Basic concepts in Epidemiology Flashcards
Occurrence of a Disease
• Incidence and prevelance
Incidence: definition
Incidence rate formula
Incidence: Describe the rate of development of a disease
in a group over a period of time.
Nbr of persons dev. a disease x unit time = Incidence rate
Total number at risk
Incidence: examples
The incidence of chickenpox in first-grade
children was 10 percent a day at the height
of the epidemic
Chick poxs
- Varicellovirus
Double stranded dna virus
- The incidence of myocardial infarction is
about 1 percent per year in men aged 55
to 59 in our community
I Prevalence: definition
Prevlance formula
Number of persons with a disease
is the most frequently used measure in epidemiology.
For a count to be descriptive of a group, it has to be
considered as proportion of a group.
Prevalence: Describe a group at a certain point in time.
Number of persons with a disease = Prevalence rate
Total number in group
Total # of dieases over number in group will give u rate of prevelance
Prevalence: examples
Prevalence of diarrhea in the children’s camp on July 13 was 33 percent
- Prevalence of significant hyperbilirubinemia in full-term infants on the third post-partum
day is 20 percent - Prevalence of electrocardiographic
abnormalities at our screening examination
was 5 percent
Morbidity rate: definition
Morbidity: incidence of illness (disease) in a population.
It includes both fatal and nonfatal diseases.
Morbidity rate could refer to either prevalence or
incidence.
Morbidity rates: examples
Morbidity rate of genital Chlamydia in Canada in 2000
was 32%.
Morbidity rate of giardiasis in Canada in 2000 was 3.4%.
These are the number of new cases for the year 2000.
Mortality rate: definition
formula
Mortality: incidence of death in a population.
Nbr of persons dead x unit time = Mortality rate
Total number in group
Mortality rate: examples
The mortality rate varied from 25% to 33% of
Europe’s population during plague epidemics
in the Middle Ages.
- The mortality rate of HIV/AIDS patients in the
USA decreased from 15.6 deaths per 100,000
people in 1995 to 11.6 deaths per 100,000 people
in 1996.
Case Fatality Ratio
Usually in an epidemiological study (often outbreak).
• The number of confirmed cases that died of the diseases.
• It is an estimate on a small sample of the mortality rate of a disease
(estimate because not all cases in outbreak has been reported)
It is usuually for people that have been confirmed based on pcr
Listeria monocytogenes
- Food path 150 cases in canad a - CFR- 15-30% - High case F R = leads people to start implementing containment early
Occurrence of a Disease the types
Sporadic disease: disease that occurs only occasionally
• Endemic disease: disease constantly present in a population
• Epidemic disease: disease acquired by many people in a given area in
a short time
• Pandemic disease: worldwide epidemic
The notifiable are usually endemic
May change if u have a way of vaccinatingg or treating ie measels
Epidem - usully unstable pop
When that goes global = pandemic
Example of a pandemic
Hiv exapmle of pandemic
1979 first cases
Luc montagnier - france
Robert gallo - usa (NIH new your
Isolate dthe virus
92-93 change of case definition gence the spike as the number befroe were probs underreporting
Case Definition of TB
A tuberculosis (TB) case is a patient that has been diagnosed as such
by a clinician, regardless if the diagnosis has been confirmed
bacteriologically or not.
• The elements necessary for defining a TB case are: the TB treatment
history, the bacteriological status, the anatomical site of the disease
and the patient’s HIV status.
• Note: any person receiving treatment for TB should be recorded as a
TB case.
• (derives from WHO guidelines)
Acute disease
symptoms develop rapidly but the disease lasts only a
short time
Chronic disease
: symptoms develop slowly
Cronic- hep c - will have acute phase followe dby cronic infectionn
Subacute disease:
: intermediate between acute
and chronic
Latent disease
causative agent is inactive for a time but then
activates and produces symptoms
tuverculosis, hep, conjuctivitis caused by herpes
Herpes simplex- the dna of virus will incorperated into dna of host cfell - 1% of people after 50 years will give an infection
Vairacella (chicken pox) - gives shingles in latent state , uaully is a nerve infectin
Herd immunity
: immunity in most of a population
Local infection
pathogens are limited to a small area of the body
Systemic (generalized) infection
an infection throughout the body
exp is strep pyogenes
Focal infection
systemic infection that began as a local infection
Sepsis
: toxic inflammatory condition arising from the spread of
microbes, especially bacteria or their toxins, from a focus of infection
Bacteremia
bacteria in the blood
- may start by a simple brushing of teeth too hard
- Does not involve growth of bact
Septicemia
also known as blood poisoning; growth of bacteria in the
blood
Toxemia
toxins in the blood
diptheria - a single unit, has an a part and b part, b is active part
Viremia
viruses in the blood
measles for unvax childrens
Primary infection:
acute infection that causes the initial illness
Secondary infection
opportunistic infection after a primary
(predisposing) infection
You may have cold or flu and u may have probkem in lungs and may develop bect which is secondary infec
Subclinical disease
no noticeable signs or symptoms (inapparent
infection)
Predisposing Factors
Gender • Inherited traits, such as the sickle cell gene • Climate and weather • Fatigue • Age • Lifestyle • Nutrition • Chemotherapy
Inherited- nRAMP
Inherited- nRAMP - 1 protien (gene)- associated with succeptability or resisiance
- The polymorphasm of this has been studied - connection to indigenous which makes them more succept to tuberculuosus
Another exampke is ccr5 gene - HIV- plymorphus - variable in dif contries
Incubation period:
: interval between initial infection and first signs
and symptoms
Prodromal period
short period after incubation; early, mild
symptoms
Period of illness:
disease is most severe
Period of decline
signs and symptoms subside
Period of convalescence:
body returns to its prediseased state
goes back to norma
Reservoirs of Infection
Continual sources of infection Human reservoirs • Carriers may have inapparent infections or latent diseases Animal reservoirs • Zoonoses are diseases transmitted from animals to humans Nonliving reservoirs • Soil and water • Food
Direct contact transmission
requires close association between the
infected and a susceptible host
Indirect contact transmission
spreads to a host by a nonliving object
called a fomite
Fomite- important for hospital infections
Droplet transmission
transmission via airborne droplets less than 1
meter
Vehicle Transmission
- Transmission by an inanimate reservoir
- Waterborne
- Foodborne
- Airborne
Vectors
Arthropods, especially fleas, ticks, and mosquitoes
• Transmit disease by two general methods
• Mechanical transmission: arthropod carries pathogen on its feet
• Biological transmission: pathogen reproduces in the vector; transmitted via
bites or feces
Fleas- eu espestos
Malaira
Mech- spreads on food by feet
Healthcare-Associated Infections (HAIs)
Acquired while receiving treatment in a health care facility
• Also known as nosocomial infections
Affect 1 in 25 hospital patients
• 2 million per year infected; 20,000 deaths
HAIs result from
Microorganisms in the hospital environment
• Weakened status of the host
• Chain of transmission in a hospital
Compromised host
an individual whose resistance to infection is
impaired by disease, therapy, or burns
Control of Healthcare-Associated Infections
Reduce number of pathogens
• Handwashing
• Disinfecting tubs used to bathe patients
• Cleaning instruments scrupulously
• Using disposable bandages and intubation
Infection control committees
Emerging Infectious Diseases
Diseases that are new, increasing in incidence, or showing a potential
to increase in the near future
• Most are zoonotic, of viral origin, and likely to be vector-borne
Emerging Infectious Diseases
• Contributing factors
Genetic recombination
• Escherichia coli O157
• avian influenza (H5N1)
Evolution of new strains
• Vibrio cholerae O139
Widespread use of antibiotics and pesticides
• Antibiotic-resistant strains (MRSA, M. tuberculosis XDR)
Changes in weather patterns
• Hantaviru
Hantavirus- associated with rockies and animal pop
Mycobacterium tuberculosis AM
resistance
Distinct subpopulations isolated from a
poorly-compliant TB patient
If the patient diesnt carry out treatmetn
The boxes are the genes of tb that have undergon mutations that will resist antibiotic
KatG gene- antibi resistance
The mutuations are addiive and they will becoem resistance to many antibiotjcos
Resistance to all antibiotics
Emerging Infectious Diseases Contributing factors (cont'd
Modern transportation Chikungunya • West Nile virus Ecological disaster, war, and expanding human settlement • Coccidioidomycosis Animal control measures • Lyme disease Public health failure • Diphtheria
Chikungunya- similar to dengu and zika
West nile- from new york
Barallia burgdorferi- can be transmitted thru a tick and deer pop
- Phylym spirochetes
Public health
- 1990 crumbling of iron current and soviet unit
- Vacci ne against dipt goes down and cases went up
John Snow
1848–1849
Mapped the occurrence of
cholera in London
ould trace it back to water pump and filitering it thru sand column
Ignaz Semmelweis
1846–1848 Showed that handwashing
decreased the incidence of
peurperal sepsis
baby birthing
Florence
Nightingale
1858 Showed that improved sanitation decreased the incidence of epidemic typhus
The Centers for Disease Control and
Prevention (CDC)
Collects and analyzes epidemiological information in the United
States
Publishes Morbidity and Mortality Weekly Report (MMWR)
Morbidity
Morbidity: incidence of a specific notifiable disease
Mortality
Mortality: deaths from notifiable diseases
Notifiable infectious diseases
diseases in which physicians are required to report occurrence
Morbidity rate:
number of people affected in relation to the total population in a given time period
Mortality rate:
number of deaths from a disease in relation to the
population in a given time
Patient with a bacteremia during a hospital stay
• Dr. Jackson wants to know the cause of the disease
- Postulate MRSA (methicillin-resistant Staphylococcus aureus)
- Culture? Phenotypic (longer but well established)
- Molecular diagnostic? PCR (faster but need to be reliable)
mannitol-salt agar
selectove medium and differential
- Sodium chloride 75 g/l (7.5%)- selective kind
- D mannatol
- Beef extract
- Phenol red - 6-8pH yellow to red , yellow is indication
○ Measure acid production to distignuish between s. epidermidis (mannitol neg so it stays red) and s. aureus
- Agar
- Proteose peptone
Blood cultures grown on mannitol-salt agar
coagulase-positive; grampositive cocci
Methicillin-resistant Staphylococcus aureus
• Strain USA100: 92% of health care strains
• Strain USA300: 89% of community-acquired strains
Methicilli n- antibiotic of familt penicilin which blocks cell wall synth
Commun- people that get infected in community - ie live on streets
80% usa 100
Use incidence 0.02-0.04% 20/100,000 and 40/100,000
Molecular Biology and Epidemiology
I Molecular strain-typing techniques (short term)
II Phenotypic methods (longer term)
III Genotypic methods (diversity of methods)
IV PCR-based methods (diversity of PCR)
I Molecular strain-typing techniques
There are 4 basic techniques in molecular biology
1. PCR
2. Hybridization
3. Cloning
4. Sequencing
All the different techniques used in molecular
epidemiology are variations of these technique
PCR (Polymerase Chain Reaction)
Pcr - dna polynerase Thermostable 90 degrees celcius - thermus aquatus Frist isolated by t d brork from yellowstoen hotspring - Primers oligonucleotied - around 20 nuc tide long single straned. A froward and reverse. One primer forwaed 5'-3', reverse: 3'-5' - Need magnesium chloride as you have to modify [] of this to optimize pcr - You need target dna - You need a positive and neg control - Thermocycler ○ 3 cycle ○ 1> denaturin g 94 degress c 2. Anneling 50-65 allowas for binding 3. Extention primer 72 - Then cycle starts again
- The promers may be targetinh very conserved areas. - Gives flexibility to look at specific group of bacteria
Hybridization
Hybirdization
- S aureus - Colonies on plate - We want to know if they vancomycin resistance - We look at van A gene - Use nylon membrane - You trat it so it crosslink s - Then u treat with piece of fna you hyberdize it and was it - If it has van a it will light up due to fluoreces and thise will be van a positive
Good way to screen several coloneis quicly and identify genotypes quicly
Cloning
Plasmid
Naturally occuring in bact
Make specific genes that are benificail
Involve dedgreation of compound or
Name comes from
Forst letter is genus
Have amp resistacne gene that doesn’t have a cloning site and will be used to eliminate bact
Can construct a plasmid with an insert
You want to identify bact with plasmid and insert
You will replace with ampicillin and amp + tetracyclin
No plasmid no growth
Cant have a plasmid with and without insert
Have lacz gene that can convert xgal to blue
White because thye cant convert x gal
Blue colony doesn’t have insert
By selecting white u know it has insert
High Throughput Sequencing
2 protiens added thu pore
The topoisomeras will unwind dna which will goto porin
By moving across membrane
The overlap of those sequences will give u the resolution
High Througput Sequencing
Several methods with different chemical principl
1: Nanopore sequencing
2. Pyrosequencing (454)
3. Sequencing by synthesis (Illumina: Miseq and High seq)
Pyrosequencing (454)
- 100bp dna
- Pcr in thousands wells
- 2nd pcr + DNA polymerase, Attp sulfurlase, luciferin , ATS->ATP
Detect light emitted
Sequencing by synthesis (Illumina: Miseq and High seq)
- 200-600 bp dna
- Dna + ardaptors small clusterrs
- Dna polymerase + dNTP terminal tors
laser
Epidemiologic problems addressed by
molecular strain-typing
Dynamics of disease transmission
•Risk determination in sporadic occurrence of
disease
•Stratifying data and refining study designs
•Distinguishing pathovars and nonpathovars
•Addressing nosocomial infections
•Identifying genetic determinants of disease
transmission
Application to epidemiology of molecular straintyping methods
When to use molecular strain-typing methods?
•How to select molecular strain-typing methods?
•Validating new molecular strain-typing methods
- Validation was a problem with covid 19 as it was genrating a lot of false pos.
•Simplicity:
•Molecular techniques may be simpler to execute and
simpler to train people to use (E. coli study in Brazil took
only 1 month to complete compared to 6 months with
classical methods)
High throughput:
•Capacity of a test to process a large number of specimens
simultaneously (especially important for power of stat tests)
•In Brazil study, only 5 -7 isolates per child could be
analyzed by classical methods, while isolates were pooled
using PCR methods allowing a greater number of isolates to
be analyzed.
Cost
Widespread use of molecular biology reagents have
reduced costs in developing countries. PCR tests have all
the same reagents except for primers.
Appropriateness
•The capacity of a test to address epidemiologic problems
not possible to address by conventional methods.
•If conventional test can be use and there is no disadvantage
to use it, then there is no need to use a molecular technique.
Ex. An unusual drug resistance pattern in Salmonella could
preclude the use of molecular strain-typing.
•But often DNA sequences allow unambiguous
identification of new infectious agents and evolution of
these agents. Ex. Identification of HIV as AIDS infectious
agents, SARS
How to select strain typing methods?
- Typeability: ability of a technique to generate an unambiguous result
for an isolate tested.
•Reproducibility: ability of a test to produce identical results when a
strain is tested repeatedly.
•Ease of interpretation: information derived from molecular
techniques has to serve as stratum in epidemiological study.
•Ease of use: (same as simplicity).
•Stability: the character use for molecular typing is not subject to rapid
evolution or lost from host.
•Epidemiologic concordance: molecular typing has to effectively
group outbreak-related strains.
•Typing system concordance: molecular typing compares
favorably with a previously validated test.
•Validity
.. of a test is its ability to correctly
predict or identify those who truly have the
characteristics the test is trying to detect , and
exclude those who do not have the characteristic
•Validating methods for pathogens causing
disease recognized to occur as outbreak
•Validating methods for pathogens causing
disease NOT recognized to occur as outbreak
II Phenotypic strain-typing
Typing by growth and morphologic
characteristics
•Typing based on biochemical characteristics
•Typing by functional or physiologic
characteristics
•Typing by serologic characteristics (serovars)
Serovars= same bacterium biut will react dif to dif antibodies
Typing by growth and morphologic characteristics
•Gram or acid fast stain (Mycobacterium tuberculosis)
•Color, shape of
colonies on agar plates (S. aureus on VogelJohnson agar are black
colonies surrounded
by a cleared yellow
zone)
Typing based on biochemical characteristics
•Targeting an enzyme associated with disease.
Lactose-fermenting E. coli cause diarrhea.
Targeting lactose fermentation for detection of
infectious agent.
• Mannitol fermentation for Staphyloccocus aureus
Like mannitol salt medium for s. auresu
This is vogal jhonson agar vja-
Vja- tryptone, yeast extract , mannitol, K2PO4,Li CL , glycine, phenol red + tellurite
- Mannitol and phenol red are for same reason as msa - Sekective part is - LiCL - Differental is manitol and ohenol - Tellurite- reduced to tellurium whoch will give black colour to staph areus
•Toxigenicity bioassays
Shiga-like toxins or verotoxins E. coli can be identify
by their cytotoxic effects on Vero cells (African Green
Monkey kidney cells)
•Toxin-producing Clostridium difficile cause cytopathic
effects on fibroblast cell monolayers
•Diphtheriae toxin in C. diphtheriae
•Survival characteristics (in vitro or in vivo)
•Based on susceptibility to stress conditions
•Multilocus enzyme electrophoresis (MLEE)
•Based on metabolic enzymes that are highly conserved
and that may reflect differences visualized by migration
of enzymes in a starch gel
•Antimicrobial susceptibility
•Betalactamase (Ampicillin), rifampin, etc.
•Phage typing
•Susceptibility to phage lysis (eg. phages PT2, PT8)
•Colicin (bacteriocin) typing
•Based on susceptibility to bacteriocins: short
peptide that inhibit other bacteria
•Cell culture assays
Enteropathogenic E. coli can be differentiated from
other E. coli by their ability to attach to HeLa cells
Typing by serological characteristics
Based on differences in antigenic determinants of
infectious agent
•E. coli can be subtype by O polysaccharide and
further subtype by flagellar protein H
•Hamburger disease (E. coli O157:H7)
•Influenza virus is typed by H and N antigenic
proteins (H5N1)
Typing by functional or physiologic characteristics
Colicin (bacteriocin) typing •Based on susceptibility to bacteriocins: short peptide that inhibit other bacteria
Typing by ELISA
Enzyme Linked
Immuno-Sorbent
Assay
Typing by Western (Immuno-) Blot
Southern- used it for dna - that goes on agarose gel - to DNA target on membrane
RNA- northern
When dealinf with protein its western
Smaller protien. Moves faster thru gel
Gel cant be hyberdizes
You need to transfer protein gel to membrane
Now you can use antibody that will bind to protein that is targeted
Can use iodine
Is a non radioactive reaction
If protein is there you will see coloured spot
III Genotypic strain-typing
- Nucleic acid extraction
- Analysis of extrachromosomal DNA elements
- Genome-based typing methods
- Restriction endonuclease analysis
- Southern blot hybridization
- Pulse-Field Gel Electrophoresis (PFGE)
- Whole genome sequence comparison
- Microarray comparisons
Nucleic acid extraction
You need a mechanical disruption
To smash cell wall and cell membrane
Then you have number of enzyme or treatment you put in you rreaction
Gel Electrophoresis of Restricted Fragments
You have an elec current
The smaller the fragment, the faster it moves
Whats important-
- Current
- Gram ov agarose/desnity of gell
- If you increase [] of agarose to 1,1.5 gel which is great to separate small markers
- Then you run sample
- The size of the fragment is a good measure of what was amplified
- Your not sure if the sequenve you amplified is the same sequence your targeting so you habe to probe it
Southern Blot of Digested DNA
You probe membrane with labeled dna prob with southern blot
You want to see if patient shares same micobacterium tb.
For micobact tb a common probe is is6110
Then you can map who has transmitted the disease
If yuou have 4 people with same pattern, u can assume tjhat its been transmitted betweene people.
Pulse-Field Gel Electrophoresis
Reslove small fragments less than 5000bp
To resolve large fragment swe go from signal current vegctor to currents generated by multiple angles and then u c an use larger pieces of dna
Microarray comparisons
Allows for identification of single pelace of dna in a sample
You can use dna to screen specific genes in a microbiome
You would grow bact under 2 dif contitions
Reverse of hybirdization where you add probe on slide and then add sanple
IV PCR-based strain-typing
•Critical in the use of PCR for diagnostic is the development of PCR primer sets •Use of - Sequence database - Software to test primers •PCR target may be: •1) coding region: gene •2) non-coding region:repetitive elements
When u select 18-25bp primer it might bind to non specific bands
Target 16s rna could be other genes as well
Patthogens use henes involved in replicating genes ie housekeeping genes
Some regions become conserved
The non cofing region gene that is not coding and not under selective pressure, basis of ips used by fungi
