EPIDEM-MIDTERM-COVERAGE-PPT-NI-SIR.pdf

VPH 81: EPIDEM MIDTERM COVERAGE Describing Occurrence of Disease 4. Attack Rate Definitions: - Population at risk for only a limited period of time.  Morbidity – th...

VPH 81: EPIDEM MIDTERM COVERAGE Describing Occurrence of Disease 4. Attack Rate Definitions: - Population at risk for only a limited period of time.  Morbidity – the amount of the disease - Proportion of animals that develop the disease  Mortality – the number of deaths - Secondary attach rate – proportion of cases of a  Temporal distribution – times of occurrence of cases of a transmissible disease that develop as a result of disease contact with the primary case.  Spatial distribution – the places of occurrence of the Formula: disease  Demography – measurement and description of the size of populations and their characteristics Structure of Animal Populations 5. Mortality 1. Contiguous Population - Cumulative mortality: - One in which there is much contact between individuals in the population and members of other population. - Population of wild animals can be enumerated by - Death rate – total mortality rate for all diseases in a aerial and ground counts. population - A common method is capture-release recapture in - Case fatality – the tendency for a condition to cause which animals are caught, marked and released. A the death of affected animals in a specified time, second sample is then captured. presented as percentage. 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑑𝑒𝑎𝑡ℎ𝑠 Formula: 𝐶𝐹 = 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑑𝑖𝑠𝑒𝑎𝑠𝑒𝑑 𝑎𝑛𝑖𝑚𝑎𝑙𝑠 ^ N = an/r Where: 6. Survival - N = estimated population size - Probability of individuals with a specific disease - a = number of individuals initially marked remaining alive for a specified length of time. - n = number of individuals in the second sample 𝑁−𝐷 - 𝐶𝑀 = 𝑁 - r = number of marked individuals recaptured in the second sample o D = no. of death observed in a specified period o N = no. of newly diagnosed cases under observation during the same period of time 2. Separated Population - Occur as discrete units such as herds and flocks - Closed – with no movement of animals into or out of 7. Crude, Specific and Adjusted Rates the unit; open – with limited movements in and out - Crude rates = summary rates based on the actual number of events in a total population over a given Measures of Disease Occurrence time period; they take no account of the structure of 1. Rates, Ratios and Proportion the population affected. - A ratio expresses the relationship between two - Specific rates = measures of disease that describe numbers (ratio of male to female births) disease occurrence in specific categories of the male:female population related to host attributes such as age, - A proportion is a specific type of ratio in which the sex, breed and method of husbandry. numerator is included in the denominator and the - Adjusted (Standardized) measures = presents one resultant value is expressed as a percentage. summary figure for a total population, but statistical - A rate is a special form of proportion that includes procedures are carried out to remove the effect of specification of time. differences in the composition of various populations (for comparative purposes) 2. Prevalence - The number of instances of disease or related attributes in a known population at a designated time, without distinction between old and new cases o Point prevalence – prevalence where time is not specified. o Period prevalence – number of cases that are known to have occurred during a specified period of time (e.g., a year) Formula: 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 ℎ𝑎𝑣𝑖𝑛𝑔 𝑎 𝑑𝑖𝑠𝑒𝑎𝑠𝑒 𝑎𝑡 𝑎 𝑝𝑎𝑟𝑡𝑖𝑐𝑢𝑙𝑎𝑟 𝑝𝑜𝑖𝑛𝑡 𝑖𝑛 𝑡𝑖𝑚𝑒 = 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑖𝑛 𝑡ℎ𝑒 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 𝑎𝑡 𝑟𝑖𝑠𝑘 𝑎𝑡 𝑡ℎ𝑎𝑡 𝑝𝑜𝑖𝑛𝑡 𝑖𝑛 𝑡𝑖𝑚𝑒8. Displaying Demographic Data - Tables 9. Bar charts 3. Incidence - Time trend graphs - The number of new cases that occur in a known - Mapping population over a specified period of time. o Geographic base maps o Cumulative incidence (CI) proportion of o Point (dot or location) maps nondiseased individuals at the beginning of a o Distribution maps period of study that become diseased during the o Proportional circle maps period o Choroplethic maps – discrete shaded units of o Incidence rate, measures the rapidity with which area new cases of disease develop over time. o Isoplethic maps (contour maps) (isomorbs and Formula: isomorts) 𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑒𝑤 𝑐𝑎𝑠𝑒𝑠 𝑜𝑓 𝑑𝑖𝑠𝑒𝑎𝑠𝑒 𝑡ℎ𝑎𝑡 𝑜𝑐𝑐𝑢𝑟 𝑖𝑛 𝑎 𝑝𝑜𝑝𝑢𝑙𝑎𝑡𝑖𝑜𝑛 𝑑𝑢𝑟𝑖𝑛𝑔 𝑎 𝑝𝑎𝑟𝑡𝑖𝑐𝑢𝑙𝑎𝑟 𝑝𝑒𝑟𝑖𝑜𝑑 𝑜𝑓 𝑡𝑖𝑚𝑒 o Geographic information system (GIS) = computerized systems for collecting, storing, 𝑇𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝑒𝑥𝑝𝑜𝑠𝑒𝑑 𝑡𝑜 𝑡ℎ𝑒 𝑝𝑟𝑖𝑚𝑎𝑟𝑦 𝑐𝑎𝑠𝑒 managing, interrogating and displaying spatial data. kting Page 1  VPH 81: EPIDEM MIDTERM COVERAGE Application of GIS - Paratenic host – a host in which an agent is - Cartography transferred mechanically, without further - Neighborhood analysis development. - Buffer generation - Intermediate host – an animal in which an infectious - Overlay analysis agent undergoes some development, frequently - Network analysis with asexual reproduction. - Three-dimensional surface modelling - Amplifier host – an animal which may suddenly increase the amount of infectious agent Determinants of Disease - Hibernating host – an animal in which an agent is A. Classification of determinants held probably without replication, in a state of - Primary and secondary suspended animation. - Intrinsic and extrinsic - Incidental/accidental host – one that does not - Host, agent or environment usually transmit an infectious agent to other B. Primary determinants – factors whose variations exert a animals. major effect in inducing disease - Link host – a host that forms a link between other C. Secondary determinants – correspond to predisposing, host species (in JE; pigs – herons – man) enabling and reinforcing factors - Reservoir host – one in which the infectious agent D. Intrinsic determinants – internal to the host normally lives and multiplies and therefore is the (endogenous) common source of infection Extrinsic and Intrinsic Determinants Vectors:  Extrinsic – determinants external to the host - Mechanical vector – an animal that physically carries  Host determinants: an infectious agent to its primary or secondary host. - Genotype - Biological vector – a vector in which an infectious - Age agent undergoes either a necessary part of its life - Sex cycle. - Species and breed o Developmental transmission – essential phase of development occurring in the vector (e.g., Agent Determinants Dirofilaria immitis)  Virulence and pathogenecity o Propagative – agent multiplies in the vector - Virulence – ability of an infectious agent to cause (virus in ticks in louping ill) disease o Cyclopropagative – combination of - Pathogenicity – quality of disease induction developmental and propagative (e.g., Babesia in  Gradient of infection ticks) - Inapparent infection - Clinical infection Associated Factors  Outcome of infection  Factors associated with spread of infection: - Carrier state (incubatory, convalescent) - Characteristic of hosts - Latent infection - Characteristics of pathogen - Effective contact Environment as a Determinant  Methods of transmission:  Location - Ingestion  Climate - Aerial transmission - Microclimate - Contact - Macroclimate - Inoculation  Husbandry - Iatrogenic (created by a doctor) - Housing - Coitus - Diet  Vertical transmission - Management - Hereditary – carried within the genome of either - Stress parent - Congenital – disease acquired either in utero or in Transmission and Maintenance of Infection ovo. Transmission can occur at various stages of Horizontal transmission development  Horizontal transmission – transmitted from any segment of the population to another Ecology of Disease - Direct – by physical contact with an infected host or Basic Ecological Concepts with discharges 1. The distribution of population - Indirect – involves intermediate vehicle living or - Vegetational zones inanimate that transmit infection between infected o Megatherms (rainforests) and susceptible hosts. o Mesotherms (deciduous forest) o Xerophiles (deserts) Host and Vector - Bronies – life zones (with particular range of plants  Types of hosts and vector: Host – a plant or animal or and animals) arthropod that is capable of being infected with and o Tropical rain forest therefore giving sustenance to an infectious agent. o Savannah Replication or development of the agent usually occurs in o Tundra the host. 2. Regulation of population size Hosts: - Balance of nature – population becomes stable with the rate of reproduction equaling the death rate. - Definitive host – a host in which an organism - Control of population size by competition – density undergoes its sexual phase of reproduction. dependent - Final host – synonym for definitive host - Dispersal – survival over large area as controlled by - Primary host – animal that maintains an infection in climate not competition for food. the endemic area. - Predation - Secondary host – a species that additionally is - Infectious disease involved in the life cycle of an agent. kting Page 2  VPH 81: EPIDEM MIDTERM COVERAGE - Home range – natural restriction to the area over  Common source and propagating epidemics: which they roam - Common source epidemic – one in which all cases - Territoriality – part of animals’ home range that it are infected from a source that is common to all defends aggressively (territory); the behavior individuals (point source) response is territoriality. h. Social dominance (peck - Propagating epidemic – caused by an infectious order) agent in which initial (primary) cases excrete the - The “Wynne-Edwards hypothesis” [- population agent and thus infect susceptible individual which control was the main purpose of group behavior constitute secondary cases. The primary case is which sometimes causes physiological stress. generally the index case 3. The Niche - one species occupying a particular position - Examples of niches relating to disease Temporal Distribution of Disease o Louse infestations Trends in the Temporal Distribution of Disease o Intracellular parasitism  Short-term o Epidemiological interference – one arc filled by - Cyclical trends – associated with regular, periodic one organisms which cannot be filled by another fluctuations in the level of disease occurrence organism. (recurrent epidemics or endemic pulsations, 3-4 yr 4. Food Chain cycle) - Different levels in food chain (trophic level) - Seasonal trends – periodic fluctuations in disease - Significance of food webs to disease transmission incidence are related to particular seasons. 5. Ecosystems – complex composed of areas occupied by  Long-term plants and animals and their physical and climatic - Secular trends features - Occur over a long period of time and represent a - Biotype – smallest spatial unit providing uniform long-term interaction between host and parasite conditions for life. - Biocenosis – collection of living organisms in a Temporal Trends biotype  Detecting temporal trends: time series analysis - Types of ecosystems: - Free-hand drawing o Autochthonous – coming for the land itself - Calculation of rolling (moving averages_ arithmetic o Anthropurgic – one created by man, e.g., average of consecutive group of measures cultivated pastures, towns - Regression analysis – a statistical technique for o Synanthropic – one that is in contact with man investigating relationship between two or more (rubbish dumps) variables. o Ecological climax – when plants, animals microbes, soil and macroclimate have evolved The Nature of Data to a stable balanced relationship Classification of Data o Ecological interface – a junction of two  Qualitative (categorical) – describe a property of an ecosystem animal (e.g., breed and sex) o Ecological mosaic – modified patch of  Quantitative – relate to amounts (e.g., body weight, milk vegetation created by man within a biome that yield, temperature, antibody titer) has reached a climax - Discrete – can have only one of the specified set of 6. Landscape Epidemiology – study of diseases in relation values, such as whole numbers (e.g., number of teats to the ecosystem in a sow) (generate counts) - Nidality (nidi – foci as natural home of a disease); - Continuous data – may have a value within a Nosogenic territory – an area that has ecological, defined range (e.g., girth of cow, body weight) social and environmental conditions that can (generates measurements) support a disease. - Objectives of landscape epidemiology. Landscape Scales of Measurement epidemiology is founded on the concept that if the 1. Nominal (classificatory) scale – involves use of number nidality of diseases is based on ecological factors (or other symbols) to classify objects; e.g., male and then a study of ecosystem enables predictions to be female coded as 1 and 2. made about the occurrence of disease and facilitates 2. Ordinal (ranking) scale – allows groups to be related to the development of appropriate control strategiers. other group (e.g., carcass condition score scale; 5 = good and 1 = poor) Patterns of Disease 3. Internal scale – distance between the ranked values Epidemic Curves 4. Ratio scale – internal scale with a true zero point. - Representation of the number of new cases of a 5. Visual analogue scale (VAS) uses a straight line. disease by a graph - Each end has a verbal description of one extreme of  Factors affecting shape of the curve: the variable that is being measured - Incubation period of the disease - Infectivity of the agent - Proportion of susceptible animals in the population - Distance between animals Data Elements  Diseases are defined at three levels in relation to: - Specific causes - Lesions or deranged function - Presenting problems, e.g., parvovirus infection (specific cause); hepatitis (lesion); ataxia (presenting problem) - Ratio scale – internal scale with a true zero point. Sensitivity and Specificity  Sensitivity of a diagnostic method is the proportion of true positive that are detected by the method  Specificity of the method is the proportion of true negative that are detected kting Page 3  VPH 81: EPIDEM MIDTERM COVERAGE The Nature of Data  Accuracy, Refinement, Precision, Reliability and Validity - Accuracy – an indication of the extent to which an investigation or measurement conforms to the truth. - Refinement – degree of detail in a datum - Precision – consistency of a series of measurements (40% +2 / 40% +5) - Reliability – degree of agreement between sets of observation made on the same animals by the same observer - Reproducibility – agreement between sets of observation made on the same animals by different observers. - Validity – the diagnostic technique measures what it purports to measure. Bias - Any systematic error in the design, conduct or analysis of a study that renders results invalid. Types of Bias: - Bias due to confounding - Interview bias - Measurement bias - Selection bias kting Page 4