MICR3001 Past Exam Paper Practices!

bye everyone.
Let’s all keep this civil and remember that the goal is to help each other to each do the best
we can! Best of luck everyone! :)
Jw is candidasis the ‘most common fungal disease’? asspergillus
Do we need to study for clinical module?? SOS!! No telling - theres been 1-2 clinical questions in the
past few exams but that doesnt mean it couldnt change - especially since some of the lectures had
example qs
Good luck everyone <3 <3
Did we get back the fungal report yet?
NO!!!!! ANGERY REACTS ONLY >:( +8
Anger intensifies +1
Any idea what we need to know for module 4 lol? +7
Not gonna study anything from module 4 (wing it) +5 its 3 weeks of content though - literally longer
than the fungal module im worried the yll be a few questions for module 4 - there haven’t been
many in past exams though? - IVE BEEN BURNED BEFORE 😰😰😰
Module 4 stuff is honestly pretty self explanatory except for the last 2 lectures
James better go easy on us for module 3 for giving our marks back so late :(
All these virulence factors are getting mixed together in my head which one belongs to which idk
My plan is to rewrite them over and over again and hope for the best (: aaaaaa
Plus 1 if you’re gonna skip the fungal module all together and hope for the best :) +7
The herpes lecture notes are soo long, and he talked so little hahahah *cries* +1 why havent there
been any herpes questions in the past
Look down at question C2 my friend. He also attached written lecture notes with it with what he
said out loud.

Honestly feel like crying tbh+7

I SHOULD'VE DONE ENGINEERING

Plus 1 if you have given up all hope and must now rely on the Cells at Work

anime +2 yall mind if i hit that YEET

Do we need to know every detail in the herpes lecture notes? +4 Not the molecular names
but the rest of it probably
COMMENT ON THE FUNGAL QNS PLS SO WE CAN WRITE UP THE
ANSWER NICELY. THANKS :)
Added a Gonorrhoeae question as A5, please feel free to answer it
JAMES FRASER IS GONNA ASK A HARD QUESTION I JUST
KNOW IT :( +1000000000000000000000001 (he is gonna rekt us)
- If he asks about how to make chocolate, i called it first here.
Added module 4 question on genomics + scarlet fever he mentioned
as example in the lecture - D6
LMS if you feel fucked by BIOC3003 :) ← hit the feels

A1. Write about the virulence mechanisms employed by uropathogenic Escherichia coli to
exert its pathogenic effect AND discuss the implications for both treatment and vaccination.
Two types of fimbriae
- Type 1: Bind D-mannose containing glycoproteins in the bladder via FimH tip
adhesin and are associated with bladder colonization (cystitis)
- P fimbriae: Bind gal-gal disaccharide in upper urinary tract via PapG tip adhesin.
Kidney colonisation (pyelonephritis)
- Both phase variable
Toxins
- Hemolysin: Pore forming, inserts into eukaryotic membrane, causes cell lysis and
triggers apoptosis, stimulates cytokine production.
- Cytotoxic necrotising factor 1 (CNF-1): Kills epithelial cells, causes actin
rearrangements and membrane ruffling.
- Secreted autotransporter serine protease (Sat): vacuolation and tissue damage.
Others
- LPS: O antigen (only specific types). Required for serum survival.
- Capsule: Offers resistance from the host immune system.
- Iron acquisition: Power/feed cell, multiple systems, often uses siderophores.
- Antigen 43: causes bacterial clumping, promotes biofilm formation, IBC (intracellular
bacterial communities) formation and therefore persistent infection
Most of these factors are kept in transposable pathogenicity islands.

Treatment
Short term: antibiotics, able to use because it’s uncomplicated and increase antibiotic
strength as strains become resistant.
Catheter infections: Broad spectrum.
Novel Treatments
Mannosides to inhibit fimH adhesion of UPEC (has good oral bioavailability)
Vaccines
FimH: target a vaccine toward fimH adhesin (using antibody specific to those binding sites)
PapG: Target a vaccine toward binding sites of PapG. (have trouble with this because P
fimbriae are phase variable, and not present in all strains)
Probiotics
Asymptomatic bacteriuria delivered to the site of infection, can inhibit colonization of the
urinary catheter by more virulent/pathogenic strains.
Do you think we should include the stuff about intracellular bacterial communities?
In a three hour exam with 7 other questions???? Nah defs not. That above is defs worth the
12.5 marks.
I mean personally I would because it’s only like 2 sentences. +1

A2. Neisseria meningitidis is an important human pathogen that causes significant morbidity
and mortality. Discuss the virulence factors that enable Neisseria meningitidis to cause
disease. What vaccines are used to prevent infections caused by Neisseria meningitidis?
Outer Membrane
- Pili: typical family of adhesins (type IV), crucial role in colonisation of host. Long
polymeric proteins.
- Opa & Opc: outer membrane protein, variable in number, size and antigenicity. Act
as adhesins. Adherence is mediated by Opc and other factors, and it can also cause
cytoskeletal changes that facilitate epithelial invasion. (Opa: CD66, Opc: Heparin)
- Porins: Two major (PorA and PorB), human antibodies recognise both of them.
React with antibodies which can enhance the immune response.
- Iron Acquisition: Grows in iron restricted environments, has receptors which can bind
hemoglobin (intracellular) and transferrin/lactoferrin (extracellular).
- Capsule: anti-phagocytic, resistant to bactericidal activities of the complement
system. Resistant to engulfment by macrophages. (composed of sialic acid
derivatives which are poorly immunogenic)
- LPS: Endotoxin (only known toxin produced by this bacterium). OM vesicles
released from cell surface, direct relationship between the blood LPS content and
patient outcomes. It activates a cytokine cascade, leading to inflammation which can
lead to death.
-
Treatment
Can be treated with antibiotics if caught early enough, however it can be hard to diagnose it
early on in the disease, as many of the early symptoms present themselves as the flu.
Vaccines
Vaccines exist for C strain and combined ACYW strains (based on capsule, don’t provide
long lasting immunity). However the serogroup B capsule is poorly immunogenic, and has
structures identical to human cells (meaning it could lead to immunopathology)
- New group B vaccine in the pipeline. This one is based on the outer membrane
proteins, the major antigens which exist on the cell surface. Currently approved for
use in Australia.

A3. Recent evidence demonstrates that at approximately 96 hours following internalization

by macrophages, Mycobacterium tuberculosis can breach the phagosomal membrane and
gain access to the cytoplasm. Describe the critical effector molecule that enables this AND
discuss the promising vaccine candidate currently under development that is exploiting this
property.
Critical Effector Molecule: ESAT-6
This molecule is a 6kDa early secretory molecule, which belongs to the ESX specialised
secretion system. The main function of ESAT-6 is perforating the phagosomal lysosome,
leading to the escape of TB into the cytoplasm.
Previous studies have shown that without this protein, there is no release of TB into the
cytoplasm of the cell, however when re-introduced back via a plasmid after being knocked
out, the perforation phenotype can be re-introduced.

The current vaccine in use for TB is the BCG vaccine, an attenuated vaccine that is only
effective in children. This is because there aren’t the right antigens present to produce an
immune response in adults.

There is a new vaccine in development however (VPM1002) which uses a recombinant

strain. This strain contains:
- Hly (listeriolysin from Listeria), which acts as a stimulant similar to those from TB
- Urease-C-deficient genes to module the pH
- Facilitates delivery of antigen to macrophage cytoplasm
- Subsequent degradation of Hly as to not impede cell.
LLO allows for the antigen present to diffuse into the cytoplasm, which helps to stimulate
not just a CD4 t cell response, but also a CD8 t cell response into the system. Similar to
how ESAT-6 works, but without the virulence that would come from including the molecule.

The answer above is great but just wondering, do we need to add in LAM and PkNG for this
question as well? How it work together with ESAT-6 to exert its effect? Or reckon the above
is sufficient?

Well if it was asking for the virulence factors yeah, but seeing as it’s just asking for the
factor that causes the breach, and its relation to the vaccine. So I guess you could add it?
But also I didn’t feel it was needed for this specific question. (+1)

(A4) Write about the virulence mechanisms employed by Streptococcus pneumoniae to

exert its pathogenic effect AND discuss the implications for vaccination.
Virulence Factors
- Capsule: coat of high molecular weight polysaccharide, key factor for survival in
the lung (if no capsule, avirulent strain). Capsule is anti-phagocytic (preventing
phagocytosis). It acts as an inert shield, prevents contact and is highly charged.
Virulence of the strain can be linked to the thickness of the capsule.
- Surface Adhesins (attach to epithelial cells): Choline binding proteins (PspA to
lactoferrin, PspC binds to the complement regulatory protein factor H to mediate
 resistance to complement). These are two different types of pili which can help
with adherence to the epithelial cells.
- Surface Adhesins (attach to ECM): Pneumococcal adhesion, virulence factor A
and Enolase (plasminogen)
- Neuraminidase: Removes terminal sugars from human glycoproteins.
- Pneumolysin: Pore forming toxin, released from cytoplasm of lysed cells, binds
to cholesterol. This can inhibit the activity of ciliated cells, and is also cytotoxic to
alveolar and endothelial cells (Activates the classic complement system).
- Inflammation: Teichoic acid and peptidoglycan are immunostimulatory molecules
(induce cytokines). This can damage the lung tissue, causing a leakage of fluid.z

Vaccines
Most vaccines are targeted to the capsule antigen. There are currently 3 types;
23V: Covers 23 strains, but is poorly immunogenic (especially in infants).
7V: Conjugated to carrier protein to improve the immune response (protects from 7
serotypes)
13V: Adds 6 new serotypes (is a second generation conjugated).
This conjugation to a carrier protein helps to generate an immune response to the
capsule, however serotype specificity is the biggest problem. (Getting the serotype
number vs effectiveness ratio correct.)

Another large issue is that S.pneumoniae can undergo capsular transformation. The
genes for CPS are on the same chromosome, at the CPS locus. This locus is naturally
transformable, readily exchanging genes. When a vaccine is introduced specific to
some strains, it puts selection pressure on those strains, meaning that newer strains
that aren’t vaccinated against become more prevalent, as old strains are vaccinated for.

A5.1. Write about the mechanisms by which Neisseria gonorrhoeae exert their
pathogenic effect and discuss the implications for vaccination. (Just wanted to add this
in so we can cover all 4 of Mark’s lectures, I think I saw this in one of the past year
papers, forgot which one).

Neisseria gonorrhoeae causes bacterial infection in the genitourinary regions (spread by

sexual contact)
Type IV fimbriae - CD46 receptor binding
Opa surface adhesin - CD66 receptor binding to facilitate intimate binding and invasion
Able to undergo phase variation (tandem repeats)
LPS - serum survival by adding host’s N-acetylneuraminic acid at the terminal tip
Lipid A component causes inflammation (Pathology is mediated by inflammation)
Binds to galactose receptor found on sperm to aid efficient transmission
Iron acquisition system - steals iron from host for metabolism
Porins - efflux and influx of nutrients

No vaccination for N. gonorrhoeae due to the lack of targetable candidates. Most

surface proteins have the capability to undergo phase variation
Ceftriaxone treatment - antibiotic resistance
Resistance through: target modification and destruction of antibodies
Receptor modification such as penA modification causing
resistance to ceftriaxone
Altered efflux system: overexpression of efflux pumps

B1. Describe with the aid of a diagram how to construct a live vaccinia virus vector
expressing a recombinant rabies virus antigen.
As above-

Phase variation= reversible, high frequency switching of antigens (genes get switched on/off) in
a random process, driven by selection. This can occur via homologous recombination, site-
specific insertion, methylation/epigenetic changes or simple tandem repeats occurring in groups
 not of three, so that a change of repeat number causes a frameshift. Switching genes on/off aids
immune evasion by changing antigen presence, leading to increased virulence.

????? V.confused on how to diagram this one +1 (There’s a diagram in that lecture, give
me a bit to find it, I’ll come back to this) (I can only find a diagram of pilS recombination for
antigenic variation? I will keep looking, but if anyone can find a diagram for this from the
notes that would be super helpful thank you! I also can’t find any diagrams on google that
look relevant...Any help would be appreciated.)
How about this diagram? Explains how slipstrand mispairing works.. But i got it off google..
Not his notes I mean, maybe? Better than we had previously, so thank you!

Also maybe this? Not as detailed but was in the lecture

Normal (6 repeat): ATG CTC TTC TCT TCT CTT CTC TCC TCT TCT CTT AAG .. …
Premature stop (5 repeat): ATG CTC TTC TCT TCT CTT CTC TCC TCT TAA (STOP)
G…..
Phase variation = reversible, high frequency switching of bacterial surface antigens (genes
get switched on/off) in a random process, driven by selection. This can occur via
homologous recombination, site-specific insertion, methylation or simple tandem repeats
(homopolymeric tr acts: di-nucleotide, tetra nucleotide and penta-nucleotide repeats).
Tandem repeats are the most common mechanism of phase variation. The opa genes
encode the colony opacity-associated outer membrane proteins which act as adhesins.
Each strain of N. gonorrhoeae contains multiple opa genes. The diagram shows that phase
variation involves the alteration in the number of 5’-CTCTT-3’ repeat units through “slipped
strand mispairing” during DNA replication, leading to frame shift mutation in the Opa open
reading frame. Thus, phase variation can give rise to a phenotypic diversity by changing
antigen presence, leading to the expression of the ideal bacterial phenotype for a particular
microenvironment within the host-niche adaptation.

I tried answering the question by using the first answer given in this doc + some of the
lecture notes information. The diagram I’m referring to is the one above which can be found
in the lecture notes. Please feel free to comment on this if you have anything to add or
remove from this answer.

B3. Variation of bacterial surface antigens has important implications for both bacterial
pathogenesis and vaccine development. Using a diagram, describe the molecular
mechanism mediating antigenic variation in the Neisseria gonorrhoeae type IV pili, and
outline the implications of this process for bacterial pathogenesis.

●
● Implications for bacterial pathogenesis
 ○ Not sure how to answer this bit other than to say it enables it to evade
host defences?
Pilin is expressed from the pilE gene and is the main cause of antigenic drift. There are
also up to 11 copies of the silent gene pilS, which cannot express pilin, BUT can
undergo recombination with pilE to alter the pilin sequence (~10^7 combinations)

In bacterial pathogenesis, this means that the pili style can change frequency,
decreasing the chance that the cell can generate memory against it. This means it could
easily re-infect again. It also means the pili are poor vaccine targets, as many different
combinations exist.

I’m pretty sure that they actually want something more like this diagram (same lecture, a
bit later on):

(this is the exact same

diagram as the one above, just different colours, and the definition above is quite similar
to what is written below) I just thought that, at least for me, this diagram was a bit easier
to understand in terms of annotation.

· Antigenic variation= changes in gene sequence which lead to amino acid alterations in
proteins so that they may no longer be recognised by specifically targeted antibodies-a
constant process
· Type IV Pili in N.gonorrhoeae are composed on Pili subunits, encoded by pilE, which
displays a high degree of antigenic variation by recombining unidirectionally with sequences
of pilS, non-expressed silent copies of the gene (up to 11 varied copies). pilE contains 6
variable regions called mini cassettes which may recombine homologously with silent pilS
sequences to generate up to 107 different versions of pili
 · The huge number of different expressed pili allow immune evasion, persistent
infection, reinfection, and make the pili a very poor vaccine target.

B4. Using diagrams, describe the three-step strategy employed by Novartis to

develop an experimental group A streptococcal vaccine. Outline why this is
a more efficient approach to antigen identification in comparison to reverse
Vaccinology.

90% sure he’s actually asking for the Venn Diagram of the three techniques,
rather than this diagram here?? (I’ve included that one as well just below, I
agree)
1. Analysing surface location (surface secretome): surface digestion and band
digestion (analysis by LC/MS/MS)
2. Antibody binding (flow cytometry), polyclonal sera.
3. Immunogenicity (Protein array)
Reasons why this is more effective than reverse:
- Eliminates a larger number of proteins/antigens to be testing, cutting down the
time and resources needed to get a clinical vaccine.
- Know it should be effective from finding the antigen, and you’ll know all the
characteristics of the target. Similar to finding the needle in the haystack using a
magnet, rather than individually picking them out.

B5. Using a specific example, illustrate how genomic epidemiology is used to

track hospital outbreaks. Explain the advantages of this method in comparison
with other technologies currently being employed to track hospital outbreaks.

Looking at a specific example: Group A Strep infection within a Sydney hospital in 2010.
- 9 perupal cases occurred between June and November 2010. Due to this, a
molecular investigation was launched. Because the most common serotype is
M28, we have a genome sequence available for use.
First, EMM sequence typing was performed, which showed no clonal species between
the isolates. Next, they moved onto performing a pulse-field gel electrophoresis, which
was able to show that strains 1, 5, 6 and 7 were similar, and 8 was discriminatory
between the other M28 isolates.

Genomic epidemiology involves whole genome sequences to monitor infection

transmission in the clinical setting. So using whole genome sequencing, they were able
to compare the SNP’s present in their isolated strains, to the database for the M28
genome itself, and compare homologies.
What was found is that there were 72SNPs shared between 4 of the strains, suggesting
a recent common ancestor. However PS001, PS005 and PS006 were virtually identical
in their sequences, despite PS005 coming from a different patient. Therefore it can be
hypothesised that these three cases came from patient-patient or patient-doctor
transmission.

Using this genomic information, it can also be established that due to the common
ancestry, this strain infecting patients may be local to the hospital itself, and be a
reoccurring infection.

Advantages of Genomic epidemiology:

· Genomic epidemiology can be used to identify more specifically the strain, serotype
and virulence genes involved in a particular infection, rather than just the species. This is
helpful in identifying whether infections are obtained nosocomially (in which case hospital
infrastructure, equipment and staff can be investigated and managed to prevent further
transmission), or from the environment. The exact gene sequence can be compared to
determine how similar the exact strains in each infection case are
· Furthermore, treatment can be better targeted; for example if resistance genes are
detected, we know not to attempt that treatment, and can use only those antibiotics and
treatments we know to be effective.
· Could also track the evolution of organisms, see how and where/when they acquire
new mutations, horizontal gene transfer, etc, which is particular useful when dealing with
nosocomial resistant bacterial and fungal strains. Also predict outbreaks, and prevent spread

***********Just a heads up guys, that the lecturers for this module (i.e. Viral module)
changed from last year. So it’s possible that the questions will be different. Here’s
hoping they don’t differ that much though. ************

Luckily it seems the lecture slides are v.similar, so hopefully questions will be v.similar.
This is true, I hope they are the same. While Dr.Suen gave Roy Hall’s lecture content
this year, it was definitely the same content. So I hope that the questions are at least
similar? Definitely go through lecture content just in case. Could also maybe ask about
WNV?

C1. Ross River virus disease and dengue are the most common arboviral diseases in
humans in Australia. Describe the viruses that cause these diseases, with details of 1)
their transmission cycles, 2) the disease symptoms they cause, 3) how they are
diagnosed and 4) how they can be treated and prevented. Include in your answer a brief
definition of an arbovirus.
• Arboviruses are arthropod-borne viruses
Transmission
(vector must survi,ve long enough to obtain at least two blood meals to become infected
by and then transmit an arbovirus)
Replicate in arthropod vector and a vertebrate host. Need: 1) High enough virus titre in
blood of amplifying host 2) Virus able to replicate & systemically disseminate in the
mosquito 3) Virus able to spread to salivary gland for transmission to new host
DENGUE
• Mosquito-transmitted flavivirus. Classical dengue: severe headaches, acute febrile illness,
vomit and diarrhoea. Severe dengue: Second infection with a different DENV serotype to that of
the primary infection
Diagnosis and Treatment
• Isolation of a Dengue virus - Detection of Dengue viral RNA - A significant rise in the
level of dengue virus-specific antibody in serum .
• Fluid replacement to alleviate shock
Control
• Mosquito control measures. - eliminate breeding sites of Ae. aegypti in urban area &
• Personal protection measures - protective clothings, repellents

Ross River virus

•Alphavirus
Transmission - PRIMARILY Wildlife-mosquito-human transmission
•Symptoms - Polyarthritis &– Rash on trunk & Fatigue & fever
Pathogenesis of arthritis
• Infection of synovial cells, myocytes, and macrophages in joints > inflammatory cell infiltrate
and mediators released Persistent infection in joint macrophages and myocytes > possible
autoimmunity > chronic arthritis/myositis
Diagnosis, Treatment
• Test for specific antibodies to RRV
•Analgesics used to reduce the pain and fevers & Anti-inflammatory agents for the
arthritic symptoms.
Prevention
• No licensed vaccine (experimental killed vaccine has been developed) ;Protection
from mosquito bites: - protective clothing, repellents, - control of vector breeding

C2. Human herpes virus 1 & 2 (herpes simplex virus types 1 & 2) and human h ce in
their host. Discuss the mechanisms of this persistence and describe the disease
consequences for each of these viruses.

So the biggest thing with these sorts of questions is, as Mark said at the final revision
lecture; just put down dot points of literally anything relevant you know. While I’m not
entirely sure how they want us to word this, because the Herpes lectures were poorly
given in my opinion, this is what I came up with, and would hopefully get a significant
number of part marks. Please feel free to add anything else anyone else can come up
with.

· As DSDNA retroviruses, Herpes viruses can integrate into the host nuclear genome to
remain latent/dormant for decades, with persistent infection that is unable to be effectively
cleared by the immune system. They can reactivate from external pressure such as host
stress, UV, and immunosuppression due to a different infection, etc. The virus is constantly
reactivating in a small amount of cells, while remaining dormant in others, leading to
persistent infection.
· HSV1 and HSV2 enter hosts through the olfactory system, penetrating olfactory
epithelium to reach trigeminal neurons. Here it establishes latency in the nucleus, and can
reactivate and travel along neuron axons to cause peri-oral symptoms and be shed in the
saliva (ie. Cold sores)
· Persistent infection is achieved by expressing few if any viral genes during latency,
and when lytic infection is reactivated, viral evasion proteins down regulate MHC I and
interferon signalling to evade immune cells.
Persistence
Ex HSV-1 after peripheral infection viral genomes enter trigeminal neurons, travel up to their nuclei
in the trigeminal ganglion and remain latent, then reactivate and travel back down neurons to re ‐ seed
peripheral infection. Latency is the key to HV persistence. It evades immune recognition by
expressing few if any viral genes. Lytic infection establishes and helps to maintain latent infection,
and drives transmission. However it is transient, because of immune attack. The window available for
lytic infection is extended by viral evasion proteins. HVs goes a stable state that is not recognized
(latency) but also does not spread, with a transient state that can spread infection (lytic) and is
protected by evasion, but is still eventually shut down by the immune response. Latent infection
intermittently reactivates. Each time the immune response has to find it and shut it down again.
Background
Herpes viruses have large dsDNA genomes with many different control factors for a virus such
as miRNAs, transcriptional elements and around ~100 genes.

Infection is common and persists for life with an estimated 40 billion ongoing infections
worldwide (multiple per person)

Cause cold sores, encephalitis, keratitis (HSV-1); recurrent genital ulcers, severe
neonatal infection (HSV‐2); chickenpox, shingles (VZV)

Pathogenesis
While most viruses require antigenic changes in order to infect a host more than once, HSV-1,
HSV-2 and VZV recur without obvious antigenic variation. This is because between episodes,
infection persists in a latent form

Alpha HSVs spread via close contact. This could be from kissing but also from skin lesions.
After peripheral infection viruses enter trigeminal neurons, travel up to their nuclei in the
trigeminal ganglion and remain latent, then reactivate and travel back down neurons to reseed
peripheral infection. HSV-1 tends to be latent in neurons and lytic in everything else.

In latency HSV-1 genomes don’t have infectious particles and exist in a stable episomal dsDNA
outside of the host chromosome in the nucleus.

During latency they don’t transcribe or only transcribe non-coding RNAs.

There are always some virions that are re-activating and as a result there are always amounts
present in the saliva.

Reactivation is dependent on ICP0 transcription This is able to degrade the ND10 which was
suppressing replication. Chromatin remodeling is also suspected to be important in reactivation.

Treatment and disease

Because of its ability to go into a latent stage there is no clear way to effectively treat alpha
herpes virus

Most drugs target viral replication in the lytic cycle

Latency also means that disease is often intermittent and will return when the immune system is
weakened

Vaccinations exist for VZV made out of a group of live attenuated strains. Wild type virus will
always circulate in the blood however it will unlikely effectively reactivate and cause serious
disease.

C3. We inhale and ingest a wide variety of viral pathogens with an equally wide range of
clinical outcomes arising from infection. Using examples, discuss the various outcomes
that can result from infection via the respiratory route and the gastrointestinal tract (use
two examples for each site). An important respiratory pathogen is influenza virus with
evolutionary change to the viral genome underpinning its ability to cause both yearly
epidemics and occasional pandemics. Briefly explain the molecular basis of the
changes to the viral genome that drives these two outbreak scenarios. Need help for
this question~ anyone>.<? This really seems like several questions all in one? So
weird…
Respiratory tract
Consists of organs nasal cavity, pharynx, larynx, trachea. Into the lungs it has bronchi,
bronchioles and alveoli.

Have an epithelial layer which is a physical barrier against pathogens.

Upper respiratory infections are the most common kind of viral infection

Most viruses will come in as aerosols

GI tract
Viruses are responsible for up to 70% of all infective diarrhoeas.

Second most common infection after upper respiratory tract infection

Can lead to local infection or be a pathway to systemic invasion

System is designed to accept food however it is a hostile environment. Acid stomach, alkaline
intestine, digestive enzymes.

Most viruses will be consumed.

Respiratory route: infection via the respiratory tract (airways, alveoli plus a large surface
area) The transmission is usually via infected droplets via an aerosol manner (sneezing,
coughing)
Some examples: RSV, Influenza, Measles
Gastrointestinal route: Eating contaminated foods, drinking contaminated water. Usually
via a local infection, or invasion of the host to produce systemic illness. Relies on acid
stability, resistance to bile, inactivation by proteolytic enzymes. Most are also non-
enveloped.
Some examples: Rotavirus, HepA

Where it says outcomes, they might want something like this? I’m not sure; this is how I
interpret that part of the question at least.
Respiratory:
· Local respiratory infections eg. Influenza, Rhinoviruses, or can be asymptomatic
or can disseminate with generalised spread from the lungs to bloodstream; from there
can infect multiple organs including skin and even CNS Eg. Measles, Mumps,
Chickenpox

Gastrointestinal:
· Local infection (eg. coronaviruses, rotaviruses), asymptomatic or spread via
invasion of tissues beyond gastrointestinal epithelial and mucosal layer to produce
systemic illness (eg. Enteroviruses, Hepatitis A

Yearly epidemics: Antigenic Drift

Antigenic drift is where there are spontaneous mutations in the HA gene, and mutants
that can escape immune surveillance are selected for. This is gradual but continuously
changing (sometimes year to year), and is the reason we need to change our vaccines
every year, and why epidemics recur every year.
This also could be asking about the cleaving of hao, the precursor of haemagglutinin. Or
the the 5 mutations in 3 genes that make H5N1 transmissible between mammals +2

Just adding some of my own stuff as well, which says pretty much the same but a little
clearer:
Influenza Epidemic vs Pandemic:
· Pandemic occurs when the Influenza strain either: gains new virulence factors or
increased pathogenicity, possibly from recombination of two viral strains, ect. OR
encounters a naïve population with no pre-existing immunity, either from change in
geographical location or a species-jump, or from a combination of these factors. This
can occur through Antigenic Shift or other means.
· Yearly epidemics are typically caused by influenza strains undergoing fairly rapid
Antigenic Shift=genetic recombination/reassortment and Antigenic
Drift=spontaneous mutations in the HA gene which select for mutants that escape
immune surveillance, a slow but continuous process of change
So are shift and drift only for endemics? Honestly I think that they both sort of contribute
to both? Hold up I’ll try to clarify...Hopefully that makes slightly more sense now? If
anyone disagrees, please correct me, just doing my best to figure it out myself, haha
Oh ok cool, thanks :) Shift absolutely applies to pandemics. That’s how we’ve gotten
some of our worst pandemics is when two influenza strains come together, and form a
new virus. (+2) H1N5 was a combination of two different influenza strains I believe?

C4. Neurological disease is a relatively uncommon consequence of virus infection.

What are the reasons for this and, using three examples, discuss how some viruses
overcome the major barriers to CNS invasion? Discuss the range of clinical
consequences of viral infection in the CNS.

Main reason it’s uncommon: Blood brain barrier is hard to cross

Why so dire: The brain is an immune-privileged site, only has an immune system
specific to it, neurons are non-renewable (if they degrade, nothing to replace) and they
are also sensitive to inflammation.
3 types of CNS diseases: Rabies, HIV and Mumps

Routes of Entry
Blood Brain Barrier
- Diffusion: increased permeability of BBB (cytokine storm), loss of tight junction
proteins (easy for virus as BBB has no defence).
- Transcytosis: through the endothelial cells. Nutrients go across the endothelial
cells. Endocytosis at one end, exocytosis at the other.
- Trojan horse: Hitchhiking in leukocytes during normal CNS trafficking (also
employed by HIV-1)
Blood CSF and CSF Brain Barrier
- Cell associated ‘Trojan Horse’ (HIV and Mumps use)
- Diffusion across fenestrated capillary epithelium.
- Infection of the choroid plexus epithelium (Mumps uses)
Transneuronal
- From the peripheral nervous system (used in Rabies). Viruses use this existing
machinery to get around, such as riding along the microtubules.
- Via olfactory route: Bypasses the BBB, nerve endings extend directly into the
brain environment.
Outcomes
- Non-cytolytic infections: Virus persistence for long periods of time.
- Cytolytic infections: Destruction of neurons, visible pathology. How this works
depends on what is being targeted. Two examples are: Meningeal stromal cells
leading to Meningitis, or Hippocampal Neuron degradation leading to behavioural
changes (Rabies)
Acute Disease
1. Encephalitis: Destructive lesions in grey matter, inflammation and usually fatal.
2. Paralysis: Destruction of motor neurons and inability to move limbs/organs. (if
organs can be fatal)
3. Aseptic meningitis: Inflammation of the meninges. Usually mild.
4. Post-infection encephalomyelitis: Demyelination of the motor neurons, usually
due to the presence of an autoimmune reaction.
Chronic
If mild, but present can lead to chronic disorders such as dementia in the case of HIV.

D1. What is the most common life-threatening mould infection of humans? Describe the
major features of the main causative agent. Are there other species that have similar
clinical manifestations? Does treatment of these infections differ? Need help for the last
two questions, just could not find any further information from the lecture notes.
Aspergillus Fumigatus:
· most common mould that infects humans, Saprophytic mould that recycles carbon and
nitrogen to use nearly any sources to grow. Produces asexual spores called Conidia.
Incredibly common, found everywhere including in the Stratosphere, inhaled constantly but
usually only infect if immunocompromised (if pulmonary macrophages/neutrophils don’t
clear), especially Cancer treatment and Organ Transplant patients. Single genotype.
· Causes variety of disease from superficial mycoses to Angioinvasion, vascular
damage, Invasive pulmonary Aspergillosis and Cerebral Aspergillosis
· Diagnostic problems: no one test is sensitive or specific enough to diagnose.
Symptoms are variable and non-specific, general ‘pulmonary infection’/flu symptoms.
However, delay in antifungal treatment can be fatal, as once set in, incredibly difficult to
clear.
 · Bacterial pulmonary infections causing pneumonia can appear similar- obviously
antibiotics will not treat fungi. Aspergillus lentulus is a cryptic species that causes similar
disease, however is naturally resistant to Voriconazole!! So we should be monitoring
cryptic species so that we actually know the exact species responsible for the infection
because response to treatment can be drastically different. Can prevent delay in
effective treatment if don’t waste time trying a treatment its resistant to
Jw is candidasis the ‘most common fungal disease’? <--candida a yeast form rather
than mould
I believe Cryptococcus share similar clinical manifestations I believe here James
actually is referring to the cryptic species I outline above, which he mentioned in
lectures, Aspergillus lentulus

But is aspergillus lentulus the most common mould infection though - Incorrect, the
most common mould infection is Aspergillus fumugatus. It’s important to remember
that Cryptic species with different clinical and treatment outcomes exist. He talked about
it a lot, so I have a feeling that that will be a question that comes up. (See D5 below)

D2. Name five classes of antifungal agents. To which does AmBisome belong?
Describe what it is and what it does.
D2.2. Name five classes of antifungal agents. To which does UK-49858 belong?
Describe what it is and what it does.

• 5 classes of antifungal – Triazoles, Echinocandins, allylamines, pyrimidine

analogues, polyenes

Antifungal agents
• Polyenes(Nystatin, Amphotericin B ‘ AmBisome’): Cell membrane ergosterol bindin, lysis
• Azoles: Inhibit P450-dependent ergosterol production
• Triazoles (Fluconazole ‘UK-49858’ ’Diflucan’, Voriconazole)
Aren’t azoles and triazole the same Are they????? YES+4
• Echinocanidins (Caspofungin): Cell wall b-1,3 glucan synthase inhibitors;
• Pyrimidine analogues (flucytosine)
D2.3. “” RE. Fluorocytosine

He didn’t really go through of this with us this year, did he? Other than Fluconazole in the PBL I
suppose? Do you think that he’ll ask about this, and the five classes?? For my own study, I’m
going to instead apply this question to Fluconazole, one of the only ones we learned about in
depth (and hope for the best):
· 5 classes of antifungals: 1. Polyenes, 2. Azoles, 3. Nucleoside analogues, 4. Echinocandins,
5. Allylamine
· Fluconazole: a fungistatic triazole which is nonspecific and used to treat a variety of species
 → inhibits the fungal cytochrome p450 enzyme 14α-demethylase to prevent the conversion of
lanosterol to ergosterol, an essential component of the fungal cell membrane with similar functions to
cholesterol in animals. This prevents fungal cell replication and can be fungicidal in a dose dependant
manner.
→ However, while mammalian demethylase is much less sensitive to fluconazole than the fungal
demethylase, the relatively high doses and long treatment courses required to effectively treat
cryptococcosis means that severe adverse reactions are not uncommon.

ANTIFUNGAL CLASSES:
1) Polyenes: Cell membrane ergosterol binding and lysis (Amphotericin B)
2) Azoles: Inhibit P450-dependent ergosterol production (Fluconazole)
3) Echinocandins: Cell wall b-1,3 glucan synthase inhibitors (Caspofungin)
4) Pyrimidine analogues (Flucytosine)
5) Allylamines (Terbinafine)

FLUOROCYTOSINE = Flucytosine
- A synthetic fluorinated pyrimidine developed as an anticancer drug
- A prodrug = metabolized after administration into a pharmacologically active drug
- Mechanism of action:
o Flucytosine is converted by cytosine deaminase into fluorouracil
Cytosine deaminase is absent in humans
o Fluorouracil = cytotoxic drug which interferes with nucleic acid biosynthesis
- Limited efficacy against moulds
- Rapid evolution of resistance from monotherapy mutation of FCY1 and FCY2
- Synergism with amphotericin B
- Only used for infections from C. neoformans and C. gattii

UK-49858 = Fluconazole/Diflucan I had no idea that these were the same thing? Thank
you!
- A synthetic azole triazole antifungal agent
- Water soluble = extensive tissue distribution and penetration into the CSF
- Broad spectrum of activity
- Adverse effects are relatively infrequent
- Delivered both intravenously and orally
- Fungistatic = inhibits growth of fungi
- Mechanism of action:
o Triazole of fluconazole binds to Fe atom at haem group of cytochrome P450
Cytochrome P450 is encoded by ERG11
o This inactivates the enzyme preventing ergosterol production
Ergosterol is the equivalent of cholesterol in fungal cell membranes
- Candida krusei = intrinsically resistant to fluconazole
o Candida glabrata = often manifests reduced susceptibility

AMBISOME = Amphotericin B
- Secondary metabolite of Streptomyces nodosus polyene discovered 50 years
ago
- Most potent antifungal used today
- Very broad spectrum of activity
- Delivered intravenously or orally
- Adverse effects are common = renal failure reduced by liposomal formulations
- Mechanism of action:
o Binds to ergosterol on cell membrane
o Forms a transmembrane channel causing lysis
- Fungicidal = kills fungi

D3. What are the Molecular Koch's Postulates? In your explanation, use Cryptococcus
neoformans in an example.
Molecular Koch’s postulates is a set of experimental criteria that must be satisfied to
show that a gene found in a pathogenic microorganism encodes a product that
contributes to the disease caused by the pathogen. The postulates are originally
described as follows:
1. The phenotype or property under investigations should be associated with the
pathogenic members of the genus or pathogenic strains of a species.
2. Specific inactivation of the gene(s) of the suspected virulence traits should lead
to a measurable loss of pathogenicity or virulence.
3. Reversion or allelic replacement of the mutated genes should lead to the
restoration of pathogenicity.
4. The genes which causes virulence must be expressed during infection
5. Immunity must be protective
Based on the molecular Koch’s postulates:
1. Melanin is one of the most extensively studied virulence factor of C. neoformans.
Masson-Fontana silver stain reveals melanised Cryptococcus. neoformans cells
in paraffin embedded brain tissue, staining not observed in non-pathogenic
Cryptococcus species(Kwon-Chung et al. 1981).
2. Melanin-deficient mutant exhibit reduced virulence.
3. This wasn’t demonstrated in the C. neoformans example he gave us was it?
They didn’t attempt to complement the mutation (neither lac1 + lac1, nor lac2 +
lac2 was reintroduced - only lac1 + lac2), therefore didn’t prove phenotype was
caused by removal of lac1.
 4. Detected in infected human brain samples as proven by the presence of melanin
ghosts (Nosanchuk et al. 2000)
5. Immunity must be protective - could not be established for c. neoformans as
immunity to melanin does not influence whether or not you will be killed by C.
neoformans < is this required?

D4. Describe the link between chocolate production and life-threatening fungal
infections. Provide information on the species involved, the type of disease it causes,
and the treatment employed to combat it.

??? anyone knows this ?? pls help

candida krusei > resistance to fluconazole but voriconazole demonstrated efficacy
I swear we never covered chocolate production :( We distinctly did, in James’ secon lecture
which covered Candida

● Chocolate comes from cacao trees. Grows pods full of cacao beans.
● To make chocolate the beans are fermented and dried. This process involves two fungi,
Candida Krusei and Geotrichum.
● Fungi are used to break down the pulp on the outside of the beans and make acetic acid
to kill the cacao embryo inside the seed, eliminating the bitterness of the beans.
● The fungi are usually naturally occuring in the cacao pods however different chocolate
companies now have their own strains that they use to give their chocolate a specific
taste.

• The fungal responsible for chocolate production and life-threatening infections are from
the same species of candida
• Candida Krusei is commonly used in chocolate production however, it may also be
responsible in causes candidiasis
• The main causative pathogen for candidiasis is candida albicans

• Candida albicans infections is associated with nosocomial infections, often after

antibiotic treatment where bacterial competition is absent allowing the growth and proliferation
of candida albicans
• It grows preferentially on moist places (toes, nails, skin, vaginal and mouth) and mucosal
surfaces
• The type of disease Candida species causes varies from superficial mycosis such as
oral or vaginal thrush or severe, disseminated infection often with skin involvement.
Disseminated infection is associated with a poor prognosis and mortality rates are high
• C. albicans is a commensal flora in our body. The route of transmission is commonly
human-human interaction, not inhaled in the same way as most other fungal pathogens
• Virulence attributes of candida albicans include pleomorphism, able to switch between
yeast and hyphae allows efficient transmission and dissemination of the pathogen
o Its association with biofilms provides the pathogen protection and survival properties,
enabling antifungal resistance, grow and proliferation of the fungal
o Quorum sensing through the secretion of farnesol in response to environmental stimuli
allows the fungal to change from being yeast to hyphae depending on cell density
o It also has adhesin proteins from adhesin-like family and Intergin-like family to mediate
attachment
o Proteolytic enzymes such as aspartyl proteinase and phospholipase and to degrade host
tissues
• However, these virulence attributes are often balance by our host immunity response
which includes – flushing / shedding mechanisms, immune and complement system activation
as well as non-specific antimicrobial substances to prevent overgrowth of C. albicans
• However, usually in immunocompromised / immunosuppressed patients, the balance is
often disrupted hence, promoting pathogen growth and infection resulting in disease

• Fluconazole, a triazole antifungal that inhibits ergosterol synthesis is effective in treating

candidiasis, however, candida krusei is shown to be intrinsically resistant to fluconazole
• Hence for candidiasis that is associated with candida krusei, voriconazole is used
instead as it demonstrated efficacy in inhibiting candida krusei growth

Both chocolate production and life-threatening fungal infections can be caused by Candida
krusei. It is a diploid yeast with no sexual cycle. It can grow in the form of yeast, pseudohyphae,
true hyphae in response to appropriate environmental stimuli. It loves to grow on mucosal
surface, causing diseases including oral thrush, vaginitis, infections in nail, skin, oesophageal
and urinary tract. It infects cocoa beans and human hosts in similar ways. Through adhesion
and colonisation on the surface, forming biofilm in its yeast form, then converts to
pseudohyphae & hyphae to penetrates into epithelial and release enzymes that break down
host tissues and defence. In cocoa’s case, C. krusei released enzyme which breaks the pulp
outside the cocoa beans, result in release of acetic acid and kills the cocoa embryo inside seed.

Because C. krusei is intrinsically resistant to one of the key antifungal drugs fluconazole, it has
to be treated with another agent that also belongs to triazole – voriconazole. Amphotericin B can
also be used to effectively treat C. krusei.
(NOT SURE IF THIS IS THE RIGHT ANSWER)

Check the candadiasis lecture

Ooo fiesty

Cacao beans have to be fermented to remove the bitter taste and break them down. This takes
place with two fungi, C. krusei, and Geotrichum. Most of the time, the two fungi are already present
on the seed pods and seeds of the cacao plant, but in modern chocolate making, specific strains are
used. Each chocolate company uses its own strains, which have been selected to provide optimum
flavor and aroma to the chocolate. The yeasts reproduce every few hours, and soon there are
thousands of individual yeast cells in a small area, which produce enzymes to break down the pulp
on the outside of the beans. This makes acetic acid, killing the cacao embryo inside the seed,
developing a chocolatey aroma and eliminating the bitterness in the beans- ermmmm its not
answering the question - it’s not. It’s additional notes from Mr Google. You can answer it if you know.

Who is this other person using the same colour as me?? >//>

D5 It is becoming increasingly apparent that cryptic species are responsible for a large
number of fungal infections normally attributed to well-known, geographically-restricted
species. Provide three examples of such cryptic species. Describe them and the
disease they cause.

· Candida krusei is a cryptic species often diagnosed as Candida albicans, as they cause similar
Candidiasis infections: → Oral thrush, vaginitis, nappy rash, skin/nail infections, UTIs and in
immunocompromised patients, disseminated infection that is potentially lethal
→ While Candida infections are most commonly treated with Fluconazole as a broad spectrum antifungal,
unlike C.albicans, C.krusei is intrinsically resistant, and should instead be treated with Voriconazole. It is
therefore for treatment and patient outcome to start differenciating cryptic species.
· Aspergillus lentulus: often diagnosed as Aspergillus fumigatus, as both cause similar appearing
Aspergillosis→ Superficial mycoses but also angioinvasion, vascular damage, invasive pulmonary
aspergillosis and even cerebral aspergillosis
→ While for A.fumigatus Voriconazole is more effective than Fluconazole, A.lentulus is resistant to
Voriconazole. Again, cryptic species need to be treated differently, so need to be recognised and
identified.
· Cryptococcus gattii: Often diagnosed as Cryptococcus neoformans, as can cause similar
Cryptococcosis symptoms→ Cutaneous infection, respiratory pneumonia, and even Cryptococcal
Meningoencephalitis, which can be fatal if untreated
→ However, while C.neoformans generally only infects the immunocompromised, specifically HIV/AIDS
patients, C.gattii can infect even the immunocompetent, and has an altered geographical districbution,
occurring in the tropics as well as Australia and some parts of the U.S.
→ Currently undertermined whether C.gattii responds differently to treatment

Histoplasma capsulatum in histoplasmosis (Primary pathogen)

Found in nitrogen rich places (bat caves) i wonder if batman have histoplasmosis before
Coccidioides immitis in coccidiomycosis (Primary pathogen)
Valley fever, desert mumps and rheumatism
Paracoccidioides Brasiliensis in paracoccidioidomycosis
Blastomyces dermatitidis Blastomycosis
Chicago disease and gilchrist

All of them are thermally dimorphic fungus that adopts a yeast form in tissues
Mode of transmission - inhalation of conidia which could either cause superficial mycosis or
disseminated infection mainly skin involvement with some having CNS involvement ( Coccidioides
immitis)
 I’m not really sure that that is what he is asking here? Those are all main species known to infect,
not their cryptic species… (+1 - Is C gattii a cryptic species?)

D6 How was genomic epidemiology used in analysing Scarlett Fever outbreaks on a global scale?
It sowhed us that Scalet fever came back even tthough we had gotten rid of it.