Measuring Disease Flashcards
Iceberg of infectious disease
There is often a larger number of infected under the surface that we cannot see because they don’t really have symptoms. Only small number of infected that we are actually aware of.
Counting deaths
- Easy to count deaths, but difficult to know what actually killed them as it may have been other complications or factors
- Introduces a bias
Johne’s Disease: Paratuberculosis
- Caused by Mycobacterium avium paratuberculosis (MAP)
- Leads to chronic diarrhea, weight loss, otherwise normal
- Similar to Crohn’s disease
- Long incubation period. Often means that one cow is the tip of the iceberg, and there is many others in the herd that are just not showing symptoms yet
o Incubation period: 3-5 yrs
o Latent period: 2-4 yrs
Parts of the Iceberg
- Clinical cases
- Non-clinical, shedding
- Non-clinical, non-shedding
- Susceptible
Incubation Period
Period from when animal becomes infected to when it shows clinical signs
Latent Period
The period from when the animal becomes infected and when they are infectious and shedding
Incubation and Latent crossover?
- Don’t need to cross over
- Latent period can be shorter, equal, or longer
Easiest way to determine incubation period/latent period
Identify individuals involved, their contacts with each other and how long it took for them to show clinical signs
Variability of incubation and latent periods
- Periods are often expressed as averages or narrow ranges. In reality, there is a lot of variation between individuals.
- Study by infecting people with pathogen, saw a lot of variation
Incubation and latent period of Rabies
- Incubation period: 3-12 weeks
- Latent period: depends on how long it takes to get to brain (where the bite occurred)
- Illness: 7 days
Characteristics of Agent in relation to communicable disease
- Infectivity
- Pathogenicity
- Virulence
- Immunogenicity
- Physical Stability
Infectivity
Proportion of those individuals exposed who become infected
Pathogenicity
Proportion of infected individuals who develop clinically apparent disease
Virulence
Proportion of clinically apparent cases that are severe or fatal
Immunogenicity
Capacity to produce specific and lasting immunity in the host
Physical Stability
Ability to survive independently in environment
Outbreak
An increase (often sudden) in the observed number of cases of a disease or health problem compared with the expected number for a given place or among a specific group of animals/people over a particular period of time
What is needed to determine outbreak?
Need to have data showing what we would expect in the population. When infected number is more than expected, than it is considered an outbreak
Ex. Foot and mouth in Canada. One case would be an outbreak
Epidemic
- The occurrence in a community or region of cases of an illness, specific health-related behaviour, or other health-related events clearly in excess of normal expectancy
- Very similar to outbreak
Difference between outbreak, epidemics, pandemics
- Outbreak used for localized epidemic (village, town, school)
- Outbreak/epidemics occur over a very wide area, affecting a large proportion of population in several countries/continents is a pandemic. Therefore pandemic= outbreak on global scale
Endemic
Endemic= a disease which is normally present or regularly found in a population
Ex. Johne’s disease is endemic in cows in North America
Issue with counting diseased animals and presenting data to public
Public often receives total case counts without a denominator
- Without denominator means we don’t know population, susceptible individuals etc.
Ex. COVID cases- we were given total number of cases but they never gave total population
What is required for counting cases?
- Need a case definition which ensures that cases are counted consistently from time and place. Also ensured that expected and observed numbers are best compared.
- Can count infected, exposed, diseases, dead
- Can help show timing of disease and the “lag time” involved in latent period and incubation period, and total duration
- Need a denominator. The size of the population at risk
Case Definition
A standard set of criteria that investigators in an epidemiological investigation use to decide whether an individual should be classified as having the disease of interest
- Does not always need a laboratory diagnostic test
- Different than a clinical diagnosis
Three categories of case definitions
- Confirmed- typical clinical features of the illness or agent as well as either a laboratory test confirming the presence of the agent or an epidemiological link to a laboratory confirmed case
- Probable- typical clinical features of the illness or agent but no lab confirmation or epi link
- Possible- fewer typical clinical features of the illness and no laboratory confirmation or epi link
Issues with identifying, finding, and counting cases
- Infected individuals may not seek health care
- Not all cases get reported
- Reported cases may not be representative of all cases. Mild disease may not be reported. There is a bias of what level of individuals get included in data
- Investigators must “case find” in order to get representative data
- Sometimes an outbreak occurs because we do a better job of looking for and identifying cases (better diagnostic tests, availability of tests, look harder)
Cluster of Cases
- A geographical or temporal group of cases that seem to be greater than the expected number of the given place and/or time
- Orienting the cases by space, time , and animal is important at population level and can determine the risk factors
Ex. outbreak is occurring in all heifers
Temporal variations of disease
- Seasonal patterns
- Cyclical fluctuations (eg. Measles)
- Secular trends (long term movement). Result of environmental changes, diagnostic changes, or medical changes
**Rarely completely random
Seasonal Patterns
- Arthropod borne outbreaks (usually has gradual build up or amplification)
- Related to environment and climate (Eg. Foot rot in feedlot cattle)
- Individuals actions during different times of year (eg. Influenza, people spend more time inside during winter)
- Related to demographics in seasonal industry (Eg. Calf scours in beef herds)
Time
- Disease events in populations all take place in a continuum of time
- Quantifiable. Provides a scale to help measure disease
Prevalence
The proportion of cases or infections in the population at one particular point of time (“Snapshot in time”)
- No distinction between old and new cases as it includes both
What does prevalence represent?
Represents the proportion of infected at a given point in time
Prevalence example (20 cows are lame in a herd of 200 dairy cows)
Prevalence of lameness= 20/200 = 0.1 = 10%
Point Prevalence vs. Period prevalence
- Point prevalence- strictly looking at the prevalence at a point in time
- Period prevalence- looking at the population of a period of time (eg. samples taken from September to December)
Prevalence and behaviours
Prevalence can also be used to assess the frequency of behaviours or characteristics that might be risk factors or protective factors for disease
Ex. prevalence of smoking
Is prevalence a proportion or a rate?
A proportion
Incidence
The measure of the occurrence of new cases of disease (or some other outcome) during a span of time
Methods for calculating incidence
- Incidence risk
- Incidence Rate
Incidence Risk (R) definition
The probability (risk) that an individual animal will contract or develop a disease during a defined time period
- Better for static populations (keeps denominator consistent)
- Only looks at new cases
- No units (range from 0-1)
- Also great for looking at specific events (eg. calving)
Incidence Rate (I)
The number of new cases of disease in a population per unit of animal-time during a given time period
- Looks at the rapidity with which new cases develop over time
Incidence risk equation
Number of individuals that become diseased during a certain period of time divided by number of healthy individuals in the population at the beginning of that period
Incidence risk and relationship with period length
The longer the period, the greater the risk
Ex. the risk of a cow having a case of clinical mastitis in the next year vs. the risk of having a case of mastitis in the next week
Attack Rates
Used to describe the frequency of disease in outbreak situations
- Calculation: Number of cases/size of population exposed
- Used in cases where the risk period is limited and all cases are likely to occur within that risk period (eg. Food poisoning from wedding)
Secondary Attack Rates
Used to describe the infectiousness of an agent/ease of spread
Calculation: (Number of cases- initial cases)/population at risk
Ex. There is a spread of a pathogen within a herd or family and not all cases have resulted from a common source exposure
One household member gets COVID and brings it home and other family members get sick
Case Fatality Rates
The proportion of animals with a specific disease that die from it (within a specified time period)
Used to describe the impact of epidemic-type disease or the severity of acute diseases
Is case fatality considered a rate or proportion?
A risk measure/proportion
What needs to be taken into account when determining case fatality rates?
Need to ensure proper denominator
- Need case definition
- How extensive was the case finding done?
- Was both severe and mild cases identified?
- How much diagnostic testing was performed?
What category does attack rate and case fatality rate fall into?
Both are specific examples of incidence risk
Ex. Food poisoning
- Attack rate: number of confirmed cases in time period
- Case fatality rate: proportion of cases that go on to die
If during one week period, 20 cats in a cattery get sick, and there are 100 healthy cats at start of the week. During the next week, 8 more cats get sick. What is incidence risk at week 1, week 2, and overall?
Week 1: 20/100= 0.2 = 20%
Week 2: 8/80= 0.1 = 10%
Overall: 28/100= 0.28= 28%
There are 50 cats in the cattery and 72 cats get sick in a 1 year period. What is the incidence rate? (years, months, weeks)
72/50= 1.44 cases per cat-year
1.44 cases per cat year= 0.12 cases per cat-month= 0.028 cases per cat-week
Incidence rate equation
Number of cases of disease in a defined period of time/ (number of animals time units at risk during the time period)
When calculating incidence rate, do you include animals that have previously been sick?
No, generally incidence rates only use the first occurrence of the disease for each animal because once an animal has the disease they are no longer considered a part of the population that is at risk even though they are still part of the population
Incidence rate (approximate method)- Equation and description
Method used to take into account the animals that leave the population of risk (withdrawals, individuals that had the disease and recovered, purchases, births)
- Assumes that they will enter or leave population at the halfway point between the time period
Equation:
Number of new cases of disease that occur in a population during a particular time period/ ((number at risk at the start of the time period + number at risk at end)/2)
Incidence rate (exact method)
- Also called incidence density
- Method that takes into account the animals that leave and enter the population, but takes into account the exact amount of time each individual in the population was at risk
Ex. 1 cow for 6 years or 6 cows for 1 year = 6 cow-years at risk
Incidence rate example: 100 cows in herd observed for 1 year (2 months= 5 cows die, 5 months= 2 cows die, 8 months= 3 cows die)
5 x2 = 10 cow-months
2 x 5= 10 cow months
3 x 8= 24 cow months
10 dead cows total= 44 months of risk in total
90 cows survive the entire year= 90 x 12 months= 1080 animal months of risk
Incidence rate= 10/ (1080 +44)= 10/1124= 0.009 deaths per cow month= 9 deaths per 1000 cow months at risk
What can cause changes in prevalence?
- Changes in incidence rate
- Change in the average duration of disease
- Change in both incidence and duration
