Pathogens Flashcards
What are the classifications of microbes
Eukaryotes (organelles)
Prokaryotes (no organelles)
Acellular organisms (non living)
Why are microbes important
They make up global ecosystems
They are saphrophytes
They are used in economic biotechnology
They can be nuisances
They can be pathogenic
Describe the bacterial genome
Located in the cytoplasm
Comprises the single circular chromosome and plasmid
Dictates metabolic and biosynthetic capacity
Bacteria with _____ genomes tend to have ____ fastidious growth requirements
Larger, less
What are the 3 types of mutations and what could they lead to
Point, insertions, deletions»_space; gain or loss of function
What are the 3 methods of DNA exchange
Transformation - uptake of free DNA
Conjugation - transfer of DNA by direct cell to cell contact
Transduction - transfer by bacteriophage
Describe the plasma membrane
Semi permeable Lipid bilayer - maintains homeostasis
Site of ATP generation
Range of transport proteins
What are endospores
Complex intra-cellular structure formed during replication of certain bacteria when growth conditions are poor
Resistant to temp, desiccation, radiation, chemical agents, enzymes etc.
Visualised by -ve staining
Cause deep tissue infections
Describe the chemical component cell wall is made of
Made of peptidoglycan
Polymer of NAM and NAG
Protects against osmotic pressure
Crosslinks can be inhibited by beta-lactam antibiotics
Describe the structure of gram positive cell walls
Thick peptidoglycan layer - molecules diffuse through interbridge gaps
Embedded in teichoic acids - attachment
Simple systems to secrete proteins
Describe the structure of gram negative cell walls
Thin peptidoglycan layer
Outer, non energised membrane - porins = transfer of molecules across / lipopolysaccharides = attachment
Molecules diffuse through peptidoglycan
Tightly regulated mvmt across PM
Many varied complex systems to secrete proteins
What is the clinical relevance of gram staining
Reveals bacterial shape and arrangement
What is different abt the cell wall of mycobacterial species
It has outer lipid layer, mycolic acids, arabinogalactan, and peptidoglycan
Detected using acid fast staining
What is flagella
External structure of bacteria
Complex structure required for bacterial chemotaxis (mechanism for bacteria to move towards nutrients or away from toxins)
Number and arrangement varies
What are fimbriae/pili
External structure
Hair like protein chains
Virulence factor - involved in attachment (to other cells or surfaces)
Mechanism for DNA transfer (conjugation) - connects bacteria and then retracts which allows for transfer of antibiotic resistance genes
What is the capsule
External structure
Polysaccharide layer beyond the cell wall
Found in both gram +ve and gram -ve
Protection from desiccation and phagocytosis
Adhesion to cells/surfaces
Can be visualised through a negative capsule stain which stains in the inside but not the capsule creating a halo effect or through transmission electron microscopy which is where the negative capsule binds to positive gold particles
what are commensal bacteria
colonise all surfaces of host
several benefits > metabolic / protection against pathogens by competing for colonisation sites
how are some pathogens also commensal
they are commensal but become opportunistic (pathogenic) in response to immunological insult such as tissue damage > provide access to deeper tissues to access more nutrients
what are primary pathogens
provide no advantage to host
not part of normal microbiome
damage the host
egg E.coli > secrete toxin
what are pathogens
disease causing agents
damage can be indirect (ie disturbs metabolic balance or nutrient acquisition) or directly (ie toxins)
structural and non structural features contribute to…
mechanism of disease (pathogenesis) and capacity to cause disease (virulence)
these allow for competition to establish infection and damage the host and cause symptoms
outline the pathogenic cycle
transmission > colonisation > proliferation > evasion > repeat
what are some transmission routes
direct contact e.g bites or wounds
indirect contact via fomites (contact w contaminated objects) > important route for Nosocomial infections
airborne
faecal-oral
food borne
zoonotic
what is ID50
infectious dose - number of bacteria needed to infect 50% of individuals
what is inoculum size
amount of pathogens an individual is actually exposed to
what is the relevance of extracellular enzymes released by bacteria
role in pathogenesis
e.g beta haemopysin is a secreted phospholipase which ha a distinct phenotype on blood agar
what are exotoxins
proteins made and secreted during bacterial growth
toxic at low doses
categorised by site of activity
two groupings = cytolysins (cause lysis) and two-component toxins (disrupt cellular processes)
what are endotoxins
bacterial structural components that have toxic activity
released on death of bacteria (meaning sometimes taking antibiotics can actually make it worse)
what are some host factors that affect outcome of infection
age, immune status, prior exposure, diet
what are outcomes of infection
clearance
asymptomatic carriage
symptomatic carriage
what factors are related to disease patterns
timing (acute, chronic, latent)
location (local, systemic)
what is an example of a bacterial pathogenesis
L.monoctyogenes - gram postive, motile
> food borne zoonosis
incubation ~3 weeks
secretes several toxins
by which process do bacteria grow
binary fission
what are the four phases of bacterial growth
lag phase
exponential phase
stationary phase
death phase
what happens in the lag phase of growth
adapt to new conditions, enzymes and new metabolites accumulate
what happens in the exponential phase of growth
maximum constant growth rate
what happens in the stationary phase of growth
oxygen and nutrient demands cannot be met > death rate = growth rate
what happens in the death phase of growth
death rate > growth rate
what factors affect bacterial growth
nutrient availability, O2 availability, pH, temperature, osmolarity
what are the oxygen requirements of obligate aerobes
require o2
what are the oxygen requirements of strict anaerobes
cannot survive in o2
what are the oxygen requirements of facultative anaerobes
more efficient with o2 but can still metabolise via fermentation when absent
what are the oxygen requirements of aerotolerant anaerobes
unaffected by presence of o2
what are the oxygen requirements of microaerophiles
require a specific o2 concentration
what are chemotherapeutic agents
chemical agents used to treat disease
kill or inhibit growth of pathogenic microbes
what are the primary mechanisms/classes of actions
inhibitors of cell wall synthesis
protein synthesis inhibitors
metabolic antagonists
nucleic acid synthesis inhibtion
what does bacteriostatic mean
inhibits growth
what does bactericidal mean
kills the bacteria
describe inhibitors of cell wall synthesis
e.g penicillins
binds to proteins involved in peptidoglycan assembly
inhibition of last step in bacterial cell wall synthesis
prevents crosslinkage of peptidoglycan strands > lysis
acts on GROWING bacteria
describe protein synthesis inhibitors
e.g aminoglycosides
either bind specifically to prokaryotic ribosome and interfere w function or inhibits stage of protein synthesis
describe metabolic antagonists
e.g sulfanomides
interfere w enzymes involved in folic acid synthesis (unable to construct basic building blocks for nucleic acids)
selectively toxic for bacteria
describe nucleic acid synthesis inhibition
e.g quinolones
block DNA replication
block transcription
not as selectively toxic
where can antibiotic resistance genes be found
bacterial chromosomes
plasmids
transposons (mobile genetic elements)
interns (gene capture system)
through what mechanisms can antibiotic resistance genes be spread
through transformation, conjugation, transduction (rare)
how do antibiotic resistance genes spread
acquisition of resistance genes from mobile genetic elements such as plasmids, transposons etc
what are resistance plasmids
can carry multiple antibiotic resistance genes
usually transferred to other cells by conjugation or transformation
carry transposons that encode antibiotic resistance
what are composite transposons
contain genes for antibiotic resistance
within a cell - rapidly move b/w chromosome and plasmids
b/w cells - can move thru a bacterial popn
what are gene cassettes
sets of resistance genes
can be part of transposons, interns, or located on bacterial chromosome
what are integrons
gene capture system > capture an expression of genes and gene cassettes
mechanism for accumulating antibiotic resistance genes in bacteria
what can be done to prevent antibiotic resistance
give antibiotics in high concentrations
give two antibiotics at once
don’t give antibiotics unless necessary
possible future solutions - dev of new antibiotics and use of alternative therapies e.g bacteriophages
describe the diagnostic schema
symptomatic patient > signs and symptoms > presumptive clinical diagnosis > specimen collection > select tests > results and interpretation > definitive diagnosis > treatment options > if patient is now asymptomatic then successful, if not, then reevaluate signs and symptoms
what is an example of a genetic test in detection and identification of bacteria
real time PCR
> amplified targets fluorescently tagged > relative fluorescent units plotted in real time hence no need for gel electrophoresis
what is an example of a serologic test in the detection and identification of bacteria
rapid immunoassay (RIA)
> relies on monoclonal antibodies (mAbs)
- capillary flow moves antigen > specific interaction b/w mAb and antigen > binding at test line results in colour change > control mAbs confirms RIA validity
indicative rather than definitive
why are multiple tests used in the process of detecting and identifying
to account for variability in sensitivity and specificity
what is an example of culturing in detection and identification of bacteria
agar plates
> selective = allows for growth of selected groups of bacteria
> differential = allows growth of a number of types of bacteria w defined characteristics
utilise agar medium elevate to specific bacteria
what is an example of a biochemical test in detection and identification of bacteria
catalyse assay
> h2o2 is a by-product of metabolism > breaks down to o2
if o2 gas generated then catalase positive
what are different types of microscopy in detection and identification of bacteria
gram stain
acid fast stain
spore stain
describe gram stain in detection and identification of bacteria
gram -ve = transparent after alcohol decolourising
gram +ve = purple
describe acid fast stain in detection and ID of bacteria
non acid fast = transparent after alcohol decolourising and then blue after counterstain
acid fast = pink
what is an example of an analytic method in detection and ID of bacteria
mass spectrometry = peaks release to specific molecules, pattern to specific bacteria
what are advantages of mass spec
rapid
high throughput
relatively high sensitivity and specificity
what are disadvantages of mass spec
in some cases requires sample culture
requires access to database of sample spectra
what are the focusses of lab stewardship
appropriate test selection
secure yet accessible data management
correct interpretation of test results
sustainable financial resourcing
what are the goals of lab stewardship
appropriate utilisation of clinical lab services
improve quality of patient care
reduce costs to patients, hospitals and health systems
what is a virus
infectious, obligate intracellular parasite comprising of genetic material, often surrounded by a protein coat or sometimes a membrane
they replicate, not grow or divide
they must make mRNA that can be translated into proteins
describe the enveloped structure of a virus
they pickup part of the cell membrane as they move out, hence they have a host lipid bilayer
have genetic material surrounded by capsid
describe the non enveloped structure of a virus
no cellular envelope ie no host lipid bilayer
spontaneous assembly of capsid structure
very stable
do viruses carry enzymes?
yes, some do
they are present if they are required prior to mRNA production
what is the function of viral enzymes
make new genomes or mRNA
what is the best cell type for viral propagation in cell cultures
primary cell lines
how do you know that a virus is replicating in a cell
causes a cytopathic effect (CPE) ie cell death
or there is syncytia formation (cell fusion)
what can CPE be used for
tell us how many viral infections there are in a sample
how do we study viruses if they do not cause CPE
use imminofluorescence microscopy to detect viral proteins
use genetically engineered genomes to detect viral proteins in real time
RT PCR to detect viral genetic material
why are in vitro viral replication methods important
assists in development of new antiviral strategies
why are animal models important in viral replication
gives better understanding of the pathogenesis of viruses
what are the main steps of viral replication
- viral entry
- translation and genome replication
- assembly and release
outline the first step of viral replication
viral entry
viruses randomly adhere to cell surfaces
if the cell surface has a specific receptor, then the virus can bind to it, allowing for the virus to enter the cell (active process as it is too large to diffuse across the PM) and transfer its genome to the inside of the cell
outline the second step of viral replication
translation and genome replication
the genome is replicated in the nucleus (DNA viruses) or in the cytoplasm (RNA viruses)
the replicated genetic material (mRNA) can then undergo translation to produce viral proteins
outline the third step of viral replication
assembly and release
the viral genetic material is then covered by a protein shell (non envelope happens spontaneous and envelope acquires a host lipid bilayer)
then the virus with the protein coat can be released from the host cell ready to infect another cell
why do positive sense viruses not need to carry their own RNA polymerase enzyme
postive strands have the same polarity as mRNA, meaning that can actually function as mRNA and be translated into viral proteins directly
why do negative sense viruses need to carry their own RNA polymerase enzyme
negative strands cannot functions as mRNA, meaning they first need to be converted into mRNA in order to be translated into viral proteins. to do this, the RNA needs to be converted into mRNA, but the host cell does not have an enzyme that is capable of converting RNA to RNA so the virus has to carry its own RNA dependent RNA polymerase
outline the replication of positive strand RNA viruses
- positive strand translation results in poly protein and production of RdRp
- RdRp used to make complementary negative strand RNA using the positive strand
- more positive strands are made which is the ultimate goal
outline the replication of negative strand RNA viruses
- negative strand uses RNA polymerase to convert to mRNA
- mRNA translated to produce viral proteins
- replicase proteins move back into the nucleus for more genome replication
- viral genetic material packaged into proteins > released
example of positive strand RNA virus
hepatitis C
example of negative strand RNA virus
influenza
example of DNA virus
hepatitis B
describe the coding capacity of DNA viruses
dependent on genome size
smaller genomes need more host proteins as they do not encode the entire replication system, hence they have a restricted coding capacity
larger genomes encode all the proteins required for DNA synthesis, so they can replicate more easily
what is viral transmission
mvmt of a virus from one host to another
what is direct transmission
direct body contact w tissues or fluids of an infected individual > physical transfer of viruses
what is indirect transmission
without close contact
fomite transmission = contact w contaminated inanimate objects
vector mediated transmission = insects feeding on infected host > transmit to new host when feeding
what is zoonotic viral transmission
transfer of virus from animals to humans either by direct body contact for indirect transmission
e.g monkeys = HIV; dogs = rabies
what are two main ways viruses can enter our body
mucosal surfaces
skin
how can a virus enter through mucosal surfaces and describe them
respiratory - small particles from breathing, coughing or sneezing > inhaled and deposited onto mucous membranes > replicate in resp tract (e.g influenza)
enteric - contaminated food or water due to faeces, urine or saliva > replicated in intestinal tract (e.g poliovirus)
sexual transmission - blood and body secretions by unprotected sexual contact (e.g Hep B, HIV)
how can a virus enter through skin and describe them
blood borne infections - exposure to infected blood > replicates and released into bloodstream (e.g Hep B, HIV)
vector borne diseases - bloodsucking insects ingest virus from infected host > replicate > pass on to new host (e.g zikavirus)
cuts, scratches w contaminated fomite
what are the four steps in pathogenesis of virus infection
- transmission
- viral replication
- spread within body
- host defence systems
what are the effects of virus infection at a cellular level
cytopathic effect
multinucleate giant cell formation
malignant transformation
inclusion bodies
no change (dormant)
describe spread within the body during pathogenesis of a virus
localised infections - stays in area of infection
systemic infection - infection of a specific area then entry into circulatory or nervous system
what determines the effectiveness of immune response to virus
rate of virus replication and presentation of antigens
size of infecting virus dose
route of infection
age of host
ability of virus to evade immune response
what are the two outcomes of a viral infection
transient virus infection
persisting viral infection
describe transient viral infection
successful clearance of infected cells
memory response developed
describe persistent virus infection
infected cells are not cleared
viral replication continues > ongoing disease and death
what are the four classifications of viral infections
transient localised
transient systemic
chronic localised
chronic systemic
what is an example of a transient localised viral infection
influenza
what is an example of a transient systemic viral infection
measles
what is an example of a chronic localised viral infection
Hep C
what is an example of a chronic systemic viral infection
HIV
what are the different types of viral infections
respiratory
GIT
liver
NS
skin
what are some common symptoms of a viral infection
high fever
tiredness
headache
sore throat
coughing
runny nose
diarrhoea
nausea
what are the 3 key cytokines involved in viral infection
type 1 interferon (IFN) - produced by virally infected cells and DC’s
IL1 - produced by infected cells and cells of innate immune system
TNF - produced by macrophages and NK cells
describe the innate response to virus
- infection involves PAMPs (pathogen associated molecular patterns) and DAMPs (damage associated molecular patterns)
- detection of infection by pattern recognition receptors (PRRs)
- production of cytokines/chemokines
- killing of virally infected cells by NK cells
what are the 3 things that triggers innate immune response to virus
presence of foreign genetic materials in host cell
release of viral genetic material into extracellular space
accessibility of viruses to phagocytes
what are PAMPs
broadly shared molecules among pathogens
what are DAMPs
components of hosts cell that are released during cell damage
what do PRRs mediate
release of inflammatory cytokines
initiation of antigen specific adaptive immunity
what are the two types of PRRs
cytosolic receptors
toll like receptors
how do CRs distinguish pathogenic RNA and DNA in the cytoplasm
- mammalian mRNA has a methyl cap whereas viral RNA do not
- presence of dsRNA in cytoplasm
- presence of dsDNA in cytoplasm
what are two ways CRs can detect a viral infection
RNA sensors
DNA sensors
what are two ways TLRs can detect a viral infection
cell surface - recognition of extracellular pathogens
endoscopes - through phagocytosis - TLR3, 7, 8, 9
how do TLRs distinguish between pathogenic genetic material and our own
bind to microbial nucleic acid that are different from mammalian nucleic acid
e.g TLR 3 recognises double stranded RNA which is rare in mammalian cells
what does TLR3 detect
dsRNA
what does TLR7 detect
ssRNA
what does TLR9 detect
DNA
what is the outcome of detection of virus infection by TLRs and CRs
expression of IFN - 1
what are the functions of IFN 1
direct antiviral effect and immunoregulatory role
what are the outcomes of IFN 1
cellular resistance to viral infection
inhibition of viral replication
impediment of viral dissemination
what are the factors that promote the emergence and spread of viruses
virus factors
virus transmission
host factors
what things do we need to think about when considering virus factors in the emergence and spread
which virus > structure, subtypes
hosts
cellular receptors and target tissues
mutations > antigenic drift/shift
what is primary transmission
animals to humans
either through direct or indirect contact
common for emerging viruses
what is secondary transmission
human to human
what things to we need to think about when considering host factors in viral emergence and spread
environment related factors > season and climate conditions/presence of animals/ecological changes/environmental changes
human related factors > living standards/living conditions/life style/demographicchanges in human behaviour
what are the 3 elements to controlling a virus infection
ID the disease causing agent
understand the epidemiology
develop control strategies
what are the 3 steps involved in developing control strategies
interfere virus transmission > public education, prevention measures, surveillance system, vector control
establish protective immunity > vaccination
establish effective treatment > antivirals, antibodies
what is the importance of vaccination
induce protective immunity to protect the individual (prime immune response > rapid secondary response) and protect the community (herd immunity)
what things make a vaccine ideal
protective
long term
safety
stable
easily administered
single or few doses
cheap
what is involved in a neutralising antibody response
form noninfectious aggregates that cannot enter cells
blocking virion attachment to cells
blocking endocytosis
blocking uncoating
what factors determine which samples are taken
clinical presentation
risk factors
test type
what factors determine what tests we do
testing for current vs previous infections
what samples would you collect for enteric virus infections
faeces/vomit
blood sample
what samples would you collect for respiratory virus infections
respiratory sample (nasal swab)
blood sample
what samples would you collect for blood borne virus infections
blood sample/heparinised blood sample
liver biopsy
what samples would you collect for sexually transmitted virus infections
vesicle fluid
blood sample
how should specimens be transported to ensure the virus is not inactivated
cold but not frozen ie around 4 degrees Celsius
what are the diagnostic methods for virus infection
grow in vitro in cell lines and ID
look directly for virus using electron microscopy
detection of viral antigens
detect genome by PCR/RT PCR
detect antibodies in serum of infected patients
what are the basic characteristics of fungus
eukaryotes
heterotrophs
cell wall composed of chitin
unicellular (yeast) or multicellular (hyphae)
non motile
decomposers, parasites, symbiotes
typically asexual reproduction
haploid or dikaryotic
what is a hyphae
multicellular fungi
what is a mass of hyphae called
mycelium ie mould
how do mycelium/moulds reproduce
produce spores
what are unicellular fungi called
yeasts
how do yeasts reproduce
budding
what are the two classifications of hyphae
septate and aseptate
septate vs aseptate
septate = many separate cells whereas aseptate = undivided mass of cytoplasm
superficial infections
infection of dead skin and hair > no living tissue invaded > no immune response
cutaneous infections
infection of skin, nails, mucosa > minimal invasion of living tissue > immune response
subcutaneous infections
infection of skin, muscle, fascia, lymphatic system > immune response
often due to traumatic injury
often caused by zygomycete fungi
systemic mycoses
invasive disseminated infections > multi organ
often acquired by inhalation or hospital environment
high mortality rates
what defences exist against fungal infection
physiological barriers e.g human body temp
non specific host defences e.g mechanical barriers and skin surface secretions
nonspecific immune response
acquired immune response
opportunistic vs primary pathogens
opportunistic lack virulence so they take advantage of impaired immune system
whereas
primary are highly virulent so they can establish an infection even with an intact immune system
what is a parasite
organism that resides on or within another living organism to find the environment and nutrients it requires for growth and reproduction
benefits of being an intracellular parasite
host supplies the food
constant environment
free transport?
new niche?
free from predation?
disadvantages of being an intracellular parasite
may require remodelling of the environment
host immune response
infection can kill the host
what are the two types of intracellular parasites
facultative (can reproduce outside of the host cell)
obligate (cannot reproduce outside of the host cell)
what is the main source of emerging viruses
zoonosis
what factors lead to emerging viral diseases
human demographics and behaviour
climate and weather
international travel and commerce
SARS-Cov-1
2002
illness begins w prodrome of fever
only infectious if symptomatic
MERS-Cov
2012
spread from camels
not very transmissible between humans
still exists today
SARS-Cov-2
2019
easily transmissible between humans
infectious even if asymptomatic
