Basic Concepts in Epidemiology Flashcards
define epidemiology
the study of occurrence, distribution, and determinants of health and disease in populations
what are the three types of epidemiology?
- descriptive
- analytical
- experimental
describe descriptive epidemiology
collecting data and describing the occurrence of human disease. The number of cases implies methods to detect the disease accurately in individuals
describe analytical epidemiology
analyzing a particular disease using case control method or cohort methide
- human groups with and without diseases are matched and possible relationship with causes are evaluated using statistical inferences
describe experimental epidemiology
conducting experiments to better understand diseases in human population
give an example of experimental epidemiology
test effectiveness of a new vaccine against AIDS. two groups with one receiving a placebo and the other vaccine and determining the level of infection in each group
what are the causes of death as reported by WHO in 2004?
- communicable disease 32%
- non-communicable diseases 58%
- injuries 9%
what is an agent?
something that has the ability to affect human health
give examples of agents
- bacteria (gonorrhea, strep throat)
- protozoa (malaria)
- virus
- prions
how can we detect agents?
- PCR
- microarray
- Elisa
- epi-florescence microscopy
what examples of vectors?
ticks, mosquitoe
what is a fomite
when an inanimate object transmits infectious diseases
examples of fomites
needles, surgical devices
what are the two main ways to control and prevent diseases?
- host level
- environment
what does host level prevention include?
- vaccines and toxoids to prevent
- antibiotics and antivirals to treat/cure
what does the environment level pertain to?
- control of vector
- hygienic procedures
- social distancing
what is molecular epidemiology?
use of molecular, cellular and other biological markers in the study, prevention, and control of health risks faced by human populations
two main approaches to molecular epidemiology
- detect a gene (NAAT, microarray, dot blots, southern blot, sequencing)
- detect a protein (ELISA followed by western blot, immunoblot) on agent or host
what plays important role in identification of TB?
IS6110 but not in pathology
what does molecular epidemiology provide?
- more accurate comparisons among groups (agent, host, or vector)
- further clarification of mechanisms
- more specialized assessment of individual risks
what is steps in traditional epidemiology?
exposure -> disease
steps in molecular epidemiology
exposure -> internal dose -> effective dose -> altered structure/function -> clinical disease -> prognostic/significance
what are biomarkers
a measurable substance in an organism whose presence in indicative of some phenomenon such as disease, infection, or environmental exposure
what do valid biomarkers provide?
- precise continuum of events
- identification of exposure to lower dose
- early identification of events in clinical disease
- reduction of misclassification of dependent and independent variables
- indication of mechanism relating exposure to disease
- better account for variability (agent and host)
- enhance individual and group assessment
what are dependent variables?
something you cannot control
example of dependent variable
tree growth
what is an independent variable
something you can control
example of independent variable
exposure of moisture for trees
what do molecular tools allow?2
early identification to resolve population issues -> prevention
what are 2 levels of molecular epi for population?
- behaviour
- environment
what are 2 levels of molecular epi for organisms?
- specific exposure
- systemic communication
what are 3 levels of molecular epi for cells?
- cell to cell communication
- substrate molecules
- genetic instructions
what is the influenze virus
an acute and infectious disease of the respiratory system caused by a virus and characterized by fever, muscle pain, headache, and inflammation of the mucous membranes in the respiratory tract
when was the last influenza outburst?
1968
what is incidence?
describes the rate of development of a disease in a group over a period of time
what is prevalence?
the number of people who have the disease at a certain point in time
what is an example which uses incidence in relation to disease?
the incidence of chickenpox in first grade children was 10% a day at the height of the epidemic
what is an example which used prevalence in relation to disease
the prevalence of electrocardiographic abnormalities at our screening examination was 5%
what scale is used when talking about prevalence and incidence rates?
prevalence: per 10,000
incidence: per 100,000
what is the formula for incidence?
(# of persons development of a disease) x (unit time)
what is the formula for prevalence?
(# of people with the disease) / (total number of people in the group)
define morbidity
the incidence of illness in a population. includes both fatal and nonfatal at a point in time. can refer to either prevalence or incidence
what is an example which uses morbidity in relation to disease?
morbidity rate of giardiasis in canada in 2000 as 3.4%
define mortality
the incidence of death in a population
what is the formula for mortality rate?
(# of people dead/total # in the group) x unit of time
give an example which uses mortality in relation to disease
the mortality rate varied from 25% to 33% of europes population during plague epidemics in the middle ages
what is meant by ‘case fatality rate’
the number of confirmed cases that died of a particular disease for a given period
what is meant by a sporadic disease?
a disease that only occurs occasionally - only in some individuals
what is meant by an endemic disease?
a disease which is constantly present in a population
what is meant by an epidemic disease
a disease which is acquired by many people in a given area in a short time
-> cannot be controlled -> starts outbreak
what is meant by a pandemic disease
a worldwide epidemic
case definition
A set of standard criteria for deciding whether a person has a particular disease or health-related condition, by specifying clinical criteria and limitations on time, place, and person.
define acute disease
a disease in which symptoms develop rapidly but the disease lasts only a short time
what is meant by chronic disease
a disease in which symptoms develop slowly
what is meant be a subacute disease
a disease in which the severity is intermediate between acute and chronic
what is meant by a latent disease
a disease in which the causative agent is inactive for a time but then activates and produces symptoms
what is meany by herd immunity
immunity in most of the population can prevent those without immunity by limiting transmission of a disease
what is meant by a local infection
an infection in which the pathogen is limited to a small area of the body
what is meant by a systemic or generalized infeciton
an infection in which the pathogen has spread to the entire body
what is meant by a focal infection
a systemic infection which began as a local infection
define sepsis
a toxic inflammatory condition arising from the spread of microbes, especially bacteria or their toxins, from a focus of infection
define bacteremia
bacteria in the blood
define septicemia
aka blood poisoning, the growth of bacteria in the blood
define toxemia
toxins in the blood
define viremia
viruses in the blood
define primary infection
an acute infection which causes the initial illness
define a secondary infection
an opportunistic infection which follows a primary infection
define a subclinical disease
an infection which produces no noticeable signs or symptoms
list some predisposing factors which can make the body more susceptible to disease
- gender
- inherited traits
- climate and weather
-fatigue
-age
-lifestyle
-nutrition - chemotherapy
describe incubation period of a disease
the interval between the initial infection and the first signs and symptoms
describe the prodromal period of a disease
the short period after incubation in which the patient presents with early mild symptoms
describe the period of illness of a disease
the period during a disease progression in which the symptoms are most severe
describe the period of decline of a disease
the period after max severity in which signs and symptoms subside
describe period of convalescence of a disease
the period at the very end of disease progression in which the body returns to its prediseased state
what are the 3 main continual sources of infectoin
- human reservoirs (carriers)
- animal reservoirs (zoonoses -> 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
droplet transmission
transmission via airborne droplets less than 1 meter (sneezing, coughing)
in what 3 ways can disease be transmitted via an inanimate reservoir?
- waterborne
- foodborne
- airborne
what are the two transmission types?
- mechanical transmission
- biological transmission
what are common vectors of disease?
arthropods such as fleas, ticks, and mosquitos
what differentiates mechanical transmission from biological transmission?
Mechanical: vector carries pathogen on its feet
Biological: pathogen reproduces in the vector and is transmitted via bites or feces
epidemics can be classified as…
- a common source epidemic
- host to host epidemic
what is a common source of epidemic
usually arises from contamination of water or food
- ie cholera
what is host to host epidemics
the disease shows a slow progressive rise and a gradual decline
- ie influenza
what is direct host-to-host transmission
infected individual transmits a disease directly to a susceptible host without the assistance of an intermediary
what is an example of a direct host-to-host transmissted illness
flu, common cold, STD
what is indirect host to host transmission
occurs when transmission is facilitated by a living or nonliving agent
- living agents = vectors
- nonliving = fomites
what do controls directed against the reservoir refer to?
- if reservoir is animal, it can be immunized or destroyed
- when humans are the reservoir, eradication can be difficult
what do controls directed against transmission of the pathogen refer to?
- immunization
- quaratine
- surveillance
- pathogen eradication
what is an emerging infectious disease
a disease which is new and either increasing in incidence or showing the potential to increase in incidence soon
what is a reemerging disease
those that have become prevalent after having been under control
What 8 main factors contribute to the emergence of new infectious diseases.
- Genetic recombination
- Evolution of new strains
- Antibiotic/pesticide use
- Changing weather patterns
- Modern transportation
- Ecological disaster/war/human expansion
- Animal control measures
- Public health failure
what are the common characteristics of emerging infectious diseases?
most are:
- zoonotic
- viral in origin
- vector borne
What is an example of a virus whose spread is affected by changing weather patterns? How?
Hantavirus is spread by deer mice, which are expanding their range because of climate change.
What was epidemiologist John Snow known for doing in 1848-1849?
He mapped the occurrence of cholera in London.
What was epidemiologist Ignaz Semmelweis known for doing in 1846-1848?
Showed that handwashing decreased the incidence of pleural sepsis.
What was epidemiologist Florence Nightingale known for doing in 1858?
Showed that improved sanitation decreased the incidence of epidemic typhus.
healthcare-associated infections
acquired while receiving treatment in a health care facility
- also known as nosocimal infections
- affect 1 in 25 hospital patients, 2 m per year infected, 20,000 deaths
what do HAI’s result from?
- Microorganisms in the hospital environment
- Weakened status of the host
- Chain of transmission in a hospital (e.g. via contaminated medical instruments)
What does Staph aureus most commonly cause in terms of HAI’s?
Infected surgical wounds
Accounts for 16% of total HA Infections
is coagulase POSITIVE - interacts w/ fibrinogen (involved in blood clotting).
Concerns w/ MRSA (Abx resistant strains), especially the spread amongst homeless population
Often to do with the community.
What are the two means by which to Control Healthcare-Associated Infections?
A) Reduce number of pathogens…
- handwashing
- disinfecting tubs used to bathe patients
- cleaning instruments scrupulously (sterilization/autoclaving)
- Using disposable bandages & intubation
B) Infection control committees
What type of media selects for Coagulase-positive, Gram-positive cocci? And what is this microbe?
Mannitol-salt agar
Selects for Methicillin-resistant Staph aureus
Flow Chart of methods used for isolation & ID of infectious pathogens
Outlines clinical and diagnostic methods
Epidemiology always starts with a clinical diagnostic
What 4 basic strain-typing techniques are used in molecular biology?
PCR
Hybridization
Cloning
Sequencing
what is PCR
- polymerase chain reaction
A technique for amplifying DNA in vitro by incubating with special primers, DNA polymerase molecules, and nucleotides.
what main components required for PCR?
- primers
- target DNA
- taq polymerase
- dNTP
- pH buffer and thermocycler
- MgCl
what are primers
short segments of DNA (~20 nt oligonucleotides) that target a specific sequence in the DNA and guide DNA polymerase to copy.
Usually single-stranded
Need both forward (5’ to 3’) and reverse (3’ to 5’)
But: There can be some mismatches –> affect the stability of the primer w/ the target DNA
What is the challenge w/ the Target DNA involved in PCR?
Contamination by molecular material from other organisms/compounds present, etc.
Therefore, requires a sophisticated extraction method.
taq polymerase
A heat-stable form of DNA polymerase extracted from bacteria that live in hot environments, such as hot springs, that is used during PCR technique
Use pfu Polymerase is used for high-fidelity sequencing
steps of PCR
- Denaturation - >90 degrees C
- Annealing - 49-65 C (depends on optimal temp. e.g. G-C’s more stable than A-T’s)
- Extension/Elongation ~72 C
What can PCR target?
A coding region (gene) or a non-coding region (repetitive element).
what is the process in hybridization?
a) Cells from specimen are affixed to filter
b) Lyse & denature (NaOH) & generate single-stranded target DNA
c) Add reporter-labelled probe; allow for reannealing to target
d) Measure hybridization directly if reporter is radioactive or fluorescent. Add enzyme substrate if reporter is an enzyme (i.e. detection via radioactive detector, fluorimeter, colorimeter/visual inspection)
what is hybridization
Is a technique that measures the degree of genetic similarity between pools of DNA sequences
- is typically used to determine the genetic differences between 2 organisms
what are the 5 phases of hybriziation
- Cells from the specimen affixed to filter
- Lyse cells and generate single stranded target DNA
- Add reporter labeled probe; allowing for re-annealing to target
- Measure hybridization directly if reporter is radioactive or fluorescent
- add enzyme to substrate if reporter is an enzyme
- whatever is bound to the membrane is what will be read - Detection
- radioactivity detector
- fluorimeter
- colorimeter/ visual inspection
what is cloning
Is a technique that the lab processes used to produce offspring that are genetically identical to the donor parent
- uses a vector insertion
what are the 3 different types of cloning
- gene cloning
- reproductive cloning
- therapeutic cloning
why do we clone?
to be able to understand more about the function of particular genes
what does cloning require
a vector
what is DNA sequencing
Is a process of determining the precise order of nucleotides within a DNA molecule
- you have multiple sequences to allow for less error
what do you need in DNA sequencing
- a radioactive primer
- typically uses radioactive P32
What happens to the reaction products in DNA sequencing?
They are separated by electrophoresis on polyacrylamide gel and identified by autoradiography
- it generates fragments of different size
What are 6 Epidemiological problems addressed by molecular strain-typing?
- Dynamics of disease transmission
-Risk determination in sporadic occurrence of dz
- Stratifying data & refining study designs
- Distinguishing pathovars and nonpathovars
- Addressing nosocomial infections
- Identifying genetic determinants of disease transmission
