What is Tularemia
Bacteria, rabbits and rodents, ticks/deer fly/dust/etc, BIOTERROR. Ucler, fever, sore throat, diarrhea, pneumonia, etc. Incubation period 3 - 4 days
Viruses
HIV, West Nile, Hanta, Rabies, Measles
Bacteria
Lyme disease, Plague, Anthrax, TB, Tularemia.
Fungi
Cave disease, Candida,
Parasites
Malaria, Giardia, Nematodes, Guinea Worm
Prions
Kuru, Bovine spongiform encephalitis, Chronic Wasting Disease, Fatal familial insomnia,
Other than Viruses, bacteria, fungi, parasites, prions, what are other “disease agents”?
Cancers, Pollutants (Environmental/occupational), Socio-economic status (mental health, poverty, exposure)
Modes of transmission?
Contact (direct/indirect), Respiratory, Airborne, Vehicle-borne, Vector Borne, Vertical transmission,
Contact (direct/indirect)
via touch. (STD, Rhinovirus)
Respiratory droplets/secretion
via cough/sneeze
Airborne route
via Airborne (droplet nuclei, dust,) Eg. TB, measles, hantavirus
Two forms of airborne falling droplets
- Large droplets fall to the ground (rain) Eg. Ebola 3 feet. 2. small drops float in the air (fog) Eg. Measles 6 ft.
Vehicle-borne
Via ingestion, injection. (food, water, intra-venous injection). Eg Salmonella, norovirus, cholera, giardiasis, botulism, HIV hep B
Vector-Borne
Either Mechanical and/or biological. Ticks, mosquitos, fleas, etc. Lyme disease, malaria, yellow fever, Chaga’s, plague, etc.
Vertical transmission
From mother to offspring. Eg. Streptococcus, Toxoplasmosis, HIV, Hep B.
What is the anatomy of disease?
“DREEMS” - Disease agent (What is it?), - Reservoir / source? - Entry into host - Exit from infected host - Mode of transmission - Symptoms
Disease agent
virus, bacteria, fungi, prion, parasites.
EIDS
Emerging Infectious Diseases
Global trends of disease agents?
Yes. Trends vs outbreaks.
What is a Reservoir
Reservoir hosts of an infectious disease serve as a source of infection and sustain the pathogen in a population.
Index Case
The initial patient in the population sample of an epidemiological investigation. (Also: primary case or patient zero)
SARS
Severe Acute Respiratory Syndrome
Epidemic Curve
a graphic depiction of the number of outbreak cases by date of illness onset
Epidemic curves provide information on:
- Disease incubation period 2. Outbreak magnitude 3. Time Trend 4. Pattern of disease spread
Latent period
Between Infection and Infectious.
Infectious period
From infectious to cure / pathogen death
Incubation period
Between infection and onset of symptoms
Symptomatic period
Between Onset of symptoms and non-diseased
Early warning (infections)
symptoms precede infectiousness
Lag warning
Symptoms follow infectiousness
What is outbreak magnitude
- How many people are infected? Magnitude in sub-populations
What is a time trend? (epidemic curve)
Tells us if the disease is still spreading.
What is it called when cases acquire the infection from the same source?
Common source
Common source - point
Period of exposure is brief, and all cases occur within
Common source - continuous
often causes epidemic curve to rise gradually
Common source - intermittent
intermittent exposure often results in epidemic curve with irregular peaks, which reflect the timing and extent of the exposure
Propagated outbreak
spread from person to person, long lasting, multiple waves of infection. Each peak is slightly taller than the previous one. Each peak separated by an incubation period.
SARS movement
- Feb 2003, From Hong-Kong to Taipei 2. March 2003, Hong-Kong to Beijing
Case fatality ratio
number of deaths / number of cases
When can you declare disease free?
When two consecutive incubation periods pass without new cases.
Zoonotic disease is…
an animal to human transmission
Prevalence
= Number positive / number tested = number of positive samples / sample size
Koch’s postulates?
Koch’s postulates to identifying disease agents. 1. The organism is always found with the disease 2. the organism is not found with any other disease 3. The organism, isolated from one who has the disease, and cultured through several generations, produces the disease (in experimental animals)
Positive results mean what? (in testing for disease)
- Agent is present 2. Contamination 3. Random events
Negative results mean what? (in testing for disease)
- Target is absent 2. Failure to work 3. Random events
True positive is…
Positive results, has the disease
False positive is…
Positive test, does not have the disease
true negative
negative test, does not have the disease
false negative
negative results, has the disease
Test Validity
the ability to distinguish between presence and absence of a disease
Sensitivity
ability of test to correctly identify cases that HAVE THE DISEASE - Practice calculating
Specificity
ability of the test to correctly identify cases that DO NOT HAVE THE DISEASE - Practice calculating
Sensitivity calculation
TP / (TP + FN)
Specificity calculation
TN / (TN + FP)
What influences test validity ?
- Test Type - Sampling time of test - Prevalence of the disease (rare or common) - Number of times test is performed
What is PPV
Positive predictive value
How do you calculate PPV
TP / (TP + FP)
What is NPV?
Negative predictive value
How do you calculate NPV?
TN / (TN + FN)
What is a cluster?
Observation of above normal number of cases
Outbreak
Sudden increase in disease cases
Epidemic
Outbreak on a large scale
Pandemic
Outbreak at international/global scale
Endemic
Normal, baseline, natural distribution/rates of disease
Epizootic
epidemic for wildlife
Enzootic
endemic for wildlife
What do maps tell us?
- Predict spread and allow instigation of control/preparations - The importance of local context & scale
Anatomy of Lyme disease?
Agent: Bacterium Borrelia burgdorferi Transmission: Vector-Borne, ticks Reservoir/source: Small mammals
Incidence
Number of new cases that occur during a specified period of time, in a population at risk for developing the disease
- Case investigation steps
- Verify that an outbreak is occurring 2. Establish preliminary hypothesis 3. Make a case definition 4. Make case questionnaires 5. Organize data (line listing) 6. Describe current outbreak information
Case definition means…
begin with a ‘loose’ case definition during initial outbreak. What is the disease? Who is a case? Who is not a case? Establish definition using disease symptoms, disease agent & stain, & likely route of exposure.
What is a notifiable case of SARS is defined as….
an individual with laboratory confirmation of infection with SARS coronavirus (SARS-CoV)
Suspected Case
A clinically compatible case without presumptive or confirmatory laboratory results
Probable Case
A clinically compatible case with presumptive laboratory results
Confirmed Case
A clinically compatible case with confirmatory laboratory results
Contact Tracing
process of locating and notifying partners (contacts) that they have been exposed to a disease (AKA partner tracing). Syphilis, gonorrhoea, TB, measles, HIV (!!!)
Line Listing
(organizing data) Common file for information
- Cause investigation
systematically review possible reservoir/source & casual agents (anatomy of disease). Remember L.E.V.EL!!! L - laboratory investigations E - epidemiologic/clinical investigations V - Veterinary/wildlife/vector investigations E - Environmental investigations L - Law enforcement investigations
Control measures
- Case investigation 2. Cause investigation 3. Control measures - ACT FAST
- Conduct analytic study with…
RISK RATIOs
Cohort
a well-defined group of subjects or patients who have had a common experience or exposure and are then followed up for the incidence of new diseases or events.
Incidence =
number of new cases that occur during a specific period of time, in a population at risk for developing the disease
Person-time units =
length of time individuals are in states of health, exposure (at risk), infection, infectiousness, etc. (or how many people and for how long??) – 10 people studied for 6 weeks. = 60 person-weeks
Fixed cohort
all people present at beginning of study; no new entries
Open cohort
people can enter study at any time
Prevalence =
number of cases / population
Retrospective cohort study
Disease outbreak is already occurring - how can we determine exposures?
Niche
set of environmental conditions within which organism can maintain populations without immigration
Statistical models
Correlation between relevant environmental dimensions and know point-occurance data
Risk factor
a variable associated with an increased risk of disease or infection. (influenced by exposure and/or susceptibility)
Susceptible hosts
What was the exposure? - Entry of disease agent - activity of host - Travel of host Host immune status
Risk calculation
n = a + b (( b is negatives, a = positives)) = # of positive samples / # of exposed
Risk rate ratio calculation
- type of ratio comparing the change in one value (numerator) per change in another value (denominator) - Delta a / delta b
Risk ratio calculation =
- risk in group 1 (exposed) / risk in group 2 (non-exposed)
Risk ratio
Disease/exposed = a No disease/ exposed = b Disease/ not exposed = c No disease/not exposed = d Risk to exposed = a/(a+b) Risk to not exposed = c/(c+d) Risk ratio = [a/(a+b)] ÷ [c/(c+d)]
What does Risk ratio tell us?
RR = 1, exposure has no association RR > 1, exposure positively associated with disease RR< 1, exposure negatively associated with disease
Batrachochytrium dendrobatidis
The Chytrid fungus, a non-hyphal zoosporic fungus. Fungus that killed a bunch of frogs
How many emerging infectious diseases are zoonotic?
73%
Majority of EIDs are:
bacterial or rickettsial
Best global predictors of EIDS?
Mammal species richness
Biodiversity should generally
reduce the prevalence of infectious diseases
The Iceberg Model
- What appears, visible behaviors. vs what’s below - Need to see the whole system “Beneath the visible level of events and crisis, there are underlying structures, paradigms of thought, and sources that are responsible for creating them.”
Practice an SIR model
now
Diseases eradicated by humans
- Measles - Rinderpest ( Morbillivirus)
Incubation period
between infection and symptoms
latent period
between infection and infectious
Index case
first initial case
Ro > 1 =
disease outbreak
Ro < 1 =
disease fades out
Ro =
average number of secondary infectious cases produced by an index case in a SUSCEPTIBLE population
Ro conditions =
- beginning of an epidemic - fully susceptible population - no control measures
SIR stands for
- Susceptible (uninfected, not exposed) - Infected - Removed (post infection, dead, recovered and resistant)
SIR model assumes
- well-mixed populations - closed population (no immigration, births, etc) - etc
Ro calculation is =
= dcp = Duration of infectiousness x contact rate x transmission probability .
Effective reproductive number =
R = average number of secondary infectious cases produced by infectious cases – Conditions: uncontrolled disease spread
CONTROL reproductive number =
Rc = effective reproductive number in the presence of control measures — conditions: control measures instigated
How to reduce R?
Reduce: 1. # of susceptible hosts 2. sources of infection 3. Infectiousness 4. contact rates 5. INTERUPT transmission 6. INCREASE herd immunity
Basic methods of disease control
- isolation 2. vaccination 3. barriers 4. eradication (disinfectant, culling) 5. treatment 6. education
Reduce Ro?
Altering: 1. duration of infectiousness 2. contact rate 3. transmission probability
Basic anatomy of disease
- susceptible hosts 2. disease agent 3. reservoir / source 4. entry into susceptible host 5. exit from infected host 6. mode of transmission
Threshold theory and vaccination equation
v > 1 - ( 1 /Ro ) v = proportion of population that are vaccinated
Herd Immunity Threshold
Vaccinating a proportion (or herd) of the population protects unvaccinated individuals.
Risk calculation =
= a / n a = positive samples n = sample size of EXPOSED persons n = a + b b = negatives
Risk ratio =
risk in group one (exposed) / risk in group two (non-exposed)
Epidemiological surveillance
ongoing systematic collection, analysis, and interpretation of health data essential to the planning, implementation, and evaluation of public health practice closely integrated with the timely dissemination of these data to those who need to know. (CDC)
Epidemiological process with surveillance
- describe disease risks and trends (surveillance) 2. evaluate control/prevention (surveillance)
Types of surveillance
- passive 2. active
Passive surveillance
Health officials report cases of illness, but no special effort is made to find unsuspected disease incidents. PRO: inexpensive, not geographically restricted CON: may under report, replies on person motivation
Active surveillance
Field investigation of disease incidence, e.g. interviews, screening, sampling PRO: accurate, high standards CON: expensive, time consuming, geographically restricted
endemic
normal, baseline, natural distribution/rates of disease
cluster
observation of above-normal number of cases
outbreak
sudden increase in disease cases
epidemic
outbreak on large scale
pandemic
outbreak at international/global scale
intrinsic incubation period
interval between the acquisition of an infectious agent by a vector and the vector’s ability to transmit the agent to other susceptible vertebrate hosts
Incidence
Number of new cases that occur during a specified period of time, in a population at risk for developing the disease. PERSON-TIME @ risk
Person-time units
length of time individuals are in states of health, exposure (at risk), infection, infectiousness, etc. (or how many people and for how long??) – 10 people studied for 6 weeks. = 60 person-weeks
Trophic Cascade
indirect top-down regulation of productivity, abundance or biomass at one trophic level (e.g. primary producers) by higher-level consumers at least one trophic level removed (e.g predators)
Muskox Lung worm
Umingmakstrongylus Pallikuukensis
Life-cycle stages of tick?
Eggs, 6-legged larva, eight-legged nymph, adult
Nymphal Infection Prevalence (NIP)
infected nymphs / number of nymphs
Number of infected nymphs = (NIN) =
Density of host species x species-specific larval burdens x #of larvae infected by host species (reservoir competence) x Species-specific molting success.
CALCULATE ! Body burden = 27.8 (se 3.3) larvae Molting % = 41.5 (3.5) Reservoir competence (%) = 92.1 (2.9) Density/ha = 0-100 – 20 mice/ha, what should the NIP be?
Body burden = 27.8 (se 3.3) larvae Molting % = 41.5 (3.5) Reservoir competence (%) = 92.1 (2.9) Density/ha = 20 Number of infected nymphs = 20 * 27.8 * 0.415 * 0.921 = 213 Number of nymphs = 20 * 27.8 * 0.415 = 231 NIP = 213/231 = 92.2%
CALCULATE ! Body burden = 36.0 (11) larvae Molting % = 41.2 (6.0) Reservoir competence (%) = 55.0 (6.4) Density/ha = 0-50 – 20 mice/ha, what should the NIP be?
Body burden = 36.0 (11) larvae Molting % = 41.2 (6.0) Reservoir competence (%) = 55.0 (6.4) Density/ha = 20 Number of infected nymphs = 20 * 36.0 * 0.412 * 0.55 = 163 Number of nymphs = 20 * 36.0 * 0.412 = 297 NIP = 163/297 = 54.9%
Density of infected nymphs (DIN)=
Number of infected nymphs / ha
Is there a predictable relationship between biodiversity and disease risk ?
No, but understanding local community ecology can help in the prediction of disease dynamics.
Meta-analysis, study requirements :
- human pathogen 2. simultaneous measurement of pathogen abundance & host diversity - test statistics : F, X^2, t, r^2
Clinical symptoms of muskox lungworm
respiratory compromise, predisposition to being preyed upon
Lyme Disease
An emerging infectious disease - Borrelia Burgdorferi
Lyme disease range expansion?
Land-use change population density surveillance case definitions media deer coyotes tick populations
Dengue
*flu-like illness * 50 -100 million infections estimated annually * over 100 endemic countries * 1/2 the world population at risk *incidence has increase 30-fold in last 50 years
Lyme disease agent
Spirochete bacterium Borellia Burgdorferi
Lyme disease mode of transmission and reservoir?
Vector-borne (ticks) reservoir rodents
When Ticks molt its called..
Trans-stadial transmission
What do maps tell us?
- they give us insight into disease ecology and disease risk - show us the importance of local context & scale
Lyme diagnostics
B burgdorferi - more detectable in EPB B miyamotoi - more detectable in blood
Small animals of California oak woodlands.
Western fence lizard - high tick burden Western gray squirrel - high pathogen transmission
“To win the disease battles of the 21st century while ensuring the biological integrity of the Earth for future generations requires interdisciplinary and cross-sectoral approaches to disease prevention, surveillance, monitoring, control and mitigation as well as to environmental conservation more broadly.” - Wildlife conservation society
“To win the disease battles of the 21st century while ensuring the biological integrity of the Earth for future generations requires interdisciplinary and cross-sectoral approaches to disease prevention, surveillance, monitoring, control and mitigation as well as to environmental conservation more broadly.” - Wildlife conservation society
Extrinsic incubation period
The time between when a mosquito acquires an infection agent and the mosquito’s ability to transmit the agent to other susceptible hosts