Page 1 of 15 Kanay Khakhria

Microbiology

Lecture 1: Interferons

LO1: List the different types of interferons, and the cell types that produce them.
Viruses are obligate intracellular parasites that use cell machinery to create more viral components and genomes. A virus
genome either comprises DNA or RNA:
DNA genomes are more stable, less error prone and can therefore be more complex than RNA genomes. They
can even have accessory genes which allow them to evade the immune response.
Viral RNA can be a maximum of 30 base pairs long. If it is any bigger than this, the virus will make so many
replication errors that it reaches error catastrophe.
Large DNA viruses such as Herpesviruses tend to cause latent infection by surviving in the host for a long period
of time. To do this they need to interact intricately with the host immune response to avoid detected. Members of
the Herpesviridae include Varicella zoster virus, Epstein-Barr virus, Cytomegalovirus as well as the Herpes
Simplex Viruses. These are extremely widespread amongst humans.
Smaller RNA viruses tend to cause rapid infection, and thus do not need to evade the immune response in a
complicated way.

In order for a pathogen to initiate any

type of response, be it innate (which
then leads to adaptive), it needs to
activate PRRs (Pathogen
Recognition Receptors). After
PAMPs (Pathogen Associated
Molecular Patterns) bind to PRRs,
they can transduce a signal with a
cascade of events to mount an
immune response. PPRs can be
cytoplasmic like RIG-I like
receptors (RLRs) or on the cell
surface like Toll-like receptors
(TLRs). They detect the viral
infection by sensing foreign nucleic
acids (those that dont have a 5 cap
and 3 poly-A tail).

Interferons are soluble cytokines

which comprise our innate
immunity against viruses (as well as
physical barriers). Type 1
interferons are secreted from all
infected cells, these include IFN-
and IFN-.

They carry out three major functions:

1. Induce antimicrobial state in infected and neighbouring cells.
2. Modulate innate response to promote antigen presentation and activate natural killer (NK) cells.
3. Activate the adaptive immune response

The INFAR (Interferon / receptor) is present in all cells. Heterodimerisation leads to the cell to produce more INF- and
INF-. While there is only one gene for INF-, there are 13/14 isotypes of INF-.
Page 2 of 15 Kanay Khakhria

Type 2 interferons are produced by activated T-cells and NK cells. IFN- is the only type 2 interferon, and signals
through its own receptor INFGR (Interferon gamma receptor). Type 3 interferons are a group of INF- molecules, whose
receptors are mainly present on epithelial surfaces. Polymorphisms in INF- are associated with improved outcome from
HCV and HBV by spontaneous clearance, and better response to antiviral therapy.

LO2: Explain how type I interferon synthesis is regulated.

After the virus enters the cell and uncoats itself, the viral RNA may be recognised by molecules such a RIG-I which
subsequently transduce a signal via a cascade of other molecules. A similar cascade may be activated through cell surface
receptors such as TLRs (Toll-Like Receptors).

Signals detected by RIG-I signal through Mavs (Mitochondrial activation of viral signalling). This leads to the nuclear entry of
various factors which bind to the promoter region of the IFN- gene. The IFN- molecule can act through autocrine
signalling or paracrine signalling to activate de novo transcription of hundreds of Interferon Stimulated Genes (ISGs).
ISGs have anti-viral effects so the cell becomes hostile to viral replication.

As well as foreign RNA, foreign DNA can be detected through cGAS. cGAS biochemically modifies bits of DNA so that it
can be detected by STING on ER to switch on IFN in the same way as RIG-I does.

LO3: Outline the canonical type I interferon signalling pathway.

INF binds to a transmembrane INF receptor which
heterodimerises. Through a series of series of
phosphorylation events Tyk2 and Jak1 phosphorylate
each other, as well as other proteins in the cytoplasm
such as STAT proteins.

The STAT proteins enter the nucleus and bind to the

promoter regions of ISGs. These promoter regions are
called the Interferon Stimulated Response Elements.

The ISGs have antiviral effects on the cell. They have

drastic effects and so cant be left switched on all the
time. The IFN response may only be maintained for
several hours.

ISGs include: PKR, 25OAS, Mx, ISG15, ISG54, ISG56,

PML bodies, APOBECs and TRIMs, ADAR as well as
100s of other genes.

Some of these genes are involved in cell cycle arrest

and apoptosis.

LO4: Explain the mechanisms of action of important type I interferon-stimulated genes.

IFITM3 (Interferon Induced TransMembrane Protein 3) is an important protein transcribed by a ISG. It inhibits entry of
enveloped viruses (such as influenza) which enter the cell via endosomes. Humans have a lot of genetic variation in this
IFITM3 gene. Genetic variation in the IFITM3 gene is associated with severe influenza e.g. the CC genotype (rather than
the CT genotype which is associated with mild influenza. CC genotype is common in Chinese people.

Mx is a GTPase that can form multimers which wrap around the nucleocapsids of incoming viruses therefore nullifying
incoming virus genomes. Mx1 inhibits influenza and Mx2 inhibits HIV.

PKR (Protein Kinase R) phosphorylates the alpha subunit of eIF2 and prevents translation in the infected host cells. It
also activates IKKb leading to NFkb release an important transcription factor in the antiviral response.

LO5: Give examples of how viruses control or evade the type I interferon system and how this
knowledge can be harnessed to make new therapies.
Viral evasion of the INF response can take place in many ways. These include:
Avoiding detection by hiding the PAMP. This results in a failure to initiate the innate and this interferon response.
Interfere globally with host cell gene expression and/or protein synthesis.
Block IFN induction cascades by destroying or binding.
Inhibit IFN signalling
Activate SOCS (Suppression of Cytokine Signalling)
Use a replication strategy that is insensitive to IFN
Page 3 of 15 Kanay Khakhria

Hepatitis C Virus contains an accessory gene that codes for the NS3/4 protease which cleaves MAVS and therefore
prevents interferon induction.

Influenza virus contains an accessory gene that codes for the NS1 protein which binds to RIG-I preventing activation of
signalling pathway and preventing nuclear processing of newly induced genes.

The Pox viruses are also large DNA viruses. More than half of their genome is comprised of accessory genes that modify
the immune response. Some pox viruses encode soluble cytokine receptors that mop up interferon so that they dont
reach their receptors. Ebolavirus also encodes an IFN-antagonist

HIV is another virus which uses accessory genes to overcome restriction factors. Such
genes include the Vif and Vpu genes:
The Vif protein product targets the APOBEC system. APOBEC3G is a mRNA-editing
enzyme which is involved in innate resistance to retroviruses and hepadendoviruses.
It usually deaminates dC to dU in minus strand viral cDNA during reverse transcription.
The Vpu, Env and Nef genes target Tethrin which is a cell surface molecule that
normally stops viral budding from the plasma membrane.

Viruses can also modulate the innate response, skewing the effects of interferon from protective to immunopathologic.
This may depend on how much interferon is made, with the amount of IFN needed for IL-6 induction being 100x greater
than for Mx. Transcriptomics reveals how Type-I IFN treatment and viral infections induce different ISG expression profiles.

Viral pathology is a combination of damage of infected cells by virus, and damage of infected and bystander cells by the
immune response. Viral induction of interferon can lead to a cytokine storm. This is the release of toxic anti-viral
mediators such as massive amounts of TNF-, which causes harm to the host. Differences in clinical outcome may reflect
vigour of innate immune system, which may vary with age. It is the cytokine storm that makes Dengue haemorrhagic
fever, severe influenza and Ebola viral infections so dangerous.

Interferon can be used as an antiviral treatment. However, it stimulates so many aspects of a cytokine and chemokine
response that it is associated with side effects like fever and aching. Pegylated IFN is used as a treatment for hepatitis C
virus infection.

Viruses that lack the ability to control interferon, produce high INF levels. This is useful in generation of live attenuated
vaccines as the high IFN levels can also induce and recruit useful immune cells; Interferon can act as an adjuvant. Cells
naturally or engineered to be deficient in IFN response can be used to grow these attenuated virus strains.
Page 4 of 15 Kanay Khakhria

Lecture 2: Viral Evasion of Host Immunity

LO1: Explain how viruses escape host cellular immune responses and list examples.
Viruses are intracellular pathogens and so their proteins are easy targets for processing and presentation on MHC
molecules. Our cellular immunity is what generally clears viral infections. It is short lived because it is toxic.

It is the internal viral

proteins which tend to be the
target of the cellular immunity.
This is good because they
vary less than surface
antigens, and also allows for
the formation of good
immunological memory.
Viruses that cause chronic
infections need to have
evolved to evade cellular
immunity as well innate
immunity.

Viral (and cellular) peptides

are fed into a proteasome
which chops the peptide
before it is fed into the
endoplasmic reticulum.
Here it is complexed with
MHC molecules which are
presented on the cell surface.

The peptide fragment can be

seen by unique T-cell
Receptors which would then
initiate the adaptive immune
system.

Viruses that survive in the

body for many years interfere
with the peptide presentation
pathway to avoid activation of
the adaptive immune system:

TAP proteins are proteins which transport peptide fragments into the endoplasmic reticulum. The Epstein-Barr Virus
encodes a protein (EBNA1) that cannot be processed by the proteasome, and therefore cannot be loaded by TAP.
Herpes-Simplex Virus produces a protein (ICP47) that blocks access of the processed peptide to TAP. Human
Cytomegalovirus goes a step further and encodes a protein (US6) which stops ATP binding to TAP, preventing
translocation.

hCMV also makes a protein (US3) which binds to tapasin and prevents peptides being loaded into MHC. Adenovirus
prevents recruitment of TAP to tapasin (through E3-19K protein). It also retains the MHC molecule in the ER preventing it
from reaching the cell surface.

Another herpesvirus, KSHV (Kaposi's sarcoma-associated herpesvirus) makes a protein (kK3) which induces
polyubiquitinylation and internalisation of MHC. Because it is ubiquinated, it is also marked for degradation by
lysosomes.

However, this poses another threat to the virus, as NK cells kill cells that dont display MHC. To overcome this, some
viruses such as CMV also encode MHC analogues (gpUL40) or upregulate MHC.

Other viruses avoid the immune system by directly attacking it. Examples include:
HIV targets CD4+ T-cells and depletes the ability to support an immune response
Ebola virus infection also results in destruction of target dendritic cells and macrophages by direct infection. As
these cells present to T-cells, Ebola also infect T-cells by bystander response. Because Ebola is much more acute
than HIV, we do not see the long-term sequelae of immunosuppression caused by it.
Page 5 of 15
LO2: Explain how antigenic variation may lead to viral evasion of host immunity using named
viruses as examples.
LO3: Give examples of the consequence of immune suppression by viruses
Antigenic variation is a form of continued rapid
evolution driven by antigen pressure from the host. An
example of this is the influenza antigenic drift where
the influenza cell surface antigens change over time.
Antigenic variation also exists as different genetically
stable serotypes that circulate between us. This is
particularly true of rhinovirus (has 120 distinct serotypes)
poliovirus and dengue, making developing vaccines
difficult.
Dengue Virus exists as 4 different serotypes. It is the
antibodies generated against previous infection that
cause Dengue Haemorrhagic Fever. This is because
they bind to, but not neutralise the similar new antigen.
We can partially account for influenza antigenic drift by
producing multivalent seasonal vaccines for antigens
predicted to be popular. However, the prediction can go
wrong at times, resulting in low vaccine efficacy. A
Kanay Khakhria
universal influenza vaccine is being developed by
targeting a more conserved region of the antigen.
Some viruses have glycoprotein antigens that are so
heavily glycosylated (mucin like) that antibody access
is hindered - eg in HIV and Ebola. Ebola virus particle
membranes have a high content of phosphatidyl serine
lipids, making them look like apoptotic bodies that are
rapidly taken up by pinocytosis away from antibody
surveillance. Ebola also codes for sGP (soluble
glycoproteins) which act as an antibody decoy. sGP
also has immunosuppressive properties, inhibiting
neutrophils.
Virus-mediated immunosuppression can be dangerous,
as in the cause of HIV and AIDS. Measles also causes
immunosuppression by infecting CD150 cells. Recent
research shows how Measles Virus infection results in a
2-3year decrease in immunological memory that leads to
morbidity and mortality from other diseases.
Page 6 of 15 Kanay Khakhria

Lecture 3: Parasitic Infections

LO1: Explain the difference between endoparasites and ectoparasites, and between protozoan
and metazoan parasites.
Infection is the invasion by and growth of pathogenic microorganisms
Parasite: An organism living in or on the
within the body.
host and dependent on it for nutrition -
causing damage.
A disease is a disordered or incorrectly functioning organ, part, structure,
or system of the body resulting from the effect of
genetic or developmental errors, infection, poisons, nutritional
Endoparasites: Ectoparasites: Live
deficiency or imbalance, toxicity, or unfavourable environmental factors;
Live inside the outside the body of
illness; sickness; ailment. body of the host the host

Protozoa include amoeba, coccidiae, ciliae,

and flagellates. They are eukaryotes
Metazoa:
(genome within a nucleus), with varied Protozoa: Single
Multicellular
pathogenesis. Some have insect vectors, such celled organisms
organisms
as mosquitos. In general, they do not produce
eosinophilia.

Metazoa (Helminths) include roundworms, flatworms and flukes. They tend to be free living, involving intermediate
hosts and vectors. Some only inhabit the guy (geohelminths), while others can invade tissues. If they invade the blood, they
can produce eosinophilia.

LO2: Explain what is meant by a vector and list two specific examples, naming the diseases they
transmit.

LO3: List the four main types of protozoan parasites, naming important pathogens of each type
and the main symptoms they cause.
Amoebae
Amoebae are a class of protozoa. Amoebae are a type of cell or organism which has the ability to alter its
shape, primarily by extending and retracting pseudopods. Amoebas do not form a single taxonomic group;
instead, they are found in every major lineage of eukaryotic organisms. Amoeboid cells occur not only
among the protozoa, but also in fungi, algae, and animals. The two clinically important parasitic amoebae
are Entamoeba histolytica and Entamoeba dispar.

Infections occur by ingestion of mature cysts in food or water, or on hands. About 10% of the worlds
population is infected with E. histolytica. It is responsible for the third most common cause of death of
parasitic infections (after malaria and schistosomiasis). Common in south and central America, and Asia
(rare in temperate climates).

90% of infections are asymptomatic with the reminder producing a spectrum of disease varying from dysentery to
amoebic liver abscess. Invasive amoebas can also affect the lung, heart, brain, urinary tract and skin. The cysts of E.
histolytica enter the small intestine and release active amoebic parasites (trophozoites), which invade the epithelial cells of
the large intestines, causing flask-shaped ulcers. Infection can then spread from the intestines to other organs, e.g. liver,
lungs and brain, via the venous system. Incubation period may be as short as 7 days; tissue invasion mostly occurs during 4
months of infection. Only E. histolytica is pathogenic.

Coccidia
The Plasmodium genus is an important member of the coccida eukaryotes. The main species include P.
falciparum, P. malariae, P. ovale, and P. vivax, which cause the disease malaria. They have two hosts:
humans and female Anopheles mosquitoes.

In 2013, there were ~198 million cases of malaria, causing an estimated 584 000 deaths, mostly among
African children (one child dies every 30 seconds). Symptoms can appear as early as 7 days, depending on
species of plasmodium. Symptoms include fever, headache, chills, vomiting and muscle pain in a
paroxysmal (sudden and intense) cycle. The longer term complication of malaria includes severe anaemia
(due to destruction of the red blood cells), and cerebral malaria (due to swelling of the brain) leading to
seizures and coma. Other symptoms include liver failure, shock, pulmonary oedema, kidney failure and ruptured spleen
Page 7 of 15 Kanay Khakhria

Plasmodium can be detected on a blood film or a more rapid antigen detection test can be done.
Usually treated with chloroquine and doxycycline.

Toxoplasma gondii is another important coccidia which causes toxoplasmosis. Humans can become
infected by eating undercooked meat of animals harbouring cysts, exposure to cat faeces, blood/organ
transplants, and also transplacentally.

Toxoplasmosis is a mild disease in immunocompetent individuals, however can pose a serious danger for
the foetus. immunocompromised patients may develop CNS disease, brain lesions, and
pneumonitis among other risks.

Cryptosporidium is a genus of coccidia protozoa that can cause diarrhoea in immunocompetent

individuals. However, it usually presents in HIV+ patients with more serious symptoms. Diagnosis is done
by stool examination. Treatment is fluid rehydration.

Ciliates
The only clinically relevant ciliate is the Balantidium coli, which as reservoir hosts with pigs, rodents, and
primates. It is also distributed worldwide. Most people infected with Balantidium coli experience no
symptoms. Immunocompromised patients may experience more severe signs and symptoms:
persistent diarrhoea, dysentery, abdominal pain, weight loss, nausea, and vomiting. If left untreated,
perforation of the colon can occur. Diagnosed with stool examination.

Flagellates
The Giardia lamblia organism is the most common water-borne protozoal infection. It causes Giardiasis
which acutely presents with diarrhoea, greasy stools which float, abdominal cramps and dehydration.
However, most people do not present with any symptoms. Giardiasis affects up to 8% of children in
developed countries, and 33% of people in developing countries.

The Trichomonas vaginalis organism is responsible for the the most common, curable, non-viral STI in the
UK Trichomoniasis, with 6000 new cases per year. In women, the organism is found in the vagina,
urethra and paraurethral glands; in men it is usually found in the urethra.

Up to 50% of people are asymptomatic. Women with symptoms experience vaginal discharge, vulval
itching, dysuria, or offensive odour. Occasionally the presenting complaint is low abdominal discomfort
or vulval ulceration. Men can also experience discharge and/or dysuruia.

Trichomonas may also enhance HIV transmission. Diagnosis of Trichomoniasis is done by microscopy
and/or a trichomonas rapid test. The infection can be treated with metronidazole.

Trypanosoma is a genus of flagellated protozoa, transmitted by tsetse flies (often in the vicinity of
animals e.g. game parks). Infection can lead to a febrile illness with lymphadenopathy and ultimately
invades the nervous system leading to alterations in consciousness causing the fatal disease of sleeping
sickness (caused by Trypanosoma brucei). African trypanosomiasis symptoms occur in two stages. The
first stage, known as the hemolymphatic phase, is characterized by fever, headaches, joint pains, and
itching. The second, neurological phase, begins when the parasite invades the central nervous system.

Leishmania is a genus of protozoa transmitted by sand flies found in warm parts of the world (mainly the
old world). It causes leishmaniasis which can present in three main ways: visceral, cutaneous and
mucocutaneous.

Visceral leishmaniasis is the most severe form, fatal if left untreated, characterised by irregular fever,
weight loss, swelling of liver and spleen and anaemia. Cutaneous leishmaniasis presents with skin
lesions on exposed body parts, often self-healing. However, can create serious disability and scars.
Mucocutaneous leishmaniasis is disfiguring, destroying mucous membranes.

Apart from the tropics, the disease also occurs around the Mediterranean and is associated with HIV
infection.

LO4: List the three main types of metazoan parasites, naming important pathogens of each type
and the main symptoms they cause.
Metazoa (helminths) are complex multicellular parasites. The adult worms cannot multiply in man, and so lay eggs,
microfilaria and larvae.

Nematodes (Roundworms)
Page 8 of 15 Kanay Khakhria

Ascaris lumbricoides are giant human roundworms that live in the lumen of the small intestine. A female may produce up
to 250 000 eggs a day, which are passed with the faeces. Infection with Ascaris is called ascariasis and usually produces
no symptoms. However, infection with a large number of worms may cause abdominal pain or intestinal obstruction.
Because adults feed on the contents of the small intestine, ascariasis can lead to malnourishment in individuals (especially
children).

Hookworms such as Ancylostoma duodenale can produce iron deficiency anaemia caused by blood loss at the site of
intestinal attachment. This is the most common symptom of hookworm infection, accompanied by cardiac complication.
Gastrointestinal and nutritional symptoms can also occur, as can local skin manifestations. Diagnosed by stool
examination.

Wuchereria bancrofti is a Filaria that causes Lymphatic filariasis (Elephantiasis) by attacking the lymphatic system.
Wucheria is transmitted via mosquito. Other filaria can cause cutaneous filariasis, and loaiasis (by Loa loa worm),
transmitted by blackflies and mango flies.

Strongyloides is an important worm infestation because the eggs produced by the adults can hatch within the host and
invade human tissue leading to severe illness especially when the host is immunocompromised. It is cause of diarrhoeal
illness in the tropics.

Cestodes (Flatworms)
Taenia (also known as tapeworms) can come from uncooked from pork (T. solium or T. asiatica) or from beef (T.
saginata). Most people have no symptoms or have mild symptoms. Taeniasis from T. saginata usually presents with more
symptoms, as the size of the worm is larger. Tapeworms can cause digestive problems such as abdominal pain, loss of
appetite, weight loss and upset stomach. The most visible sign of taeniasis is the active passing of tapeworm segments.
Taenia solium is the most common cause of acquired epilepsy worldwide.

Trematodes (Flukes)
Schistosoma are responsible for a group of highly significant infections termed schistosomiasis. The main culprits are S.
haematobium and S. mansoni. Within days, patients can experience itchy skin or a rash. Within two months,
schistosomiasis presents with fever, chills, cough, and muscle aches. Children who are repeatedly infected can develop
anaemia, malnutrition, and learning difficulties. After years of infection, the parasite can also damage the liver,
intestine, lungs, and bladder.

LO5: Name two ectoparasites, explain the symptoms they cause, and how they are diagnosed.
Sarcoptes scabei produce the disease called scabies. They burrow into the upper layer of the skin,
causes temporary itching due to dermatitis; but do not multiply on the human host.

They are diagnosed on the appearance of a rash and presence of burrows. Infection can be treated with
scabicides.

Lice such as Pediculus humanus capitis, Pediculus humanus corporis, Pthirus pubis; may be
asymptomatic or cause tickling feeling, itching, allergic reaction; can serve as vectors for Rickettsia
prowazekii (epidemic typhus), Bartonella quintana (trench fever), and Borrelia recurrentis (louse-borne
relapsing fever).
Page 9 of 15 Kanay Khakhria

Lecture 4: Immunity to Fungal Infections

LO1: List the major antifungal immune effector cells.

The innate immunity has a direct role in antimicrobial activity and fungal killing. It also has a facilitative role through the
production of pro-inflammatory cytokines and chemokines, and antigen presentation.

Each distinct growth form of a fungus is called a morphotype. As the morphotype of the fungus changes, the innate
response varies.

The three major antifungal immune effector cells include:

Neutrophils are involved in the phagocytosis of opsonised (by both complement and antibodies) and
unopsonised fungi. They are also involved in the oxidative killing of fungi as well as produce cytokines to help with
the response.
Macrophages are also involved in the phagocytosis of opsonised and unopsonised fungi. They have a key role in
granuloma formation and in the release of pro-inflammatory cytokines in order to maintain latency of
response. Macrophages also act as antigen presenting cells.
The main role of the dendritic cell is in antigen presentation, and therefore in Th1/2 polarisation. They can
also phagocytose and kill fungi as well as produce cytokines.

LO2: Explain mechanisms of cell-mediated antifungal defence.

As mentioned above, phagocytes can kill internalised microbes by both oxidative and non-oxidative mechanisms.

The NADPH oxidase enzyme complex is a multi-subunit enzyme complex which mediates the respiratory burst.
During phagocytosis, oxygen consumption is increased through the activity of NADPH-oxidase generating superoxide
anion !" and hydrogen peroxide #" !" . These metabolites give rise to yet other reactive oxygen species that are strongly
anti-microbial, but which may also cause tissue damage and apoptosis. The role of ROS (Reactive Oxygen Species) by
neutrophils in fungal killing is essential, and successfully kills internalised Candida albicans.

Neutrophils can also produce NETs (Neutrophil Extracellular Traps) which are extracellular fibres derived from chromatin
and coated with granule proteins. The production of NETs requires ROI-mediated signalling cascades. This type of
mechanism is important in the killing of Aspergillus fumigatus and is an example of where ROS plays a part in killing that is
distinct from direct killing.

Simply phagocytosis itself by alveolar macrophages plays an essential role in the defence against Cryptococcus
neoformans as it leads to cytokine secretion. This recruits, other immune cells, and leads to the activation of CD4+ Th1 cells
which is essential in the clearance of infecting fungal cells. However, from phagocytosis, there may be a latency phase, or
survival of C. neoformans before escape and CNS infection. Aspergillus fumigatus are internalised and killed by
macrophages. On the other hand, Candida albicans experiences nutrient starvation inside the macrophage
phagolysosome, prompting germination and escape.

LO3: Summarise the sequence of events leading to effective clearance of infectious fungal cells.
A number of cell wall components of the fungi act as PAMPs, detected by PRRs (Pattern Recognition Receptors). TLRs
(Toll-like Receptors) are one of the activators of innate and adaptive immunity to fungi. Dectin-1 is a major fungal pattern
recognition receptor (PRR) which not only senses fungi at the cell surface but its also responsible for the internalisation
of fungi.

Some fungal PAMPs are specific to certain morphotypes, while certain morphotypes may be able to evade recognition all
together.

Most fungi are detected and destroyed by the innate immune system hours before even an early inflammatory response.
Opsonisation is done by pentraxin 3 and mannose-binding lectin, allowing phagocytes to more easily recognise the
pathogens. If the organism breaches these early lines of defence, the adaptive immune system will ensue.

This mainly involves the generation of antigen-specific T-helper, CD8+ T-cells and Treg cells and B-cells. This response
specifically targets the pathogen and induces memory cells that prevent subsequent infection.

Dendritic cells sample fungi at the site of infection, transport them to the draining lymph nodes and activate T-cells.
TReg cells might serve to dampen the excessive inflammatory reactions and contribute to the development of memory
antifungal immunity.
Page 10 of 15 Kanay Khakhria

LO4: Explain how immune status determines risk of fungal infection.

The risk for type of fungal infection differs depending upon which aspect of immunity is impaired. The immune response to
fungi varies with respect to fungal species, morphotype and site of infection.

Fungal Pathogen/Infection Host Factor

Candida (mucosal infection) Impaired cell mediated immunity
Candida (disseminated infection) Impaired mucosa, breach of epithelial barrier,
neutropenia, chronic granulomatous disorder (CGD-
difficulty forming ROS such as superoxide)
Aspergillus Neutropenia, high dose corticosteroids, CGD
Crypococcus Impaired cell mediated immunity and high dose
corticosteroids.

Immunosuppression can therefore leave you susceptible to fungal infections. Surgery also provides a route for
opportunistic infections to infect the body.

Hereditary conditions can affect our immune response towards fungi. For example:
Human Dectin-1 deficiency leads to mucocutaneous fungal infections. It also leads to impaired macrophage
binding to Candida albicans and increase susceptibility to Aspergillosis
Human CARD9 deficiency. A functional CARD9 is needed for TNF-a production in response to -Glucan
stimulation. It is also required for Th17 differentiation in humans.
Plasminogen alleles defects can lead to increased susceptibility to Aspergillus fumigatus as plasminogen binds
directly to that fungus.

There is a damage-response continuum to define fungal pathogenesis as both the pathogen and the host response are
responsible for damage. There are two types of fungal infections in terms of the damage-response continuum:
Class 1 pathogens cause damage in hosts in hosts with a weak immune response or in the setting of a normal
host response. The curve plotted host-response against damage, would show as the host response increases,
damage to the host decreases. Such organisms include Candida albicans and Cyrtpococcus neoformans.
Class 2 pathogens cause damage at the extremes of both weak and strong immune responses. At low
immune responses it is the pathogen that directly causes the damage, while at high immune responses, the
pathogen causes the damage through the toxic immune response.
Page 11 of 15 Kanay Khakhria

Lecture 5: Community Acquired Infections

LO1: List important bacterial virulence factors.

Bacteria can come in many shapes and forms. The main shapes are cocci, bacilli and spirochete. They can be further
categorised based on how they group. For example, cocci that clump are called Staphylococci, while cocci that form a line
are called Streptococci.

Common virulence factors (factors that contribute to bacterial pathogenicity) include:

Diverse secretion systems
Flagella (important in movement and attachment)
Pili (important in adherence factors)
Capsules (can protect against phagocytosis) Streptococcus pneumoniae
Endospores (metabolically dormant forms of bacteria) that are resistant to heat, cold, desiccation and chemicals
Bacillus and Clostridium species
Biofilms (organised aggregates of bacteria embedded in a polysaccharide matrix, making it antibiotic resistant)
Pseudomonas aeruginosa and Staphylococcus epidermidis

As well as the above structures, bacteria can also produce a range of exotoxins:
Neurotoxins are exotoxins that act on the nerves or motor endplates to cause paralysis. Such exotoxins include
the tetanus or botulinum toxins.
Enterotoxins are those that act on the GI tract to cause diarrhoea. They inhibit NaCl reabsorption, activate NaCl
secretion or kill intestinal epithelial cells.
o Infectious diarrhoea occurs when bacteria colonise and bind to the GI tract, continuously releasing
their enterotoxin locally. Examples include Vibrio cholerae, Escherichia coli, Shigella dysenteriae and
Campylobacter jejuni
o Food poisoning occurs when bacteria grow in food, releasing the enterotoxin into the food. The digested
toxin is ingested resulting in symptoms. Bacillus cereus or Staphylcoccus aureus are bacteria that do this.
Pyrogenic exotoxins work by stimulating the release of cytokines i.e. Staphylcoccus aureus or Streptococcus
pyogenes.
Tissue invasive exotoxins allow the bacteria to destroy and tunnel through tissue. They are enzymes that destroy
DNA, collagen, fibrin, NAD, RBC and WBC.
Bacteria can also produce miscellaneous exotoxins are specific to the species. Endotoxins are toxins only produced by
Gram+ bacteria as they are the lipid A moiety of LPS outer membrane and are shed in steady amounts from living
bacteria. Treating a patient with a Gram- infection can sometimes worsen their condition because when bacteria are lysed
they release large quantities of endotoxin/LPS leading to septic shock.

LO2: Define an outbreak of infectious disease.

LO3: Explain how outbreaks are identified.
An outbreak is a greater-than-normal or greater-than-
expected number of individuals infected or diagnosed with a
particular inflection in a given period of time, and/or a particular
place.

An example of an outbreak is the E.coli outbreak in Germany

2011. This particular strain was entero-aggregative and
shiga-toxin producing, causing gastroenteritis and
haemolytic-uremic syndrome.

Heamolytic-uremic syndrome is characterised by a triad of acute renal failure, haemolytic anaemia, and
thrombocytopenia. E.coli strains that cause haemolytic-uremic syndrome are called EHEC stains (enterohaemorrhagic
E.coli). They cause these symptoms though the production of shiga-toxin, which inhibits protein synthesis in eukaryotic
cells, as well as affecting the microflora of the gut.
Page 12 of 15 Kanay Khakhria

You can use PCR to define if an infection is caused by the outbreak strain or not different countries have different
regulations what is accepted and what is not accepted for diagnosis. Through genome sequencing it was found out that the
bacteria responsible for the outbreak was a EAEC strain (enteroaggregative E.coli) that had been infected with
bacteriophage that transferred genes from the EHEC strain, to form a fusion EAHEC strain.

Normally, EAEC strains can colonise both the small and large bowels. This is through the production of (virulence factor)
aggregative adherence fimbriae (AAF). This is required for adhesion to erythrocytes, allowing for biofilm formation.

An outbreak can be identified through surveillance and good and timely reporting systems.

LO4: List bacterial pathogens that cause community acquired infection.

LO5: Explain the routes and types of infection caused by these bacterial pathogens.
The communicable diseases in Europe can be roughly split into six categories:

Respiratory Diseases
These commonly include influenza, animal influenzas, SARS (Severe Acute Respiratory Syndrome), Legionnaires
disease and Tuberculosis.

Legionella Pneumophilia Mycobacterium tuberculosis

Gram- Causes legionnaires disease Mycolic Causes tuberculosis. The bacterium

through infecting and growing in can enter a dormant state, causing
alveolar macrophages. latent tuberculosis.

Important virulence factor is the type The Mycolic acid layer has an extra lipid
IV secretion system which allows layer which makes treatment more
secretion of effector proteins that allow difficult. Treated with six months of
replication in a LCV (Legionella Isonizid and Rifampicin.
containing vacuole) in the host cell.

Sexually Transmitted Infections

These commonly include chlamydia, gonorrhoea and syphilis (caused by Treponema pallidum) and infections caused by
HIV, HepB and HepC,

Chlamydia trachomatis Neisseria Gonorrhoeae

It is an obligate intracellular pathogen Gram- Causes gonorrhoea through

Gram-
(can only grow and divide within host establishing infection in the urogenital
cells, so cannot be cultured outside tract. The bacteria interact with non-
host cell. ciliated epithelial cells.

It is the most frequent STI in Europe. Important virulence factors include pili
It is also popular in other parts of the to aid in adherence, and antigenic
world where it is responsible for 3% of variation to escape detection and
the worlds blindness. clearance by the immune system.

Food and Waterborne Diseases

These importantly include:
Anthrax caused by Bacillus anthracis.
Cholera is an acute severe diarrheal disease caused by Vibrio cholera which uses fimbria to deliver the cholera
toxin.
Listerosis caused by Listeria monocytogenes. Particularly affects immune-compromised patients, the elderly, and
pregnant patients. Can also corss the blood-brain barrier.
Shigellosis caused by Shigella species.
Salmonellosis caused by Salmonella species is one of the most common GI infections in Europe. Mainly
contracted through undercooked poultry. Small children (0-4 years) are the highest risk group. Type III secretion
systems are ecoded on pathogenicity islands.
Escherichia coli causing haemolytic-uremic syndrome.
Campylobacter jejuni is the most commonly reported infectious GI disease in Europe. Small children (0-4 years)
are the highest risk group. Infection is most likely though undercooked poultry. Uses flagella and type IV secretion
systems.
Page 13 of 15 Kanay Khakhria

Emerging and Vector-Borne Diseases

These importantly include:
Malaria
Plague caused by Yersinia pestis (Gram-)
Q fever caused by Coxiella burnetti (Gram-)
Severe acute respiratory syndrome (SARS)
Smallpox (an eradicated virus)
Viral haemorrhagic fevers (VHF).
West Nile fever
Yellow fever

Vaccine Preventable Diseases

These include:
Diphtheria caused by Clostridium diphtheriae (Gram+)
Invasive Haemophilus influenzae disease caused by Haemophilus influenzae (Gram-)
Invasive meningococcal disease caused by Neisseria meningitidis (Gram-)
Invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae (Gram+)
Pertussis caused by Bordetella pertussis (Gram-)
Tetanus caused by Clostridium tetani (Gram+)
Measles
Mumps
Polio
Rabies
Rubella
Page 14 of 15 Kanay Khakhria

Lecture 6: Hospital Acquired Infections

LO1: Explain why patients in hospital are particularly at risk from acquiring new infections.
Healthcare-associated Infections (HAI) are infections that occurs >48h after exposure to healthcare. 3.2 million patients
a year acquire healthcare-associated infection in the EU each year. About 37,000 of them die as a direct consequent of this.
The most frequent types of HAI are surgical site infections, urinary tract infections, pneumonia, bloodstream infections
and gastrointestinal infections.

Hospitals are a source of infections due to three main reasons:

1. Interventions performed, such as central lines, catheterisation, intubation, chemotherapy, prophylactic antibiotics,
inappropriate prescribing and prosthetic material.
2. Dissemination of infection by people moving from ward to ward.
3. Concentration of people hospitals have a large concentration of people, who also tend to be
immunocompromised, increasing the chance of infection.

LO2: List examples of common hospital infections caused by bacterial pathogens.

LO3: Explain the routes and types of infection caused by these bacterial pathogens.
The most common pathogens, also tend to be resistant (not all) to certain antibiotics. The mnemonic ESCAPE can be used
to remember the names of the pathogens:
Gram positive
Enterococcus faecium (vancomycin resistant)
Staphylococcus aureus (methicillin resistant)
Clostridium difficile (can establish infection more easily if previous antibiotic treatment had wiped out normal gut
flora)
Gram positive
Acinetobacter baumanii (highly drug resistant)
Pseudomonas aeruginosa (multi drug resistant)
Enterobacteriacae such as E. coli, Klebisella pneumoniae, and Enterobacter species (multi drug resistant)

Our therapeutic options for these pathogens are so extremely limited that clinicians are forced to use older, previously
discarded drugs, such as colistin. These drugs are associated with significant toxicity and for which there is a lack of robust
data to guide selection of dosage regimen or duration of therapy.

Pathogenic E.coli is the most frequent cause of bacteraemia by a Gram- bacterium. It is also the most frequent cause of
community and hospital acquired UTI. There has been an increase in multi-drug resistant strains, especially resistance to
cephalosporins. Most isolates that are resistant to cephalosporins express the extended spectrum beta lactamase
virulence factor. They still seem to be sensitive to carbapenems.

Cephalosporins are a class of -lactam antibiotics which inhibit peptidoglycan

incorporation by binding to transpeptidase enzyme [Pharmacology 31].
Extended spectrum beta-lactamase enzyme encoded on the E. coli plasmid, cleaves the
cephalosporin.

Carbapenems are also a class of -lactam antibiotics, therefore inhibiting

peptidoglycan wall synthesis. However, beta-lactam ring cannot be cleaved
by ESBL, but can instead be cleaved by carbapenemase enzyme bla(kpc)
which is encoded on a transposon mobile genetic element.

Klebsiella pneumoniae is an important cause of UTI and respiratory tract infections, particularly in
immunocompromised patients. A high proportion of cases are resistant to cephalosporins, fluroquinolones, and
aminoglycosides in Europe. CRKP (carbapenems-resistant Klebsiella pneumoniae) on the other hand is the most commonly
encountered species in the United States.

Pseudomonas aeruginosa is an important cause of infection in the immunocompromised. A high proportion of strains
are resistant to several antimicrobials, in particular to carbapenems.

MRSA (Methicillin Resistant Staphylococcus Aureus) is the most important cause of

antimicrobial resistant infection worldwide.

Methicillin is also a -lactam antibiotic and therefore normally inhibits peptidoglycan

incorporation. Resistance is produced by expression of additional penicillin-binding protein
PBP2A has a low affinity for methicillin and can still function in he presence of the antibiotic.
Page 15 of 15 Kanay Khakhria

LO4: Explain why prudent antibiotic use is important in limiting hospital acquired infections.
LO5: Explain the problem of antibiotic resistance.
People die, its sad.