M16: Emerging Infectious Diseases Flashcards
Definitions in Epidemiology:
Incubation period
Infectious period
Latent period
time from exposure to development of disease
length of time a person can transmit disease
period of infection without being infectious. This may occur right after exposure or late in the disease
Definitions in Epidemiology:
Epidemic
Endemic
Pandemic
occurrence of cases of illness in excess of expectancy.
An epidemic whose incidence remains stable for a long period
a global outbreak
Definitions in Epidemiology:
Incidence
Incidence rate
Denominators can be expressed _
number of new cases in a given time period in a given population
Example: 93 new cases of HIV infection in Allegheny County in 2008
number of new cases per population at risk for the disease over time
Example: 23 cases of C. difficile acquired at hospital A (500 beds) over a month with full occupancy = 23 / (500 x 30) = 0.00153 cases / patient-day
as any population at risk:
• Ventilator-days
• Central-line days
Definitions in Epidemiology:
Prevalence
This is of little interest if an infection is of (short / long) duration (ex) but more important if an infection is of (short / long) duration (ex)
total number of disease cases / # individuals in the population of concern.
short
Ex. measles
long
Ex. chronic hepatitis B, HIV
Definitions in Epidemiology:
Attack rate
Primary cases
Secondary cases:
proportion of exposed individuals who become ill
The person who infects a population
Those who subsequently contract the infection
Definitions in Epidemiology:
Case fatality
This is a function of the _ of the infection and is heavily influenced by _
Virulence
- indicated by _
- Rabies: (very / not very) virulent
- Hepatitis A: (more / less) virulent
proportion of infected individuals who die of the infection.
severity
how many mild cases are not diagnosed
the degree of pathogenicity within a group or species of microorganisms or viruses
- case fatality rates (CFR) and/or the ability of the organism to invade the tissues of the host
very
less
Definitions in Epidemiology:
Reservoir
Vector
Zoonosis
ecological niche (vs source which is the actual object).
any organism (usually an arthropod like a mosquito or tick) which harbors infectious agent and transmits it to susceptible individuals (e.g. Lyme disease, malaria)
infections that can spread from vertebrate animals to man.
Definitions in Epidemiology:
Formula: Ro =
Ro: The basic reproductive rate is _
b is the attack rate: _
k is the number of _
D is the duration of _
b x k x D
the number of secondary cases following a single introduction into a fully susceptible population
how infectious
potentially infectious contacts the average person in the population has per unit time
infectivity of an infected person
Ro = the basic reproductive rate
If Ro < 1, then _
A population that is _ or became _ affects disease spread
If Ro = 1 then _
If Ro > 1 then _
every new generation of infection will affect fewer individuals and the disease will die out.
vaccinated (polio) naturally immune (hepatitis A)
approximately the same number of individuals are infected with every new generation causing endemicity (West Nile virus)
there is an ever increasing number of infected individuals causing epidemic or pandemic (Influenza)
Definitions in Epidemiology:
Herd immunity threshold
The higher the Ro of infection, the (larger / smaller) the number of immune people is required to confer herd immunity.
For example: measles has a Ro of 15; the need of herd immunity (vaccination coverage) to interrupt transmission of measles is (high / low) in a population
the fraction of a population that must be immune to a given microorganism to prevent an outbreak beyond one index case.
larger
high
Outbreak
You should suspect an outbreak when there are (#) cases of an illness with similar characteristics linked by _, _, or _.
When investigating an outbreak it is important to first decide about a case definition, and then collect data to determine (4)
2 or more
time, location or contacts
- Reservoir
- Transmission route
- Incubation time
- Value of Ro (limited outbreak, epidemic or endemic)
Different causes of acute pneumonia:
Bacterial (4)
Viral (6)
Streptococcus pneumoniae
Legionella
Chlamydia
Mycoplasma
Influenza, Avian Influenza Para-influenza virus Adenovirus Respiratory Syncitial virus (RSV) Metapneumovirus Coronaviruses (SARS)
Severe Acute Respiratory Syndrome (SARS):
The spread of SARS could be linked to a primary (_) case and the infectivity was very (high / low). Transmission was mainly _, but also by _.
SARS elicited the first global response to an outbreak. In a record time of 6 weeks after recognition of the new disease _ was isolated and identified as a new pathogen. Koch’s postulates were fulfilled in monkeys in 8 weeks and the genome sequence was available in 10 weeks. All advances were instantly available through the internet and published online in a matter of days.
index
high
respiratory
aerosolized feces (fomites)
SARS-CoronaVirus (SARS-CoV)
Severe Acute Respiratory Syndrome (SARS):
There were 8000 cases of SARS identified, causing 775 deaths (mortality 10%). SARS-CoV is an (enveloped / unenveloped) RNA virus and is stable in _ and _ (1-4 days). It is killed by _ and _.
The latest serology data on SARS suggests it was not previously endemic in people. Reservoir consists of _ (civet cats, fruit bats) that can carry _ that are homologous to SARS.
Early transmission from animals to humans was inefficient, but then CoV adapted to human-human transmission through mutations (_ virus). Ongoing introduction from the reservoir to humans was demonstrated by a repeat mini-epidemic in Dec 2003-Jan 2004. This was associated with the re-opening of “wet” markets in China where live animals were sold.
enveloped
feces and urine
disinfectants and heat
healthy animals
coronaviruses (CoV)
RNA
Severe Acute Respiratory Syndrome (SARS):
_ are now thought to be the natural reservoir for many viruses, including SARS-CoV, rabies, Nipah & Hendravirus and Ebola & Marburgvirus.
They chew, suck and then regurgitate _ and _, remnants tainted by _ containing these viruses are dropped under the trees that they live in and contaminate the surrounding area.
Animals (pigs, civet cats) or humans come in contact with _ and can get infected. Adaptation to the host is facilitated by the high mutation rate of _ viruses.
Proximity of humans to _ (_) and easiness of _ increase the chance of rapid dissemination causing epidemics or pandemics.
Bats
fruits and insects
bat saliva
bat droppings
RNA
animal reservoirs (animal husbandry) travel
Avian Influenza:
Avian Influenza in birds is caused by _, _, and _ strains.
Most are of (high / low) pathogenicity (_) and are carried (symptomatically / asymptomatically) in the respiratory and GI tract of birds.
(High / Low) pathogenicity (_) strains cause disseminated disease and death.
The _ strain is predominant since 2004 and continues to cause illness and death mainly in birds but also in other animal species including humans: Over 648 human cases and 384 deaths (59% mortality) have been reported as of August 10th 2012.
Until now no efficient transmission to humans has been documented due to a different _.
Conditions for a pandemic exist when a new virus subtype emerges (H5N1 or next) and _ takes place; genetic material is exchanged between _ and _ viruses - facilitating the gradual process of adaptive mutation resulting in an increased ability to bind to human cells in subsequent infections.
The virus can then infect _, spreading easily between humans (Ro>1) causing an epidemic or pandemic.
H5, H7 and H9
low (LPAI)
asymptomatically
High (HPAI)
H5N1
tissue tropism (interspecies barrier)
reassortment
human and avian
humans
Avian Influenza:
1) The currently circulating _ has an expanding host range including humans, tigers and cats while some new reservoirs excrete the virus without becoming _. H5N1 viruses are now endemic in _ and spread by migrating wild birds as well as by illegal fowl trading.
2) Severe consequences are anticipated since there the mortality is (high / low) while there is no pre-existing _ to the strain unless a vaccine is developed and administered widely throughout the world.
3) In addition, this avian influenza is resistant to _ and _ possibly caused by using these antivirals in birdfeed. Resistance to _ has also been reported.
H5N1
ill
Asian domestic fowl
high
immunity
amantadine and rimantadine
oseltamivir
Metapneumovirus:
Was first described in 2000. It was discovered by “fishing” with PCR primers in a cohort of children with _.
It is a common cause of _ infections in children and adults and has been prevalent for decades. New techniques can discover “new” diseases.
undiagnosed pneumonias
respiratory
Different causes of meningitis, encephalitis, encephalopathy in the USA:
Bacterial (3)
Viral (4)
Fungus (1)
Prion (2)
Streptococcus pneumoniae
Neisseria meningitidis
Listeria
Enterovirus
West Nile virus
Herpes Simplex virus
Arboviruses
Cryptococcus
CJD
vCJD
West Nile Virus:
Several cases of _ occur.
An outbreak of a communicable disease was investigated when this illness was previously absent and when >2 of these cases were associated in time and place. The investigation yielded 8 human cases that met the case definition of which 3 died. They all were active outdoors and lived in a 2-by-2 mile area in northern Queens.
Serology was positive for _ against _ species. In the meantime, an excess of dead crows in the NYC parks was observed. Brain tissue from dead crows was collected and viral cultures on eggs were positive.
Nucleic acid analysis of the cultured virus was analogous to West Nile Virus (WNV) in the flavivirus family, linking the cause of the death of the crows to the observed illness in humans. Antibodies for WNV have since been found in many _ and _ species The incidence of WNV+ mosquito pools coincided with ill humans and horse and infected birds.
encephalitis
IgM
flavivirus
bird and mosquito
West Nile Virus:
WNV infection is (symptomatic / asymptomatic) in only 1:5 people infected (by serology).
It causes a _ only in 1:150 people. WNV is widespread in Africa, Middle East, Eastern Europe and now endemic in the USA.
The reservoir is _ and transmission occurs per _ that are viremic for life.
Preventive measure are mosquito control by spraying and eliminating water pools (tires), by personal protection against mosquito bites (DEET/clothing) and screening of organ and blood donations during the period of endemicity (summer and fall).
symptomatic
meningo-encephalitis
birds
mosquitoes
New variant Creutzfeldt Jacob Disease (vCJD):
_ are diseases of humans and other animals.
Some of these are _ and some are _ by either inherited or spontaneous mutations.
Although the cause of some of these encephalopathies are _ and thus infectious, they are not caused by live micro-organisms but by _.
Spongiform encephalopathies
transmissible
genetic
transmissible
abnormal (dead) proteins or prions
- Transmissable and genetic spongiform encephalopathies in humans (5)
- Spongiform encephalopathies in animals (3)
-Sporadic Creutzfeldt-Jakob disease (sCJD)
-New variant Creutzfeldt-Jakob disease (vCJD)
–Kuru (Fore tribe members in New Guinea eating human brains)
–Gerstmann-Straussler-Scheinker disease (GSS)
–Fatal familial insomnia (FFI)
–Scrapie (sheep)
–Bovine spongiform encephalopathy (BSE)
–Chronic wasting disease (CWD) in elk and deer
New variant Creutzfeldt Jacob Disease (vCJD):
The cause of spongiform encephalopathy is a protein found in high quantities in the _ (and much lower levels in other tissues). This protein, called _ is present in all brains without _, but when the protein takes on an abnormal shape it accumulates unless _ by normal pathways.
In susceptible individuals with the 129 MM genotype, elevated levels of this abnormal protein kill _ and cause the clinical symptoms of the disease.
Human to human transmission of prion disease has been documented by (4)
brain
prion (PrP)
any harmful effects
destroyed
brain cells
cannibalism, use of corneal transplants, contaminated neurosurgical devices and blood transfusions
New variant Creutzfeldt Jacob Disease (vCJD):
Abnormal prions are _ proteins and survive the rendering process (highly resistant to _ and _).
_ spread between cows in the UK when left-over bovine carcasses (bone meal) were used as animal feed. The emergence of _ was noted and changing feed practices have decreased the incidence.
When patients were reported with unusual presentations of _ (younger age at onset and causing rapid death) a link with BSE suspected. Named “variant Creutzfeldt-Jakob Disease (vCJD)” caused clinical symptoms in humans that were very similar to BSE symptoms in cattle. The disease is uniformly _ and has been casually linked to the consumption of either _ or _. Cumulatively ~230 human cases have been reported (mainly in the UK) as of 2013.
denatured
heat and chemicals
BSE
Mad Cow Disease (BSE)
sporadic CJD
fatal
BSE meat contaminated with brain tissue or the consumption of brain tissue itself
Different causes of acute gastroenteritis:
Bacterial (6)
Viral (2)
Parasites (2)
Toxins (5)
E. coli Salmonella Campylobacter Yersinia Vibrio cholera Bacteroides fragilis
Norovirus
Rotavirus
Giardia
Cryptosporidium
Staphylococcal toxin Bacillus cereus Botulism Ciguatara Scombroid
Norovirus:
(formerly named Norwalk virus) was first described as the cause of an outbreak of _ in Norwalk, Ohio (1968). As part of the investigation bacterial cultures of feces were negative. Then a human experiment was conducted to test Koch’s postulates:
1) Feces was _ (bacteria and parasites were _)
2) Filtrate was fed to volunteers who all developed _, this was suggestive of a viral etiology.
3) Pre-treatment of the filtrate with _ did not destroy infectivity: The virus did not contain a _ which would have made it environmentally unstable. Viruses with lipid membranes need _ such as wet hands, snot, or genital tract but typically do not survive harsher environments such as the _ or .
4) Electron microscopy showed viral particles (1972), confirming it was a virus with a _ that offers the unstable inside protection against (4). These viruses flourish in the _.
gastro-enteritis
filtrated
removed
gastro-enteritis
soap
lipid envelop
moisture
gastro-intestinal tract or dry surfaces
capsid
RNA genome
high temperatures, drying, acid and detergents
GI-tract
Norovirus:
Norovirus causes a self-limited _ (24-48 hours) with nausea, vomiting, abdominal pain and diarrhea. It is very _ and has caused many outbreaks in schools, cruise ships and hospitals. Diagnosis can be made by PCR and EM of _, and by serum testing for _ by ELISA.
Reservoir is _ and transmission is indirect by _ (hands/food/door handles) and _ with viruses (vomiting). There is no available _ or _
Preventive measures are:
- _ after touching contaminated surfaces and prior to eating
- harsh chemical _ of environment
acute gastro-enteritis
contagious
stool
antibodies
humans
oral-fecal route
airborne fomites
treatment or vaccination
washing hands
cleaning
Re-emerging Infections:
Tuberculosis:
Tuberculosis was previously thought to be nearly _ in the resource rich world but is now resurging due to _ and the increasing pool of _ hosts (HIV).
In addition, the spread of _ and _ TB is causing great concern, especially in Sub-Saharan Africa and the former Russian Republics.
eradicated
immigration
immunocompromized
Multi Drug resistant (MDR)
Extreme Drug resistant (XRD)
Re-emerging Infections:
Polio:
Polio has re-emerged in _ and _ in areas where it had been eradicated.
Most of the outbreaks have been due to re-introductions of polio from _ areas to people with low herd immunity - _ because religious beliefs.
Some outbreaks have occurred due to reverting of _ polio vaccine strains back to _ poliovirus.
Africa and Asia
endemic
not vaccinated
attenuated
wild-type
Re-emerging Infections:
Measles and Pertussis:
Other vaccine-_ diseases such as measles and pertussis have re-emerged due to _ with immunization recommendations.
This is mainly driven by some parents who are more concerned about potential rare _ of vaccinations rather than maintaining the herd immunity against these devastating illnesses.
preventable
non-compliance
side effects
Re-emerging Infections:
Salmonellosis:
Salmonellosis which nearly disappeared from the first world with improved _ and treatment is now re-emerging with wider distribution of _ and more _.
hygiene
food supply
antibiotic resistance
Re-emerging Infections:
Because re-emerging infections are per definition not from _ microorganisms, the real challenge in preventing them is constant public health surveillance.
In the United States, this occurs largely at the local and state level. Each US state decides which infectious diseases are _ for the purposes of counting cases, a system of passive surveillance for organisms of public health significance.
Physicians are legally required as a condition of licensure to _, but in practice few actually do this.
Most reporting occurs via _ and _, which automatically report notifiable diseases. In most states, they also forward bacterial and viral isolates to state reference typing laboratories on a standing or as-requested basis, depending on the pathogen.
novel
reportable
report suspected cases of these notifiable diseases to the local/state health department
hospital and outpatient microbiology laboratories
Re-emerging Infections:
At the national level, the Centers for Disease Control, a division of the US Public Health Service, coordinates national outbreak investigations between state _ and _ (MDs, veterinarians, and epidemiologists) in the Epidemic Intelligence Service (EIS) to investigate outbreaks of foodborne and other reportable illnesses that cross state lines.
The entire system is voluntary, and CDC must coordinate with _ (FDA, USDA) if control measures must be taken.
health departments
field officers
food safety enforcement agencies
Foodborne Illnesses:
Foodborne illnesses sicken more than 4,000,000 people per year in the U.S. alone. Detection of outbreaks of foodborne illness can be (easy / difficult) given modern large-scale agriculture and widespread food distribution networks. A significant number of cases of cases can occur nationwide from a single point source without _.
The genus Salmonella is a Gram (positive / negative) bacterium which is a _ without much host specificity.
It ends up in meat products where _ comes in contact with said foods, and eggs can be internally contaminated as well. The virulent serotype of _ causes typhoid fever, a potentially fatal infection in humans, but this disease has become rare with improved sanitation in the America’s and Europe. Infections by other foodborne serotypes (S. enterica serotypes Typhimurium, Enteriditis, Cholerasuis etc.), however, are on the rise.
These cause disease states ranging from self-limited _ in the normal host to _ in the elderly and immunocompromised. The usual case fatality rate for non-typhoidal Salmonella is ~ 0.03-0.06%.
difficult
attracting the notice of a local or state health department
negative
zoonosis
animal fecal contamination
Salmonella enterica Typhi
gastroenteritis
septicemia/death
Foodborne Illnesses:
To monitor for foodborne outbreaks of Salmonella that would escape local detection, the CDC uses a voluntary molecular epidemiology program called _, part of CDCs FoodNet safety research arm.
State health departments collect Salmonella bacterial isolates from all diagnosed cases and type them using _, a visual band-based typing system for bacteria based on the unique patterns that result when genomic DNA from a strain of Salmonella is digested by a restriction enzyme and run on a high-resolution agarose gel.
The banding pattern for each Salmonella tested by a health department is uploaded to a CDC website. Epidemiologists can then monitor for _ and assist local health departments in tracing outbreaks to suspect foods.
Once a food has been implicated as the source in an outbreak, the CDC’s only role is to continue _ the success of any interventions that other enforcement agencies take (USDA, FDA, and state agricultural regulators); CDC has no legal enforcement authority over the _.
PulseNet
pulsed field gel electrophoresis (PFGE)
unique PFGE types
monitoring
food supply
Important factors in emerging infections (5)
Interspecies crossing Adaptation of a virus Susceptible hosts Global warming Improved diagnostic tests
Important factors in emerging infections:
- Interspecies crossing
Close human proximity to (3)
Encroachment to new _ (humans handling jungle meat-Ebola) - Adaptation of a virus to the human host
Change (human) as incidental _ to reservoir (SARS)
Improved human-human _ (HIV)
_ can determine pathogenicity (diarrhea in SARS) - Susceptible hosts
International _ increases the size of population at risk (SARS)
_ exposes non immune humans to a “new” disease (H5N1)
Decreased _ rates due to concerned parents (measles) - Global warming
Expansion of _ habitats (Dengue, chikungunya) - Improved diagnostic tests
Reveal new _ of existing syndromes (Metapneumovirus)
birds, pigs (Influenza) and bats
reservoirs
host
transmission
Tissue tropism
travel
Antigenic shift
childhood vaccination
mosquito
pathogens
