MODULE 2 - Epidemiology of Infectious Diseases and Principles of Antimicrobial Therapy Flashcards
what is epidemiology?
the study of distribution and determinants of health-related states or events (including disease) in specified populations and the application of this study to the control of disease and other health problems
what does epidemiology involve?
counting cases or health events and describes them in terms of time, place and person
dividing the number of cases by appropriate denominator to calc rates
comparing these rates over time or for different groups of people
what are the 5 W’s of epidemiology?
what - health issue of concern (case definition)
who - person (age, gender, ethnicity etc.)
where - place
when - time
why/how - causes, risk factors, modes of transmission
first 4 are descriptive epidemiology, 5th is analytical epidemiology
what is cholera?
acute diarrhoea illness which can lead to dehydration, coma and death
intestinal infection with vibrio cholera and transmission by contaminated food or water
how is frequency (how many) important to epidemiology?
relationship of no. of health events to population size allows comparison of disease occurrence across different populations
measures are prevalence and incidence
how is pattern important to epidemiology?
occurrence of health events by time (when), place (where), and person (who)
what is prevalence?
the proportion of a population that have the disease at a given point in time (i.e. existing cases)
how do you calculate prevalence?
prevalence = number w disease/total number in population
what is incidence proportion?
proportion of people who develop a disease during a specified time period (i.e. new cases)
how do you calculate incidence proportion?
incidence proportion = number who develop disease during a time period/total number at risk at the start of time period
what is the incidence rate?
how quickly people are developing the disease (i.e. new cases)
how do you calculate the incidence rate?
incidence rate = number of people who develop disease during time period/number of person-years at risk
what are determinants?
the causes and other factors that influence the occurrence of disease and other health-related events
i.e. identify the risk factor which leads to the disease via a causal pathway
what measures are associated with determinants?
relative risk
risk difference/attributable risk
odds ratio
what is relative risk (risk ratio) and how do you calculate it?
relative risk = incidence in exposed group/incidence in non-exposed group
how do you calculate the risk difference?
incidence of exposed group MINUS incidence of comparison group
when would you use an odds ratio?
when you don’t know the number of people exposed and is risk cannot be calculated
how do you calculate an odds ratio?
odds of exposure = number of exposures/number of non-exposures
odds ratio = odds of exposure in cases/odds of exposure in controls
what are the two main types of studies in epidemiology?
observational (cross-sectional, cohort, case-control)
experimental (randomised controlled trials)
what is a cross-sectional study?
observational
randomly select sample of source population
at same point in time measure exposures of interest and outcome of interest
calculate prevalence of exposures and outcomes
descriptive only
what is a cohort study?
observational
randomly select a sample of source population
measure exposure state of participants at beginning of study
group participants by exposed or not
follow-up for period of time
count who develops the outcome during follow-up
calculate incidence, relative risk and risk difference
what is a case control study?
observational
select cases with outcome of interest
select controls (without the outcome of interest) from the same source population
measure exposure status of both cases and controls
calculate odds ratio
what is a randomised controlled trial?
experimental
randomly select a sample of the source population
randomise sample participants into groups (intervention or control)
follow-up participants for period of time
measure outcome
calculate incidence, relative risk, and risk difference
what is a confounding factor?
a third variable distorting results
independently associated with exposure or outcome
does not sit on causal pathway
what is bias?
systematic error e.g. selection bias (differences between the groups or how they behave during study)
what does precision involve in epidemiological studies?
95% confidence intervals
P-values (probability that observed result would occur when null hypothesis is true)
sample size
how do you calculate infection rate?
cases per year/total population
how do you calculate mortality rate?
fatal cases per year/total population size
how do you calculate case fatality rate
fatal cases/cases of disease
how do you calculate infection fatality rate
fatal cases/cases of infection (including asymptomatic cases)
how do you calculate the secondary attack rate?
person exposed who then became infected/total persons exposed
what is R?
average number of people each person with a disease goes on to infect
what is R0?
assumes everyone in population is susceptible to infection and no control measures (however during epidemic people become infected or immune and are no longer susceptible)
what is Rt
effective reproduction number
potential for epidemic spread at a specific time (t) the under control measures in place
what happens if Rt > 1
virus will spread out and disease will become epidemic
what happens if Rt = 1
virus will spread locally and disease is endemic
what happens if Rt < 1
virus will stop spreading and disease will disappear eventually
what are the tasks of epidemiology in public health?
- public health surveillance
- field investigation
- analytic studies
- evaluation
- policy development
(1 and 2 are outbreak identification, 2 and 3 are outbreak investigation)
what does sporadic mean?
occasional cases of infection (no common source)
what does endemic mean?
infection is always present in the community
what does epidemic mean?
sudden increase in incidence of an infection locally
what does re-emerging mean?
previously a major threat, decreased dramatically, and now increasing again
what does pandemic mean?
a global epidemic
what does zoonotic mean?
disease transmitted from animals to humans
what does enzoonotic mean?
endemic transmission in animals (endemic in animals)
what does epizootic mean?
epidemic in animals
what is measles?
a respiratory disease caused by measles morbillivirus (fever, cough, conjunctivitis followed by head to toe rash)
can have serious complications
highly contagious and been circulating for thousands of years
vaccine available
most deaths are children <5
sporadic in NZ
because of the high R0 of measles, what do you need to do to prevent sporadic outbreaks becoming epidemics?
high vaccination levels
what is rhinovirus?
endemic (always present in community)
respiratory virus responsible for most common colds
> 100 different types meaning reinfection v common
detected all year round and can cause complications e.g. pneumonia
what is the definition of outbreak?
same as epidemic (sudden increase in incidence of an infection locally) but used for more limited geographic area
when do epidemics occur?
when a pathogen and susceptible hosts are present in adequate numbers, and the pathogen can be transmitted from a source to the susceptible hosts
what might an epidemic result from?
recent increase in amount or virulence of pathogen
recent introduction of the pathogen into a setting where it has not been before
enhanced mode of transmission so that more susceptible persons are exposed
change in the susceptibility of the host to the pathogen e.g dropping immunisation rates
factors that increase host exposure or involve introduction through new portals of entry
what is monkeypox?
a zoonotic orthodox DNA virus
human-to-human transmission through large respiratory droplets, close/direct contact with skin lesions, fomites
only recently efficient human-to-human transmission
2022 outbreak sexual contact main means of transmission
what is syphilis?
re-emerging
STI with severe long-term consequences if untreated
Treponema pallidum subsp pallidum
spirochete
primary infection - painless ulcer
secondary - disseminates through body causing rash/swollen lymph nodes
(those are two most infectious stages)
latent/asymptomatic phase
tertiary syphilism - gummas, neuro/cardio issues
congenital syphilis (mother to baby) can occur
what are the three types of plague which occur from yersinia pestis?
bubonic - buboes, fever, headache, chills, 30-60% fatality, can lead to next two
septicaemic - fever, weakness, shock, chills, abdominal pain
pneumonic - fever, headache, weakness, rapid developing pneumonia, 100% fatality, airborne
what is plague (Black Death)?
caused by yersinia pestis
enzoonotic between fleas and rodents
humans and domestic animals can become infected from flea bites - highest risk during epizootic cause fleas jump from dead hosts
little genetic change since Black Death
what is Spanish flu (influenza)?
has segmented genome where each segment encodes a different gene and it can reassert the segments between different viruses if you get co-infection (antigenic shift)
can change and evade immune response by:
- accumulation of mutations (antigenic drift)
- genetic reassortment of genetic segments (antigenic shift)
what are the two major surface proteins of spanish flu/influenza and what does reassortment of these result in?
haemagglutinin (HA)
neuraminidase (NA)
reassortment of HA and NA results in major changes in antigenicity giving it pandemic potential
what are the usual reservoirs for influenza?
wild birds and infection usually asymptomatic
also can infect a wide range of host e.g. swine, humans but causes disease in these
potential for zoonotic infection and pandemics
what are the possible outcomes of a pathogen entering a person?
it could be immediately eliminated
it could replicate which could then lead to elimination also, transmission, colonisation of normal microflora, asymptomatic or symptomatic infection
what does a bacteria need to do to be successful?
colonise a host, reproduce a lot and transmit to a new host
from a pathogens perspective, causing disease can be…
helpful (e.g. helps it transmit), neutral or unhelpful (clears it out of host)
would the coughing and sneezing disease symptoms caused by rhinovirus help it reproduce?
yes cause it leads to more transmission
would the penile discharge caused by chlamydia help it reproduce?
no cause people less likely to have sex so less transmission
would the disease symptoms caused by tetanus (paralysis) help it reproduce?
no - we are just an incidental host and tetanus usually lives in the soil
would the accesses caused by MRSA help it reproduce?
nah cause more likely to isolate yourself but also maybe yes cause it could make transmission easier
what is an acute infection?
remains in host short-term and causes short-lived disease
what is a chronic infection?
remains in host long-term (persistently replicating) and can cause disease or be asymptomatic
what is an asymptomatic infection?
remains in host (persistently replicating) but no symptoms of disease
what is a latent infection?
remains in host (dormant/not replicating) and shows no symptoms of disease
what is reactivation?
latent infectious agent starts replicating again, which can be asymptomatic or result in disease
what is colonisation/carriage?
part of normal microflora
what is environmental/animal reservoir?
humans are not main reservoir
what are the differences/similarities between latent infection and asymptomatic infection?
in latent infection host shows no symptoms and the pathogen isn’t replicating
in asymptomatic infection there are also no symptoms but pathogen is replicating
what is a chronic infection like with hepatitis C?
asymptomatic but high level of replication then disease occurs later on
what is a chronic infection like with HIV?
symptomatic early on but then immune system controls it and person is asymptomatic for ages but during this time virus infection CD4 T cells and eventually these are lost and person gets immunocompromised and loses control of virus
what is HSV and VZV (chickenpox) infection like?
latent infection (once infected it won’t go away) and can reactivate later on
what type of infection do rhinovirus and influenza cause?
acute infection
outline the key points of Salmonella enterica serovar Typhi (typhoid fever) infection?
human restricted pathogen, acute infection causes disease (headache, fever, GI symptoms), not normal microflora, not sick during chronic carrier state, always replicating/contagious
chronic asymptomatic infection occurs after acute infection in gall bladder of 3-5% of infected (can go on for decades and infected highly contagious but asymptomatic)
outline the key point of Varicella zoster virus infection?
human restricted pathogen, acute infection causes disease, not normal microflora, not sick during latency, not contagious during latency, can reactivate and become contagious
in primary infection cause chickenpox (varicella) (airborne transmission) but then immune system controls so it sets up latency in neurons
reactivation can occur with loss of immune control causing herpes zoster (shingles)
what might favour overgrowth of a pathogen such as Candida albicans?
normal flora disruption with antibiotics allowing candida (part of normal microflora in digestive tract) to overgrow
immunosuppression
is Candida albicans colonisation common or uncommon?
common - grows at many mucosal sites on the skin
does Candida albicans have human carriage?
yes cause commonly colonises skin
what types of infection does Candida albicans cause?
acute, chronic and asymptomatic (also disease doesn’t really help transmission and is related to load)
what are the two types of disease caused by Candida albicans?
mucocutaneous and invasive
what are the main aspects of cryptosporidium infection?
protozoal parasite which can form oocysts and has animal reservoir
causes acute and self limiting disease in immunocompetent host and chronic disease in immunocompromised host
what are the main aspects of tuberculosis infection?
causes acute (latent tb), chronic and latent infection which can reactivate and then transmit (post primary/ extra pulmonary tb)
airborne transmission and most people clear the acute infection
has a human reservoir
what is streptococcus agalactiae (group B streptococci)?
beta-haemolytic streptococci which is part of normal GI tract microflora in 20-40% of people and causes different disease in different hosts
neonatal infection (infection soon after birth) causing bacteraemia, meningitis, pneumonia
invasive disease in elderly and immunocompromised hosts (soft tissue, bone, joint infections)
invasive disease (food borne from raw fish) causing bacteraemia, meningitis (animal reservoir!)
how does group B streptococci cause neonatal infection and what are the three types?
pregnant woman vagina and/or rectum may be colonised with group B strep (10-30%) and can transmit to neonate during or after birth and occasionally during pregnancy
congenital infection (spread during pregnancy) leading to still birth
early onset infection during delivery can cause meningitis
late-onset infection (>1 week post natal) more likely to cause meningitis and mode of infection unclear
leading cause of sepsis, pneumonia and meningitis in infants, causes acute infection and involves human carriage
what antibiotic treatment is there for neonatal infection caused by group B strep (GBS)?
giving antibiotics during birth if we know woman colonised can prevent early onset disease (called intrapartum antibiotic prophylaxis) but doesn’t prevent late onset disease
what is meningitis?
infection of the meninges and subarachnoid space
what is a reservoir?
the habitat in which the agent normally lives, grows and multiplies
bacterial isolates of the same species are related to differing degrees, what is a way we can exploit this for epidemiological purposes?
strain typing
what is the core genome?
genes common to all strains within a species
these are defining genes of a species
e.g. any individual E. coli you sequence will have around 4800 genes in its genome, but only around 3000 common to all E. coli genomes (core genome)
what is the pan-genome?
entire set of genes from all strains within a clade
e.g. E. coli pan genome >16000 (remember a single E. coli has 4800 genes)
what causes genetic differences between bacterial isolates?
horizontal gene transfer (conjugation, transformation and transduction)
why can two different E. coli have very different capacity to make people sick?
due to genomic plasticity within bacterial species
what is a strain?
a genetic variant or subtype of a micro-organism within a species
why do we need to subtype?
to link, source and track infections and epidemics
e.g. if you got swabs from three infected individuals in hospital and culture and isolate them, are they all the same strains or different, if all same strains could be an outbreak, is the swab from a nurse same as patient i.e. she infected him and so on
what is a point source outbreak?
all coming from one food vehicle
what is subtyping used to determine?
similarity between bacterial isolates
what are some non DNA-based ways to distinguish strains?
antimicrobial susceptibility pattern (antibiogram)
serotyping
phage typing
what are some DNA-based ways to distinguish strains?
restriction length polymorphism
amplified length polymorphism
rule field gel electrophoresis
multi locus sequence typing
genome sequencing
what is serotyping?
using antibodies to detect specific surface antigens (H, K and O) to see if different strains have the same ones
composition of antigens varies so much between bacteria that they are antigenically distinct
so an antibody that can bind to one might not be able to bind to another i.e. they are different serotypes
what are some common surface antigens in bacteria assessed during serotyping?
flagella (H antigen)
capsule (K antigen)
lipopolysaccharide (O antigen)
of the 700 E. coli serotypes, what antigens determine serogroup and what ones determine serotype?
O antigen determines serogroup
O + H antigens determine serotype
what is E. coli strain O157:H7?
makes cell wall antigen O157 and flagella antigen H7 (which are not responsible for making people sick). However, when we see O157 and H7 they usually accompany other highly undesirable genes e.g. shiga toxins which help it adhere to gut
why is E. coli strain O157:H7 so good at making people sick?
it has a variable gene collection including two shiga toxins and genes that help it adhere to gut
how do we do a serotype test?
latex beads are coated with antibody, if they encounter their antigen (while being stirred with bacteria) they agglutinate (make a clump)
what does phage typing look at?
do strains have the same susceptibility to the same bacteriophages
uses a broad collection of bacteriophage to determine the susceptibility to those different viruses i.e. how well can these viruses replicate (if well they will lyse bacterial cell)
how does phage typing work?
successful phages multiply and cause lysis
there is a diverse collection of bacteriophages
each phage has a different mechanism of action so it will act on a different set of molecular targets. Therefore different strains which have genetic differences will be differentially susceptible to each phage
how is phage typing done in real life?
entire plate is bacterial lawn
divide in a grid, inoculate one unique phage per square
each spot with lysis represents susceptibility to that phage
the “which phages kill it” pattern can be used to distinguish strains
what is a real-world application for phage typing?
can be used to distinguish S. aureus strains
it is fast and cheap
what is restriction fragment length polymorphism (RFLP)?
to look at variations in DNA sequence of presence/absence of certain bits of DNA
to do it: purify DNA from isolate of interest, cut with restriction enzymes which recognise particular sequences (usually short enzymes) in DNA, separate through gel electrophoresis, blot it and prove against insertion sequences or other repetitive regions
restriction fragment length polymorphism patterns are mainly determined through what?
through the specific combination of restriction enzymes and DNA probes
what are the steps of amplified fragment length polymorphism (AFLP)?
- digest DNA with two restriction enzymes (frequent cutters)
- ligate restriction fragments with end-specific adapters
- selective amplification of fragments by PCR
- analysis by automated DNA sequencer or gel electrophoresis
all we are measuring is whether restriction sites have been gained or lost and whether there’s deletions in between
what is pulse field gel electrophoresis (PFGE)?
gold standard for typing
differs from RFLP and AFLP in that it uses restriction enzymes but it uses ones which are rare cutters within the genome resulting in large fragments of DNA which can’t move seperate from standard gel electrophoresis. So to get them to move through gel we use PFGE. If there is a mutation in restriction enzymes site (can’t detect mutations outside of restriction sites cause large fragments) we see different numbers of bands
what are the steps to multi-locus sequencing typing (MLST)?
amplification of seven housekeeping genes (sequences constrained because of essential function of encoded protein)
sanger sequencing
identify species specific alleles by comparison to database
assignment of sequence type
what does multi-locus sequencing typing do?
uses DNA sequencing to uncover allelic variants in several conserved genes
what are the downfalls of multi-locus sequencing typing?
use of highly conserved housekeeping genes often fails to detect the variability of closely related strains
sequencing seven genes is costly and time consuming
what are the pros and cons of whole genome sequencing (WGS)?
pros: exactly which genes are there, exactly which mutations are present, you can do things you cannot do with other subtyping methods i.e. much higher sub typing resolution
cons: still relatively slow and expensive
Streptococcus pneumoniae has over 90 capsular serotypes, what does this mean in regards to serotyping it?
genome sequencing shows that sometimes serotyping is very inaccurate due to capsular switching
why are heavy metals antimicrobial?
because they are toxic to cells and not specifically bacterial ones so fuck everything up
key point is they are non-specific
e.g. mercury binds to and damages many proteins very non-specifically
what is the principle that every antimicrobial works on?
maximise toxicity to pathogen while minimising toxicity to host
every drug has a therapeutic dose and a toxic dose, what is the therapeutic index calculated from and what does it mean?
calculated from the ratio of the toxic dose to the therapeutic (effective) dose
a higher therapeutic index means a safer drug
which is better for an antimicrobial, a narrow therapeutic margin or a wide therapeutic margin and why?
wide therapeutic margin is better cause bigger gap between therapeutic dose and toxic dose
what is the easiest way to make a highly effective and safe drug?
target cell processes that humans don’t have
this means there will be a good therapeutic index and a wide therapeutic margin
can you target two different types of microbes e.g. bacteria and protozoa?
yes but its uncommon
why is penicillin selectively toxic for bacteria?
it inhibits cell wall synthesis by inhibiting peptidoglycan cross linking
peptidoglycan has a glycan backbone with N-acetyl muramic acid and N-acetyl glucosamine alternating and the glycan backbones are given stability by peptide bridges which require a transpeptidase to join them up. This links the peptide chains together which results in the peptidoglycan layer having structural strength which is important for bacteria’s survival
penicillin binds to the penicillin binding proteins (transpeptidases) and activates them preventing cross linking of peptidoglycan layer
why has penicillin got a good therapeutic index?
peptidoglycan cell wall processes (which it targets) are specific to bacteria
what is the most important part of penicillin and what does modifying it do?
the beta-lactam ring because it irreversibly binds to PBP
modifying the R group alters its spectrum and pharmacokinetics
modifying beta-lactam ring creates other classes of beta-lactam
what does it mean if a drug is bactericidal and give example?
they kill their targets
e.g. penecillin
what does it mean if a drug is bacteriostatic and give example?
keep the bacteria from growing when drug is present but the bacteria can start growing again as soon as the drug is gone
e.g. sulphonamides
why is the difference between bacteriostatic-bactericidal important and what is the 60:40 rule?
the difference important for immunocompromised patients where you might need to use bactericidal drug rather than a bacteriostatic one you would have used for immunocompetent person who’s immune system could’ve done the rest
60:40 rule is to cure someone this should be 60% by their own immune system and 40% the antibiotic
this is because a fully functioning immune system is best for antimicrobial therapy
what are pharmacokinetics?
what does the body do to the drug
what are pharmacodynamics?
what the drug does to the bug
what are the four main questions to ask when deciding on the right drug to use for an infection?
what do we know about the bacteria?
what do we know about the host?
what kind of infection and where does the drug need to go?
what do we know about how the drug behaves?
when might it be a good idea to use antimicrobials in combination?
if we don’t know whats causing the infection
if infection is polymicrobial
to preven emergence of resistance
synergy (two antibiotics work better when combined)
combining will allow reduction of dose of a toxic antimicrobial
what is the disk diffusion test?
each disk saturated with antibiotic and is dropped on bacterial lawn creating a gradient of antibiotic
zone of inhibition size corresponds to the diffused concentration of antibiotic that will inhibit bacteria growth
what are the three possible outcomes of the disk diffusion test when testing multiple antibiotics?
indifference (antibiotics don’t affect one another)
synergy (one makes the other work better)
antagonism (one inhibits the other)
what are some common benefits and drawbacks of antibiotics?
benefits: shorter less severe infection, cure infection, prevent infection (prophylactic), reduced morbidity and mortality
drawbacks: side effects, allergies, resistance emergence, secondary infections
what are some common mechanisms of antimicrobial resistance?
modifying antibiotic target (antibiotics target specific cell processes) e.g. MRSA have a new penicillin binding protein that can cross-link peptidoglycan in presence of beta-lactam cause it doesn’t bind beta-lactam
inactivate the antibiotic e.g. beta-lactamases produced which hydrolyse beta-lactam ring
restrict access of antibiotic to its target e.g. decreasing permeability so antibiotic can’t get into cell or efflux pumps which pump out antibiotic
what are the two kinds of resistance bacteria can have to an antibiotic?
innate resistance - chromosomally encoded and predictable i.e. they always genetically have been
acquired resistance - encoded on chromosome or plasmid, not predictable
what is antibiotic-mediated selection
lots of germs (a few drug resistant)
antibiotics kill bacteria causing illness as well as good bacteria protecting the body from infection
the drug-resistant bacteria are now allowed to grow and take over
how does antibiotic use promote resistance by selecting for point mutations that confer resistance?
lots of germs (a few drug resistant)
antibiotics kill bacteria causing illness as well as good bacteria protecting body from infection
drug-resistant bacteria now allowed to grow and take over
point mutations lead to resistance
what is an example of a point mutation causing antibiotic resistance?
no quinolone binding
how does antibiotic use promote resistance by selecting for bacteria that have acquired genes by horizontal gene transfer?
antibiotics kill of all germs expect drug resistant so the drug resistant can take over
some bacteria give their drug resistance to other bacteria causing more problems
what is an example of antibiotic resistance being acquired through horizontal gene transfer?
acquisition of mega gene encoding PBP2A that doesn’t bind beta-lactams
why is horizontal gene transfer more preferable to bacteria than a point mutation when it comes to gaining antibiotic resistance?
its easier and better to acquire resistance genes from other microbes
just cause a lot more difficult to get an effective mutation occurring when the best methods selected for and can just be got from your neighbour
which came first, antibiotic use or antibiotic resistance?
antibiotic resistance e.g. soil microbes
cause antibiotics are from the environment and have been around forever
do antibiotics treat viruses?
no
is it only misuse of antibiotics that creates a selection pressure for antibiotic resistance?
nah even appropriate use
any use does
why is antibiotic resistance such a major problem for agriculture?
it is used way more than in normal medical treatment
e.g. for growth promotion, prophylaxis, disease treatment
it also doesn’t go away when antibiotic usage is stopped
what makes MRSA resistant?
MRSA has a gene called mecA which encodes a penicillin-binding protein (PBP2A) that gives resistance to all beta-lactams
mecA acquired through HGT not point mutation
MRSA can also gain other resistance genes and is only treatable with vancomycin
what is Pantone-valentine leukocidin (PVL)?
a clinically important pore-forming S. aureus toxin which forms pores in monocytes and neutrophils leading to lysis
there are also many other S. aureus pore forming toxins this one just most important
what is MSSA?
methicillin sensitive s. aureus
if it acquires mecA it becomes MRSA
are the genes for methicillin resistance and PVL acquired together?
NO but they often are
PVL acquired by transduction
both acquired independently but you do often end up with both in the same organism
true or false - MRSA often carries resistance genes for other antibiotics?
true
how can using one antibiotic select for resistance of another antibiotic?
there is often cross resistance and these gene care genetically linked i.e. travel together on the same plasmid etc
