3 Epidemiology of Infectious Diseases

Introduction
Epidemiology basically started as a science for the study of infectious diseases. Why infectious diseases? It is because since the beginning of times, infectious diseases have been the main cause of mortality in the world. For this reason, it is said that infectious diseases created epidemiology as a science that study health phenomena, especially disease, and mainly transmissible diseases. Also, it can be said that without infectious diseases, there is no epidemiology.^[1] That is the reason for this chapter to exist ahead of the majority of topics covered in the rest of this textbook.

How things got started?
Everything started with the epidemiologic triangle and its components – already covered at the beginning of this book. I am posting the image again to refresh the concept. See below:

In this model, for disease to occur, there is need to have a host, an agent, and an environment. ^[2] The variable, time was added, later. In this manner, the interaction among host, agent and environment happen in a certain period of time.

The agent (also, called, infectious disease agent, or, pathogen
It is accepted that the agent is one of the major factors, without an agent there is no disease [because this is biologic/medical model]. Common agents include: bacteria, viruses, fungi, other microbes and parasites.^[3], ^[4] Examples of common agents include, the viruses. See picture below:

Electronic picture of a virus. Photo by Judy Schmidt, Image from PIXNIO. Public Domain.

The host
The host can be a person, or an animal that harbors the disease. ^[5] As described later in the textbook, a host can show symptoms of the disease, or, can be free of symptoms.

The environment
In general it is accepted that the environment is everything that surrounds the host, or, promote the existence of the agent.^[6] It is is the external (to the host or, agent) set of factors that contribute to the development of the disease. Time It refers to the duration of the disease, it includes incubation periods (not symptoms are manifested during this period), or, the manifestation of the whole set of symptoms that characterize the disease.

Disease Transmission
In addition to the definitions above, it is customary to review additional concepts that help to explain how infectious diseases occur. The first of this is, transmission.

Common ways of transmission
Transmission goes together with the concept of chain of infection [also visited before in this book]. See image below about the general process of transmission.

Image of The chain of infection. CDC. Public Domain.

In this context, diseases can be transmitted directly or, indirectly. Direct transmission is the spread of disease from person to person. Examples, kissing, touching and infected person (or, the person who has the disease). It can occur through direct physical contact, or direct person-to-person contact, such as touching with contaminated hands, skin-to-skin contact, kissing, or sexual intercourse. And, in other situations, the direct transmission occurs while a person is coughing or, sneezing in which the droplets (of infection) spread from an infected person to a susceptible hostsusceptible host^[7]

Indirect Transmission, in this case, the spread of the infection occurs through an intermediate source called, vehicles, fomites, or, vectors. These terms require the use of some definitions starting with vehicle, which is the medium that contains the infection agent. Examples of vehicles include used needles contaminated with blood, which is common among IV substance users, or, in the case of needles accidentally contaminated with hepatitis. Another common example of a vehicle is contaminated water.

Other forms of Indirect transmission, airborne, in this situation, the disease is spread via droplets when a person sneezes, coughs, or talks, spraying microscopic pathogens. It can also happens when dust particles are spread by fans in abandoned buildings.

The mechanism for airborne indirect transmission. Example, when an infected person coughs or sneezes, tiny particles containing droplet nuclei are expelled into the air.

‘Airborne transmission,’ image from Wikimedia, Licensed CC BY 4.0 International.

Since its importance, the concept of droplet nuclei is defined here, which is a particle 1-5 micron in diameter that contains the infectious agent inside (see image below).  The droplets nuclei can remain suspended in the air for several hours, depending on the environment. The most effective droplet nuclei tend to have a diameter of ≤ 5 μm. ^[8]

‘The Droplet nuclei’, Image prepared by Giovanni Antunez, Licensed CC BY 4.0

To have an idea of the generation of droplets’ nuclei, it helps to compared how many of these droplets can be generating while coughing, talking, or, sneezing. See image and comments below:

	In general it is accepted that one cough can generate 3000 droplet nuclei. Talking for 5 minutes can generate 3000 droplet nuclei and singing can generate 3000 droplet nuclei in one minute Sneezing generates the most droplet nuclei by far (tens of thousands), which can spread to individuals up to 10 feet away.[9]
‘Sneezing,’ image from CDC PHIL, Public Domain.

Ways in which Indirect transmission occurs. Examples include, waterborne, vehicleborne, foodborne, and vectorborne. Details of these forms of transmission are discussed in more detail below:

Shigella’ bacteria, image from Medicinenet.

‘Sarcoptes scabei’ image from Wikimedia.	‘Pediculosis capitis‘, the cause of a head lice, image from Flickr.	‘Pediculosis pubis’ the cause of Pubic lice, from Wikimedia.

Vectorborne, although redundant, the disease is transmitted by a vector such as mosquitoes, ticks, etc. For some these are considered simple mechanical processes, as when the pathogen uses a host (a fly, flea, lice, or rat) as a mechanism for a ride, for nourishment, or as a physical transfer process in order to spread -this process is called, mechanical transmission.

In the same manner, when the pathogen undergoes changes as part of its life cycle, while within the host/vector and before being transmitted to the new host, it is called, biologic transmission. This process is easily seen in malaria, in which the female Anopheles mosquitoes blood  meal is required for the Plasmodium protozoan to complete its sexual development cycle. This can occur only with the ingested blood nutrients found in the intestine of the Anopheles mosquito. See the process in an image below:

‘Malaria Cycle,’ Image from CDC, Public Domain.

Reservoirs
This term refer to humans, animals, plants, soil, or inanimate organic matter (feces or food) in which infectious organisms live and multiply. For example, the reservoir for Clostridium tetani that causes tetanus is

‘Soil’, image by Jayme Burrows at The Spruce.

commonly contaminated soil. This information is very important especially for individuals who do gardening, or, work in occupations that require handling of soil and have open wounds that could be contaminated with the Clostridium spores. ^[10]

Fomite(s) which is inanimate objects that may become contaminated with the infectious agent. A common example are contaminated diapers in a day care center. Diapers are also fomites that may contribute to the spread of some infectious agents, especially, gastrointestinal and respiratory infections.^[11]

Image from Diapers.

Another example is personal protective equipment (PPE) used for decontamination. Although fomites seem important in the transmission and spread on an infectious disease, fomites are not effective (they not always contribute) to the transmission of disease.

The last of the terms in the topic of indirect transmission is vectors, it refers usually to insects and small animals that contribute to the spread of disease as part of their life cycle. Common examples of vectors are fleas, mites, flies, mosquitoes, small rodents, etc. These vectors contribute to the spread of disease in an effective manner, so, their control is part of the preventive measures of well-known infectious diseases such as malaria, zika virus, west nile virus and others.

Common Disease Vector, the mosquito that transmit malaria, image from Wikimedia, Public Domain.

‘Zoonosis,’ Image from Texas Health Dept.

The concept of carriers
Carrier, is the process that can contribute to the spread of disease. A carrier contains, spreads, or harbors an infectious organism. It is accepted that there are at least six types of carriers: active, convalescent, healthy, incubatory, intermittent and passive. Some of them will be defined as follows:

 

Active carrier, this term refers to an individual who has been exposed to and harbors a disease-causing organism and has done so for some time, even though they may have recovered from the disease. An example of this is that, worldwide as 2020, there is an estimated 257 million chronic carriers of Hepatitis B virus.

‘Prevalence of Hepatitits B virus worldwide,’ image from CDC.

Healthy carrier, the situation refers to an individual who has been exposed to and harbors a disease-causing organism (pathogen) but has not become ill or has not shown any of the symptoms of the disease. An example of this is, the prevalence of healthy carriers of N. meningitidis in a unvaccinated population with high serum titles of the pathogen but asymptomatic.

“An electronic picture (microscopic) of N. Menigiditis, ‘ Image from Blogspot.

Intermittent carrier, this is when an individual or, animal; who has been exposed to and harbors a disease-causing organism (pathogen), and who can intermittently spread the disease at different places or intervals. Examples, chronic salmonellosis (S. typhi/enterica) in human and animals (reptiles, exotic pets, and cattle). The human or animal shed the salmonella bacteria in their feces, and if the persons with this problems don’t wash its hands after defecation, the disease can be spread to others, as it is the case, of cooks who cook and serve food for others. For this reason, it is a public health measure to regularly check people working in the food industry, especially cooks for salmonellosis, so, the intermittent or chronic carrier does not infect passively other people.^[13]

‘Geographical distribution of typhoid fever,’ Image published in Lancet, but originally developed by the World Health Organization, Public Domain.

How an infectious agent entries in the body
Other information that is commonly covered in a principles of epidemiology textbook is the concepts of how disease entry to the body or, organism and how it lefts (or, exit) the host; this is known as, Portals of Exit and Entry of infectious diseases. Most books and similar offer complex tables of information that can be found elsewhere,^[14],^[15], ^[16]but the following image should summarize what most student need to know for a principles of epidemiology textbook. I developed the following slide using a mnemonic that will assist with remembering the main portals, the mnemonic is COCONUT.

Image prepared by Giovanni Antunez, Licensed CC BY 4.0

Some of the entrance for disease in an organism, or, host are more effective than others, for example, blood (Intravenous, or, trans-placental) is probably the most efficient, followed by inhalation and oral.

There are other definitions (or, terms) that are related to the concept of disease transmission, the most important will be reviewed. These are, incubation period, inapparent infection, generation time, herd immunity.

Incubation period, most (if not all) infectious diseases have a period in which the signs and symptoms are not manifested. The person has the infection but it is asymptomatic. Most of the time, this period called, incubation period helps the clinician and the epidemiologist to prepare in advance for the appropriate response to a disease outbreak. The incubation periods for common infectious diseases are also presented in several tables that can be found online, or, in epidemiology textbooks, for now, let’s use a slide that I prepared for this topic.

Image prepared by Giovanni Antunez, Licensed CC BY 4.0

As seen in the image, some infectious diseases have such as short incubation period while for others, it may take moths, and years to manifest. In the case of food contamination (commonly called, food poisoning), the incubation period is a matter of hours, and depending of the infectious agent, the severity of the disease may lead to dehydration, complications, or even death. Another example of short incubation period is the common cold, the person exposed (and contaminated) to the infection may start the symptoms as early as 12-24 hours after exposure.

Inapparent infection, this is a concept that has clinical significance, because it refers to asymptomatic persons who have the disease but its condition has not reached the level to be clinically obvious (with symptoms). With the advent of COVID-19, this category has raised attention because asymptomatic individuals can transmit the disease to other susceptible hosts. These individuals with no symptoms can be unknown carriers. ^[17]

Generation Time

In general, this term refers to the time that takes an infectious disease to elevate at the level of case, which is usually when the full set of symptoms manifest, and the person seek health care. Another way to see the term, is to look at the time interval between the presence of an infectious agent in a host and maximal time of communicability. The practical application of this concept is that for some diseases the maximum period of communicable can be longer, while for others is short. Both assists the epidemiologist or, any other public health professional to work in the prevention and control of infectious diseases.

Another way to see the process described above is presented in the image below:

‘Concept of Incubation period,’ image from Wikimedia, Licensed CCO 1.0 Public Domain.

Herd immunity
In general and for those of us whose English is a second language, the word ‘herd’ can be confusing, but one way to understand its usage is when we refer to groups of sheep, cattle or, any other ‘herd’ that needs protection (from the wolf, or, the possum). So, the word 'herd' is mostly synonymous of protection. In simple terms, herd immunity refers to the percentage of people or, animals that can be protected by immunization. The higher the number of immunized individuals, the higher the protection for those who are not immunized. In the past, this concept was highly regarded, and it was the belief that with at least 70% of vaccinated individuals, the protection was accomplished. But over the years, and with the advent of so many infectious diseases (old, and new), there is some consensus that the number should be at least 95% (the number varies by disease) of vaccinated in order to get herd immunity for those who are not immunized.^[18],^[19],^[20],^[21]

‘A graphic representation of the concept of herd immunity’, This image is excerpted from a U.S. GAO report.

It is important to mention that herd immunity does not work for all infectious diseases, that is another reason for the concept to be considered a ‘weak’ and ‘old’ concept to refer to this method (vaccination) used to control the spread of an infectious disease. Maybe the key is to add to the vaccination other effective features that have been used in public health for centuries, good sanitation, soap and water to wash hands and other surfaces, mask covering and social distance among other measures that we have seen working during the COVID-19 pandemic.^[22].

Methods commonly used to prevent and control infectious diseases (also, called, communicable diseases)
The following section will cover the essential methods used commonly to prevent an infectious disease, it starts with the use of vaccines, sanitation, isolation, quarantine and additional measures that had been used for centuries but that are becoming relevant these days with the COVID19 pandemic. In addition, there are three key factors that are considered essential, 1) Remove, eliminate, or contain the cause or source of infection, 2) Disrupt and block the chain of disease transmission, and 3) Protect the susceptible population against infection and disease. In this context, and additional set of recommendations are also prescribed, and discussed in the following paragraphs:

Vaccines (also, called, Immunizations)
In the history of medicine and public health (including, epidemiology), vaccines have been considered the major weapons  of defense especially on the prevention of infectious diseases, especially those common childhood infectious diseases.^[23] See below a list of common vaccines that are available:

Image prepared by Giovanni Antunez, Licensed CC BY 4.0

In general, vaccines are used to prepare the body to resist infection. Most of them are inactivated bacteria, viruses, or microbe toxins. This process is called, an ‘antigen-antibody reaction’. In other word, the vaccine acts as the antigen (a substance capable of stimulating the formation of antibodies). These antibodies protect the person against the infectious agents that are the cause of the disease. ^[24] See image of this process:

Image from how vaccines work.

Until recent years, most of the vaccines contained the infectious agent, but in recent years, especially during the COVID-19 pandemic in which two vaccines (Pfizer–BioNTech and Moderna) are developed using using mRNA technology, which changes the paradigm that a vaccine to combat this disease should contain an attenuated form of the infection agent. However, more time will be needed to use the mRNA technology to develop effective vaccines in the future, especially for new emerging, and re-emerging infectious diseases.^[25]

Sanitation
Hand washing has been the oldest of the measures used to prevent infection. For centuries, public health has promoted hand washing as the number one activity to keep people out of disease (infectious disease).^[26], ^[27]Together with this measure, it is important to put attention to personal hygiene (frequent bathing, regular

‘Hand washing’ image from Pixbay.

grooming, teeth cleaning, and maintenance, changing clothes frequently), and also to keep ventilation in homes, and buildings as the cleaning of surfaces that can act as Fomite(s) or, inanimate transmitters of an infectious agent.^[28]

In addition, face mask covering and personal protective equipment or PPE are also considered

Family mask, image from Pixabay.

especially for health care workers who are considered more at risk due to their exposures with infected clients, and surfaces.^[29]

Environmental controls to prevent infectious diseases

This measure is aimed at providing clean and safe air, water, milk, and food. It also includes the management of solid waste (trash, and garbage); liquid waste (sewage); and control of vectors (insects and rodents) of disease.

 

Host-related control & prevention
Based on the concept model of the epidemiological triangle of infection, the host-related control is intended to protect the host from contagious diseases and infections the following protective measures are used: quarantine and isolation.

 

Quarantine
The original meaning of this word is that quarantine means, forty days, however in recent years, the word quarantine refers to specific amount of time considered in which a person is isolated, or, separated from those who are not infected with the agent, and it is not necessarily forty days, it can be as short a week, two weeks, depending on the situation as it has been used during the COVID-19 pandemic. ^[30], ^[31]

‘Quarantine’, image from PNGmart.

In addition, it accepted that there are four levels of quarantine used in public health: 1) Segregation, 2) Personal surveillance, 3) Modified quarantine, 4) Complete quarantine. Most of the mentioned levels are very much self explanatory but more details can be found in the Internet and epidemiology and public health literature. ^[32]

Isolation
This method is mainly used for limited number of cases as it is in the case of humans, and also for animals. There are six levels of isolation: 1) In a private isolation room, 2) The use of separate and infection control gowns, 3) Staff must wear masks, 4) All staff must gloved with interacting, treating, or working

‘Quarantine versus isolation’, Image from Dept. of Health, City of Philadelphia, Pennsylvania.

with or on the patient or subject (e.g. an animal), 5) Hands washing is required upon entering, and leaving the patient’s room, 6) All contaminated articles or possible contaminated articles including linen, dressing, syringes, instruments, etc., must be disposed properly.^[33]