Infectious Diseases
Weekly Objectives
- Model the direct transmission of an infectious disease through a susceptible population.
- Evaluate when it is appropriate to quarantine or isolate individuals.
- Describe the role of Social, Economic, and Political Forces on sexually transmitted infections
- Develop an intervention strategy for reducing the burden of directly transmitted infections
- Identify timely global infectious disease issues pertaining to directly transmitted infections.
Direct Transmission
Mechanisms of Direct Transmission
- Understanding how diseases are transmitted help to design prevent and control strategies.
- Direct transmission refers to person-to- person transmission.
- Examples include:
- Contact (Touch ex: Skin- to- Skin, kissing)
- Respiratory droplets (cough/sneeze)
- Mother-to-child (transplacental or breastfeeding)
- Sexually transmitted infections
- Examples include:
Match Disease to Direct Transmission
- Diseases & Mechanisms
- Tuberculosis – Respiratory droplets
- Human Pappillomavirus (HPV) – Sexually transmitted
- Cytomegalovirus – Mother-to- child (though it can be transmitted other ways.
- Clostridium difficile – Fecal oral
Tuberculosis
- Tuberculosis is a bacterial infection, with 5-6% showing resistance to multiple drugs.
- It is transmitted via respiratory droplets. It has a latent phase, which means that people may be infectious without having symptoms, making it very dangerous.
- It has a very large disease burden- in 2020 the World Health Organization reported 10 million cases, with 1.5 million deaths worldwide. It is one of the top infectious disease killers.
- There is an element of social determinants of health with this disease, which we will talk about more on the next slide. The key takeaway is that it affects low-middle income countries more than high income countries.
- On reason it is so deadly is that it is a common co-infection with HIV. It can push people who are HIV positive into AIDS.
- Treatment is difficult and time consuming. Most successful treatment is called “Directly Observed Therapy”. This means that someone (healthcare worker, community worker) goes to each person’s residence who is on DOT and ensures that they have the medication and are taking it appropriately each day.
Tuberculosis deaths by income
- Here we see the burden of disease based on income. As you can see, low-middle income countries have it listed as the 7th overall leading cause of death, worsening from 2019, and 4th leading infectious disease. Upper- middle income countries doesn’t have it anywhere on their list.
- Why do you think this might be?
Human Papillomavirus
- The Human Papillomavirus is one of the most commonly transmitted STIs worldwide. There are 40 different subtypes, 13 are probably or confirmed to be carcinogenic.
- HPV is the only cause of cervical cancer that we know of. It is a leading cause of anogenital (including penile), and oropharyngeal (neck and throat) cancers. This has been on the rise in recent years due to oral sex.
- According to WHO, in 2020, there were 604 new cases and 342,000 deaths.
- HPV can produce genital warts.
- It is sexually transmitted- it is through contact with mucosal layers on skin, not necessarily intercourse.
- Prevention:
- HPV Vaccine protects against 70% of common subtypes since most people acquire HPV between 18 and 25, so it is important to target people under 18 for maximum protection.
- Screening:
- HPV can be detected through PAP smears (cervical swab during pelvic exam). Recently genetic testing has been developed and is effective in detecting HPV. Since pelvic exams are not required every year and not everyone has a cervix, the genetic testing has helped detect more HPV and reduce the discomfort of screening on some patients.
- Treatment:
- Much like other treatments of cancer (surgical, radiation, chemotherapy). If the lesions are found early, they can be removed through cryotherapy, lop electrosurgical excision procedure.
Cytomegalovirus
- Cytomegalovirus is common. Like HPV, prevalent but many people don’t experience active symptoms.
- Spread through contact with saliva, feces, and other bodily fluid.
- Often affects children at daycare
- 1 in 200 babies are born infected with cytomegalovirus. It can cause premature birth, low birthweight, microcephaly. Most commonly, it can cause hearing and vision loss.
- Treatment with antivirals should be initiated once it is detected.
Clostridium Difficle
- Clostridium difficile (aka c. diff) is a bacterial infection commonly found in healthcare facilities (“nosocomial” infection)
- It is spread through fecal-oral transmission
- Antibiotic resistance is a concern when determining the types of treatment you can use
- US had an estimated incidence of 223,900 cases in hospitalized patients per year, and 12,800 deaths in 2019.
- Treatment is a special combination of antibiotics, and experimental fecal transplanation, which can help restore the microbiome to what it was before the infection took hold.
Exercise activity
- As an exercise, try to draw the infectious disease triangle that we learned about from last week’s lecture, using one of the four diseases we just discussed.
- Draw the infectious disease triangle for your disease
- List one factor for each of the triangle elements that would influence disease transmission
- Provide at least one possible intervention strategy- label it as primary, secondry, or tertiary prevention
- Calculate case fatality
SIR Models and R0
Basic SIR Model
- Each letter in the “S-I-R” model stands for a different state that the person could be in.
- Compartmental model looks at a population, not a broader model
- Assumptions:
- Working with a fixed, stable population. No one travelling or moving to or from the population
- Random mixing of individuals within the population.
- Full recovery (moving from infectious back to susceptible) or death
- Each letter represents a state that each person in the population is in: they could be susceptible (have not yet gotten the disease but is able to), infectious (actively has the disease), recovered (no longer experincing the disease). When you add these three together, you should have the total population.
- Consider what factors can affect populations in each state.
- Ex. If more people are infected, what happens to S?
- As people move from each state, each has an impact on another- they’re all dependent on each other
- Susceptible:
- For susceptible, the only way people could move into the susceptible state, is if they are born, recovery.
- For now, we are not going to introduce a background mortality rate, but typically, this is also something that could affect susceptibility.
- Infectious:
- The infectious state is impacted by the contact rate between individuals (how often you interact with others), Probability of infection (what is the probability of giving the disease to someone with each interaction?), and people that move out of this state and recover.
- Recovered:
- Recovered, meaning those that survive infection.
- The probability of being in the recovered state is also impacted by the probability of death post-infection.
- Other factors that could impact this include co-morbidities that may worsen your outcome or make you vulnerable for other diseases.
- We talk about the recovery rate (expressed as “a”) and the infection rate (expressed as “b”) when looking at them as a function of how the different states affect each other.
- a(lt)= Number of infectives that are removed in day “t”, meaning how many people moved from the infectious state to the recovered state within a certain time frame.
- b(StIt) = Number of susceptibles that got infected in day “t”, meaning how many people from the susceptible state became infected within a certain time frame.
Basic Reproductive Number (R0)
- Understanding the basic reproductive number (R0, which is pronounced like R-naught) is an important concept in mathematical modeling
- It is defined as the number of new infections that would result from one infected individual entering a fully susceptible population.
- We could envision this as if a person who is infectious walks into a room full of susceptible people, how many would become infected?
- Understanding the baseline of infectiousness helps us understand how many people we need to protect (i.e. with a vaccine) in order for a disease to die out, by running out of people to infect.
- One simple use of R0 is by looking at its relative magnitude. Based on whether or not the R0 is greater, equal to, or less than 1. If it is greater than 1, then the disease willl take off and there will be an outbreak or epidemic. If it is equal to 1, it will be sustained, neither taking off nor dying out. If it is less than 1, the disease will run out of people to infect and will eventually die out.
- If R0 > 1, there will be an epidemic
- If R0 = 1, the disease will be sustained within the population
- If R0 < 1, the disease will die out
- We calculate R0 as a function of the susceptible population size times the infection rate times the recovery rate.
- R0 = population size * infection rate * recovery rate
- R0 = S0 * b * a
Guerra (2017) – R0 and Measles
- Let’s apply the concepts from the readings and combine them with the SIR model.
- The mathematical modeling inputs can vary by context. That has implications for the interventions and controls that we recommend.
- For example, the more R0 increases, the higher vaccination coverage needs to be in order to ensure herd immunity and keep R0 less than 1.
- Measles was used as an example in your reading and is often times cited as one of the most transmissible disease, with an R0 of 12-18. This means that each person infected with measles would infect 12-18 people, in a totally susceptible population.
- Population density changes how transmissble a disease will be, since it is assumed that people will not interact as much. The authors estimated that the R0 in a low density setting would be closer to 12.6 and in a high density setting, 15.9.
- Birth rate also matters – a low birth rate would bring the R0 down to 10.4 and a high birth rate would bring it up to 12.9.
- Consider why this might R0 be higher in high density and high birth rate settings?
- Consider why this might be?
- So when we factor everything into our calculation, the R0 can range from 3.7 to 203.3, which is huge.
- Factors that can influence this is also include region and level of development.
- Why do you think this would be?
- In what ways would an SIR model be inadequate to describe outbreak of measles?
ISOLATION AND QUARANTINE
- Now we are going to talk about a common prevention method for highly transmissble diseases- isolation and quarantine.
Definitions
- Isolation
- refers to removing sick people from the healthy population
- The isolated person is exhibiing symptoms.
- Quarantine
- refers to removing someone who has been exposed to a sick person but is not yet sick themselves, from a healthy population.
The Ethics of Isolation, Quarantine and Exposure
- Isolation and quarantine are some of the oldest control strategies – this was not always well accepted by communities. In some cases, it was later reflected upon as to whether isolating an entire community actually allowed it to spread faster. There have also been cases where community leaders conceived communities that it was the best approach.
- The four Beachamp and Childress principles were adopted by the founding principles of bioethics:
- First consider harm – restricting freedoms of individuals can only be justified if it is to reduce the harm caused to others
- Least restrictive or coercive means should be used. Any action justified by harm should always use the mildest possible measures. Education and discussion should precede any prohibition.
- Societies within which public health measures are implemented should be expected to be compensated for the distress they experience.
- All stakeholders affected by public health measures should be involved in the decision-making process and all processes should be as clear as possible.
- Quarantine Governance and Public Health Law and Ethics
- Local and state laws apply if the threat is confined to a city, or state. If the disease is important from a foreign country (often the case with tropical disease or something like COVID) or transmitted across state lines.
- The Public Health Service Act grants the Secretary of DHHS authority to make and enforce regulations to prevent the introduction, transmission or interstate spread of communicable diseases… detain, or conditionally release infected with “quarantinable diseases” (usually those diseases that are most communicable.
- There are also limits on isolation and quarantine intended to protect individuals who are affected.
- There must be evidence that the person being quarantined/isolated was actually infected with or exposed to an infectious disease.
- There must be a safe and healthful environment for those subject to isolation and quarantine.
- Cannot target specific groups outside of their infectiousness or exposure.
- Each individual is entitled to procedural due process- just like any other legal proceeding.
- What can we say about this with respect to COVID-19? When do you think isolation or quarantine is “just”, when is it not? How have the stay-at-home orders for the general public differed from quarantine or isolation?
- Numerous other ethical issues and controversies have arisen during the COVID pandemic. Your reading this week by Kramer et al address this. Consider while completing your reading the following questions.
- Debates highlighted:
- Professional responsibilities of healthcare workers in treating patients with this virus, given the demostrated high risk of being infected as they care for them?
- Contact tracing Vs patient confidentiality
- Who should be screened when COVID-19 tests are limited?
- How do we allocate scarce resources, such as ICU beds, ventilators, and medications?
- What ethical concerns are there with relaxing FDA rules and criteria for certification into the medical field?
Computer-Assisted Modeling for SIR
- This is the activity for this week, in lieu of a discussion post
Modeling Diseases- Worksheet
- SEIR Model
- Disease with exposed, but latent, period
- Using the Excel file found in the Assignments section for this week, answer questions from the worksheet.
- Show your work and submit for credit
- Answer will be provided next week to check your understanding.
- You will be modeling a disease with an exposed state as well, in addition to the SIR.
Discrete SIR infectious disease model, Part 1
