virus uses host cell machinery to replicate, it is hard to find a drug that combats just viral replication but leaves host cell replication intact

This means that most antivirals are specific for the viruses that they target: they usually target viral

that have been found to differ from our own or viral replication by acting as nucleoside

that are chain terminators. This causes difficulty because an accurate diagnosis is needed to make sure that the virus is targeted specifically

Viruses may also develop resistance to the drugs if drugs are used individually, this problem is overcome by using multiple drugs to eradicate the virus

Antiviral drugs are usually, but not always either

or they specifically target viral enzymes (as before)

Acyclovir, a guanosine analogue, is used to treat

It is a chain terminator: The chain is terminated because there is no

group for the adjacent 5’ phosphate group to bind to

Only activated inside a virus infected cells • Higher affinity for viral DNA polymerase than for host cell polymerase • Resistance is rare but maps to thymidine kinase

Strategies must be undertaken to make new drugs that are antiviral. This means looking at existing chemicals and seeing if they work, or looking at viral structure and proteins to see if there is anything to inhibit their function without interfering with the host cell

Antivirals against influenza:

hese need to target a unique and essential gene of the virus and affect multiple strains

Byproducts of petroleum refinement,

were seen to have an effect on influenza A.

They were seen to block the

on the influenza virus

When the crystal structure of neuraminidase was figured out, it allowed for rational drug design. Inhibitors- sialic acid, relenza and

Drugs targeting HIV: Entry inhibitors e.g. enfuvirtide and maraviroc NNRTI e.g. Efavirenz and Viramune NRTI e.g. Zidovudine and Stavudine Integrase inhibitors e.g. Raitegravir Protease inhibitors e.g. Atanzavir