Unit 8 Slides Epidemiology PDF

EPIDEMIOLOGY • Epidemiology is study of disease patterns in populations • Epidemiologists (health detectives) ! ! ! ! ! Collect, compile data about sources of disease and risk factors Design infection control strategies Prevent or predict spread of disease Use expertise in diverse disciplines incl...

EPIDEMIOLOGY • Epidemiology is study of disease patterns in populations • Epidemiologists (health detectives) ! ! ! ! ! Collect, compile data about sources of disease and risk factors Design infection control strategies Prevent or predict spread of disease Use expertise in diverse disciplines including ecology, microbiology, sociology, statistics, and psychology Influences our daily lives (hand washing, waste disposal, restaurant/food inspection, water treatment) PRINCIPLES OF EPIDEMIOLOGY • Communicable (contagious) diseases ! ! ! Transmitted from one host to another ! E.g., measles, colds, influenza Transmission determined by interactions between environment, pathogen, and host Control of any of these factors may break infection cycle ! E.g., improved sanitation (prevent infection); antimicrobial medications (kill or inhibit pathogens); vaccination (increase host resistance) • Non-communicable diseases ! ! ! Do not spread from host to host Microorganisms most often arise from individual’s normal microbiota or environment (e.g., Clostridium tetani) Legionnaire's disease causes outbreaks and has an “infection cycle” that must be broken (find and clean the contaminated water supply) but the bacteria doesn’t spread from person to person. RATES OF DISEASE IN A POPULATION • Epidemiologists less concerned with absolute number of cases than rate (consider small vs. large city) • Attack rate is percentage of people who become ill in population after exposure ! Reflects infectious dose, immune status of population • Incidence rate is number of new cases/time/population ! Measure of risk of an individual contracting a disease • Prevalence is total number of cases at any time or for a specific period in a given population ! ! Reflects overall impact of disease on society; includes old and new cases, as well as duration of disease Both expressed as cases per 100,000 people RATES OF DISEASE IN A POPULATION • Morbidity reflects the burden of disease in population at risk ! Contagious diseases (e.g., influenza) often have high morbidity rate: infected individual may transmit to several • Mortality is overall death rate in population ! ! In developed countries, most often associated with non-communicable diseases (e.g., cancer, heart attack) Infection is major cause of death in developing countries • Case-fatality rate is % of population that dies from a specific disease ! ! Plague feared because of very high rate Rate for AIDS has decreased from improved treatment; prevalence has increased as more with disease survive THE 2014-2015 EBOLA OUTBREAK Ebola in Guinea, Sierra Leone and Liberia - cases as of March 2015 Confirmed) Cumula&ve) cases) Cases)in)past) 21)days) 14,333) 384) Probable) 2556) Suspected) 7045) TOTAL) 23934) 384) Cumula&ve) deaths) 9792) The)overall)case)fatality)rate)is)9792/23934)=)41%) EBOLA OUTBREAK 2014-2015 The overall case fatality rate is 9792/23934 = 41% In Guinea = 66% In Liberia = 44% In Sierra Leone = 31% (spent $62 per person per year on health in 2011) (spent $92 per person per year on health in 2011) (spent $192 per person per year on health in 2011) (Canada = $4541 per person in 2011) THE 2014-2015 EBOLA OUTBREAK cumulative number of confirmed and probable Ebola cases as of March 2015 data from World Health Organization (www.who.int) The outbreak started exactly one year prior – March 2014 The incidence rate in Liberia is 144 people per 100,000 this year RATES OF DISEASE IN A POPULATION • Endemic diseases constantly present in population E.g., common cold • Outbreak is a higher than expected cluster of disease cases over a specific time in a population • Epidemic is unusually large number of cases – usually over a larger region ! Introduced or endemic disease • Pandemic is global (e.g., AIDS) 8 Percent)of)deaths) ! 10 6 ) Epidemic threshold Seasonal (endemic) baseline Actual percentage of total deaths in the population 4 ) 0 ) ) 5 15 25 35 45 5 15 25 35 45 Year 1 Year 2 ) ) 5 15 25 35 45 5 15 25 35 45 Year 3 Year 4 Weeks of the year ) 5 CDC,)MMWR)45(6):)135,)1996) Copyright © The McGraw-Hill Companies, Inc. www.cdc.gov, March 8, 2015 DESCRIPTIVE STUDIES Collect data that characterize occurrence (time, place, individuals affected) of an outbreak – used to compile risk factors for spread • The Person: Determining profile of people who become ill ! E.g. age, gender, ethnicity, occupation, personal habits, previous illnesses, socioeconomic class, marital status may all yield clues about risk • The Place: Geographic location helps pinpoint source, yield clues about potential reservoirs, vectors, or boundaries that may affect transmission • The Time: Season important; also rate of spread OUTBREAK EPIDEMIOLOGY • Common-source epidemic/outbreak: ! ! ! Rapid rise in cases suggests exposure to single source of pathogen Example: Food poisoning from a contaminated product Requires tracing to find what all victims have in common ! Did they eat at the same restaurant? Visit the same park? • Propagated epidemic: slow rise in cases suggests contagious disease spreading in population ! ! first case is called the “index case” or “patient zero” requires contact tracing to find potential new victims • Some have features of both common-source and propagated epidemic. SINGLE SOURCE – FOOD POISONING AT A LOUISIANA PSYCHIATRIC HOSPITAL MMWR August 17, 2012 / 61(32);605-608 MEASLES OUTBREAK 2015 = SINGLE SOURCE (DISNEYLAND) TRIGGERING A PROLONGED OUTBREAK DUE TO PROPAGATION Zipprich J, Winter K, Hacker J, Xia D, Watt J, Harriman L. Measles outbreak—California, December 2014-February 2015. MMWR. 2015:64(Early Release):1-2. ANALYTICAL STUDIES Determine relevancy of risk factors from descriptive study • Cross-Sectional Studies: Surveys range of people at a single point in time for presence/absence of disease ! May suggest associations between risk factors & disease but does not establish cause of disease • Retrospective Studies: Actions and events following outbreak compared ! ! Case-control study attempts to identify causative chain of events leading to disease Individuals who developed disease vs. healthy controls • Prospective Studies: Looks ahead from prospective studies ! ! Predicts tendency to develop disease Cohort groups with known exposure to risk factor are selected and followed over time OUTBREAK CONTAINMENT • Critical to containing an outbreak of contagious disease like Ebola or measles is aggressively tracking down those who may have been exposed through “contact tracing” ! ! ! Interview patients and families Check hospital records for where and when patient stayed and who was in the same ward Inform and monitor contacts for disease CS250727A CONTACT TRACING – MEASLES 2015 • Contact tracing was visible during the measles outbreak of 2015. • York Region Public Health contacted everybody who had been to a clinic on the same day that a measles patient had been there. Those people were told to monitor themselves for the next two weeks for disease. • A mother of a 15-day old infant who had been to the clinic that day posted an angry Facebook post to anti-vaxers saying “I blame you” if her son developed measles. The post went viral. • The child did not get measles. QUARANTINE VS. ISOLATION • Isolation (common) ! A person who carries the disease causing microbe (sick or not) is placed in special isolation units that separate them from the rest of the patient population. • Quarantine (rare) ! An outwardly healthy individual showing no signs of disease is held in isolation in case they carry the disease to prevent spreading it to others. The “Yellow Jack” flown on a ship indicates it is under quarantine RESERVOIRS OF INFECTION • Natural habitat in which pathogen lives ! In or on animal, human, or in environment (soil, water) Environment Animals (domestic) Humans • Identification important in disease control ! ! E.g., control of rats, mice, prairie dogs (reservoirs of Yersinia pestis) prevents plague epidemics in U.S. Can prevent contact with disease Animals (wild) (top):)©)Amanda)Clement/GeQy)Images;)(boQom):)©)Corbis)Digital)Stock)CD) Copyright © The McGraw-Hill Companies, Inc. RESERVOIRS OF INFECTION Human Reservoirs • May be exclusive or exist in other animals, environment • Often easier to prevent and control ! E.g., Smallpox (vaccination, identification of infected humans) • Symptomatic infections: obvious source of pathogens ! Precautions can usually be taken (incubation period) • Asymptomatic infections: harder to identify, may not realize they habor pathogen or show clinical symptoms, can shed/spread to others ! ! Up to 50% of women infected with Neisseria gonorrhoeae are asymptomatic, easily transmit Many people carry Staphylococcus aureus RESERVOIRS OF INFECTION Non-Human Animal Reservoirs • Common ! ! E.g. Chicken (Campylobacter & Salmonella) E.g. Raccoon, skunks, bats (Rabies virus) • Zoonoses (zoonotic diseases) primarily exist in animals but can be transmitted to humans (e.g., plague, rabies) Environmental Reservoirs • Difficult or impossible to eliminate ! E.g. Soil (Clostridium botulism, Clostridium tetnai, Nagleria) DISEASE TRANSMISSION • Vertical transmission is pregnant woman to fetus or mother to infant during childbirth, breast feeding • Horizontal transmission is person to person via air, physical contact, ingestion of food or water, or vector Airborne Indirect contact Direct contact Vectors Food/water (phone): © Ryan McVay/Getty Images; (hands): © Randy Allbritton/Getty Images; (sneeze): © Kent Wood/Photo Researchers; (tick): Courtesy of University of Nebraska/Department of Entomology; (foods): © Mitch Hrdlicka/Getty Images; Copyright © The McGraw-Hill Companies, Inc. PORTALS OF ENTRY AND EXIT • Entry or exit route for pathogen ! ! ! ! ! Eyes Broken skin Digestive Intestinal tract: ingestion of microbe in tract water or food - shed in feces (e.g., Vibrio cholerae, E. coli, Salmonella, Norovirus) Respiratory tract (e.g., M. tuberculosis, respiratory viruses like influenza) Genitourinary tract: semen, vaginal secretions (e.g., Neisseria gonorrhoeae, HIV) Bloodstream (HIV by contaminated needle or blood transfusion, malaria by mosquitos) Ears Respiratory tract Broken skin Genitourinary tract Copyright © The McGraw-Hill Companies, Inc. DISEASE TRANSMISSION • Direct Contact (infected individual has to touch uninfected person): handshake, sexual intercourse ! ! ! ! Some pathogens cannot survive in environment, require intimate, usually sexual, contact (e.g., Treponema pallidum, Neisseria gonorrhoeae) Infectious dose important (e.g., E. coli can happen from handshake) From hands, can be ingested: fecal-oral transmission Hand washing considered single most important measure for preventing spread of infectious disease • Indirect Contact with inanimate objects (fomites) ! Clothing, table-tops, doorknobs, light switches, drinking glasses DISEASE TRANSMISSION • Droplet Transmission: respiratory droplets generally fall to ground within a meter from release – considered contact transmission ! ! Important source for densely populated buildings (schools, military barracks) Spread minimized by covering mouth when sneezing CDC image library DISEASE TRANSMISSION • Air: respiratory diseases commonly transmitted through the air ! Talking, laughing, singing, sneezing, coughing, airborne particles (dust, soil) generate ! Droplet nuclei (microbes attached to dried material) remain suspended • Particles >10µm usually trapped by mucus lining nose and throat (all):)©)Joan)K.)Mann) • Air sample cultures - number of bacteria in air proportionate to number of people • Airborne transmission difficult to control ! Ventilation systems, negative pressure, HEPA filters attempt to prevent spread Copyright © The McGraw-Hill Companies, Inc. DISEASE TRANSMISSION • Food and Water: can become contaminated, infect digestive tract ! ! ! Municipal water systems can distribute to large numbers ! E.g., 2000 E. coli outbreak in Walkerton, Ontario. Cross-contamination: transfer from one food to another ! Refrigeration & good foodhandling practices are key to prevention Animal products (meat, eggs) have pathogens from animal’s intestines DISEASE TRANSMISSION • Vectors: living organisms that can carry pathogen ! ! ! Most commonly arthropods: mosquitoes, flies, fleas, lice, ticks Can carry internally or externally, can be mechanical or biological ! E.g. Malaria, plague, lyme disease (internal); E. coli, Shigella (external) Vector control important in preventing diseases Mechanical vector Biological vector Copyright © The McGraw-Hill Companies, Inc. PATHOGEN FACTORS THAT INFLUENCE EPIDEMIOLOGY OF DISEASE Virulence: ability to cause disease and how severe ! Factors that allow pathogen to adhere to or penetrate host cell, thwart immune defenses, damage host Dose: minimum number of pathogens required ! ! Doses below minimum necessary may produce asymptomatic infection: immune system eliminates organism before symptoms appear Very large dose (e.g., laboratory accident) may produce serious disease even in normally immune individual Incubation Period: influences extent of spread ! Long incubation period can allow extensive spread ! E.g., 1963 typhoid fever in ski resort in Switzerland ! 10,000 individuals drank water containing Salmonella enterica serovar Typhi; 10–14 day incubation allowed spread to at least 6 different countries HOST FACTORS THAT INFLUENCE EPIDEMIOLOGY OF DISEASE Immunity to Pathogen: previous exposure, immunization • Herd immunity protects non-immune individuals in population; >90% immunity typically sufficient • Antigenic variation can overcome (e.g., avian influenza) General Health: malnutrition, overcrowding, fatigue • Developing world more susceptible • Good general health increases resistance or asymptomatic disease Age: very young, elderly generally more susceptible • Immune system less developed in young; wanes in old • Elderly also less likely to update immunizations HOST FACTORS THAT INFLUENCE EPIDEMIOLOGY OF DISEASE Religious and Cultural Practices: • Breastfeeding provides protective antibodies to infant • Consumption of raw fish can increase exposure (e.g., freshwater fish and tapeworm Diphyllobothrium latum) • Burial practices spreading Ebola in Africa Gender: • Women more likely to develop urinary tract infections ! ! Urethra is shorter; microbes more likely to ascend Pregnant women more susceptible to listeriosis Genetic Background: • Natural immunity varies widely • Specific receptors may differ (e.g., lack of receptor on red blood cell yields immunity to Plasmodium vivax; lack of receptor on white blood cell reduces susceptibility to HIV) A mysterious illness arrives in Toronto • Late 2002: Cluster of unusual pneumonia-like cases occur in southern China • February 2003: Travellers from Hong Kong spread illness to Vietnam, Singapore and Canada • March 2003: Disease spreads throughout Toronto hospitals • April 12: Canadian scientists publish the genome of the virus • April 23: WHO issues travel advisory for travel to Toronto • July 2003: Global outbreak is declared over Centers for Disease Control and Prevention, 2017 Emerging infectious diseases Newly emerging • Recognized to infect humans for the first time • Example: Ebola emerged in humans for the first time in 1976 • Example: SARS emerged in humans for the first time in 2002 Re-emerging • Increasing after years of decline, or in a more pathogenic form, or in a new geographic location Ebola virus. CDC • Example: Tuberculosis and malaria, partly due to emergence of antimicrobial-resistant pathogens • Example: Measles and pertussis, due to reduced vaccination Mycobacterium tuberculosis bacteria. CDC NIH Zoonotic pathogens as emerging diseases Where do diseases emerge from? • 60-80% of human diseases likely originated in animals (rodent, bats) • Bats are the natural reservoir for a number of highly pathogenic viruses • Direct or intermediate transmission Natural host Transmission host Terminal host Bean et al. Nature Reviews Immunology (2013) Factors contributing to emergence of disease Microbial agent Genetic adaptation and change Polymicrobial diseases Examples: • Development of antimicrobial resistance O139 • Vibrio cholerae serotype O139 gained ability to produce a capsule • Infection with the measles virus increases susceptibility to Mycobacterium tuberculosis O1 0.1 μm Adapted from Meno et al. Arch Microbiol (1998) Adapted from Morens DM, Fauci AS (2013) Emerging Infectious Diseases: Threats to Human Health and Global Stability. PLOS Pathogens 9(7): e1003467. https://doi.org/10.1371/journal.ppat.1003467 Factors contributing to emergence of disease Human Host Human susceptibility to infection Human demographics and behaviour International trade and travel Intent to harm (bioterrorism) Occupational exposures Inappropriate use of antibiotics CDC: Overview of Tuberculosis Epidemiology in the United States Examples: • Complacency regarding tuberculosis led to a resurgence in the USA • Leishmaniasis in adventure travelers to South America • Deliberate release of infectious agents (bioterrorism) Adapted from Morens DM, Fauci AS (2013) Emerging Infectious Diseases: Threats to Human Health and Global Stability. PLOS Pathogens 9(7): e1003467. https://doi.org/10.1371/journal.ppat.1003467 Factors contributing to emergence of disease Human Environment Climate and weather Changing ecosystems Economic development and land use Technology and industry Poverty and social inequality Lack of public health services War and famine Lack of political will Animal populations Examples: • Acanthamoeba infections associated with wear of contact lenses • Increasing temperatures can increase the geographic range of vectors that may carry disease • Deforestation two years before an ebola outbreak The Guardian: Joerg Boethling/Alamy (2017) Adapted from Morens DM, Fauci AS (2013) Emerging Infectious Diseases: Threats to Human Health and Global Stability. PLOS Pathogens 9(7): e1003467. https://doi.org/10.1371/journal.ppat.1003467 • • • • Emerging viral pathogen: MERS coronavirus First identified in humans in 2012 Respiratory illness; often fatal Reported in 27 countries, with a fatality rate of 35% Reservoir may be dromedaries Centers for Disease Control and Prevention, 2017 World Health Organization , 2017 • • • • Emerging viral pathogen: MERS coronavirus First identified in humans in 2012 Respiratory illness; often fatal Reported in 27 countries, with a fatality rate of 35% Reservoir may be dromedaries Centers for Disease Control and Prevention, 2017 Human Host World Health Organization , 2017 • • • • Emerging viral pathogen: MERS coronavirus First identified in humans in 2012 Respiratory illness; often fatal Reported in 27 countries, with a fatality rate of 35% Reservoir may be dromedaries Centers for Disease Control and Prevention, 2017 Human Host Microbial agent World Health Organization , 2017 Emerging viral pathogen: Candida auris • Causes bloodstream infections in healthcare settings around the world Countries from which Candida auris cases have been reported, as of September 30, 2017 Centers for Disease Control and Prevention, 2017 Emerging viral pathogen: Candida auris • Causes bloodstream infections in healthcare settings around the world Why is C. auris a problem? Centers for Disease Control and Prevention, 2017 • Resistant to the most common class of antifungal, azoles • Some isolates have shown resistance to the other classes of antifungals • Appears to be transmitted through healthcare settings Centers for Disease Control and Prevention, 2017 Emerging viral pathogen: Candida auris • Causes bloodstream infections in healthcare settings around the world Why is C. auris a problem? Centers for Disease Control and Prevention, 2017 • Resistant to the most common class of antifungal, azoles Microbial agent • Some isolates have shown resistance to the other classes of antifungals • Appears to be transmitted through healthcare settings Centers for Disease Control and Prevention, 2017 Emerging viral pathogen: Candida auris • Causes bloodstream infections in healthcare settings around the world Why is C. auris a problem? Centers for Disease Control and Prevention, 2017 • Resistant to the most common class of antifungal, azoles Microbial agent • Some isolates have shown resistance to the other classes of antifungals • Appears to be transmitted through healthcare settings Human Host Centers for Disease Control and Prevention, 2017 Recent outbreak of Vibrio cholerae Bacterial pathogen • • Extremely virulent, causes acute diarrhoea • Secretes a toxin that binds to epithelial cells in the intestine • Two patterns of disease: endemic and epidemic Centers for Disease Control and Prevention, 2017 What caused the current outbreak? • As of October 1, 2017: over 750,000 people in Yemen have been infected, and over 2000 have died • Civil war in Yemen lasting almost 2 years • Lack of food, clean drinking water and healthcare infrastructure NY Post, AP, 2017 Recent outbreak of Vibrio cholerae Bacterial pathogen • • Extremely virulent, causes acute diarrhoea • Secretes a toxin that binds to epithelial cells in the intestine • Two patterns of disease: endemic and epidemic Centers for Disease Control and Prevention, 2017 What caused the current outbreak? • As of October 1, 2017: over 750,000 people in Yemen have been infected, and over 2000 have died • Civil war in Yemen lasting almost 2 years • Lack of food, clean drinking water and healthcare infrastructure Human Environment NY Post, AP, 2017 Response to emerging infectious diseases Worldwide • The World Health Organization has a major role in tracking emerging infectious diseases worldwide • Curates a list of top priority emerging diseases Canada Public Health Agency of Canada • Provide federal leadership in managing national public health events Public Health Ontario • Shapes policies and practices to prevent illness and promote health Communicable disease epidemiology and modeling Ashleigh Tuite, PhD MPH MSc ep·i·de·mi·ol·ogy The study of how often diseases occur in different groups of people and why 2 Why are communicable diseases different? • A fundamental property of communicable diseases is transmission • Current cases produce future cases Osteoporosis 3 Why are communicable diseases different? • A fundamental property of communicable diseases is transmission • Current cases produce future cases Measles • When current cases produce on average > 1 new case, have an exponential increase in case numbers, a.k.a., an “epidemic” 4 What’s the big deal with exponential growth? 600,000 R0 = 2 Number of cases 500,000 400,000 300,000 200,000 100,000 0 0 2 4 6 8 10 Generation 12 14 16 18 20 What’s the big deal with exponential growth? 1,400,000,000 1,200,000,000 R0 = 3 Number of cases 1,000,000,000 800,000,000 600,000,000 400,000,000 200,000,000 R0 = 2 0 0 2 4 6 8 10 Generation 12 14 16 18 20 Basic reproduction number (R0) • Average number of secondary infections generated by a primary infection in a susceptible population • For an epidemic to grow in the early stages of spread, more than one new case must be generated by each primary case (i.e. R0>1) • When R0 = 1, disease stays endemic 8 BASIC REPRODUCTION NUMBER (R0) How long is a person sick and able to infect others? How many people does the sick person come into contact with while they’re sick? What is the probability that the sick person infects a healthy person if they do come into contact? We rarely observe the basic reproduction number in real life • When we recognize a communicable disease outbreak, we generally react: • Implementation public health control measures • Change our behaviours • Over time, as people become infected, we may become immune to reinfection • Susceptible people provide the “fuel” needed to sustain outbreaks • Immunity, either through recovery from infection or vaccination, deprives epidemics of the fuel they need to grow 11 Effective reproduction number (Rt) 12 • Average number of secondary infections generated by an infected individual at a given point in time • Does not assume a completely susceptible population or no interventions • Useful for monitoring epidemic control – essentially a snapshot of current transmission https://covid19.sph.hku.hk/ What is an epidemic model? • Models are simplified representations of reality • Structured way of thinking about the dynamics of an epidemic Available knowledge + Plausible assumptions à Logical implications • Allow us to evaluate counterfactual/“what-if” scenarios to try to understand what might happen if we make different policy decisions • Can be useful tools for decision making and identifying areas where we don’t have enough information 13 What is an epidemic model? • Many different types of models used to explain how communicable diseases spread in populations 14 Phenomenological Compartmental Describe epidemics without seeking to reproduce mechanisms Describe disease as ‘flow’ of infection between compartments, with feedback loops Deterministic Get the same result every time Agent-based Model populations as individuals Stochastic Incorporate random chance Models allow us to explore counterfactual scenarios Model projections • Can be really important in public health where we want to prevent bad things from happening • Models can help quantify the impact of prevention • E.g., how many infections averted or lives saved when a vaccination program is implemented in a population? Summary • When studying communicable disease epidemiology, need to account for transmission and the fact that a case is also a risk factor for other people • The basic reproduction number is an important characteristic of communicable diseases: • It tells us how transmissible a pathogen is and how difficult it may be to control it • By understanding the components of R0, we can also understand how and why we can use different tools to control transmission in populations • Epidemic models are useful tools for quantifying the impact of public health prevention measures, allowing us to simulate “alternate universes” where we take different courses of action 16 Thank you!