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HNSC 3162 Biological Concepts in Public Health (Cai)

Professor Patricia Cai OER

Topic 1: A Brief History of Infectious Disease, its Rise and Spread

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • explain variolation.
  • recognize the scientists and their contribution to the advances of the study of infectious disease: Edward Jenner, Charles Louis Alphonse Laveran & Ronald Ross, Jonas Salk, Maurice Hilleman.


Citation: Texas Medical Association. (May 11, 2021) Stamping Out Disease - A History of Infectious Diseases. (9:38)

Knowledge Check

Topic 2: Characteristics of Infectious Disease

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • Distinguish between signs and symptoms of disease.
  • Explain the difference between a communicable disease and a noncommunicable disease.
  • Compare different types of infectious diseases, including iatrogenic, nosocomial, and zoonotic diseases.
  • Identify and describe the stages of an acute infectious disease in terms of number of pathogens present and severity of signs and symptoms.


  • In an infection, a microorganism enters a host and begins to multiply. Some infections cause disease, which is any deviation from the normal function or structure of the host.
  • Signs of a disease are objective and are measured. 
  • Symptoms of a disease are subjective and are reported by the patient.
  • Diseases can either be noninfectious (due to genetics and environment) or infectious (due to pathogens). Some infectious diseases are communicable (transmissible between individuals through either direct or indirect mechanisms) or contagious (easily transmissible between individuals); others are noncommunicable, but may be contracted via contact with environmental reservoirs or animals(zoonoses)
  • Nosocomial diseases are contracted in hospital settings, whereas iatrogenic disease are the direct result of a medical procedure
  • An acute disease is short in duration, whereas a chronic disease lasts for months or years. Latent diseases last for years but are distinguished from chronic diseases by the lack of active replication during extended dormant periods.
  • The periods of disease include the incubation period, the prodromal period, the period of illness, the period of decline, and the period of convalescence. These periods are marked by changes in the number of infectious agents and the severity of signs and symptoms.

Knowledge Check

Topic 3: How Pathogens Cause Disease

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • recognize Koch’s postulates and explain their significance and limitations.
  • summarize the premise of molecular Koch’s postulates and its limitations.
  • explain the concept of pathogenicity (virulence) in terms of infectious and lethal dose.
  • distinguish between primary and opportunistic pathogens and identify specific examples of each.
  • summarize the stages of pathogenesis.
  • recognize pathogens that are capable of crossing the placental barrier.
  • explain the roles of portals of entry and exit in the transmission of disease.


For most infectious diseases, the ability to accurately identify the causative pathogen is a critical step in finding or prescribing effective treatments. Today’s physicians, patients, and researchers owe a sizable debt to the physician Robert Koch (1843–1910), who devised a systematic approach for confirming causative relationships between diseases and specific pathogens.

Koch’s Postulates

In 1884, Koch published four postulates (Table 15.3) that summarized his method for determining whether a particular microorganism was the cause of a particular disease. Each of Koch’s postulates represents a criterion that must be met before a disease can be positively linked with a pathogen. In order to determine whether the criteria are met, tests are performed on laboratory animals and cultures from healthy and diseased animals are compared (Figure 15.4).

Koch’s Postulates
  1. The suspected pathogen must be found in every case of disease and not be found in healthy individuals.
  2. The suspected pathogen can be isolated and grown in pure culture.
  3. A healthy test subject infected with the suspected pathogen must develop the same signs and symptoms of disease as seen in postulate 1.
  4. The pathogen must be re-isolated from the new host and must be identical to the pathogen from postulate 2.

Microbiology book's Table 15.3

figure 15.4

Microbiology book's Figure 15.4 The steps for confirming that a pathogen is the cause of a particular disease using Koch’s postulates.

In many ways, Koch’s postulates are still central to our current understanding of the causes of disease. However, advances in microbiology have revealed some important limitations in Koch’s criteria. Koch made several assumptions that we now know are untrue in many cases. The first relates to postulate 1, which assumes that pathogens are only found in diseased, not healthy, individuals. This is not true for many pathogens. For example, H. pylori, described earlier in this chapter as a pathogen causing chronic gastritis, is also part of the normal microbiota of the stomach in many healthy humans who never develop gastritis. It is estimated that upwards of 50% of the human population acquires H. pylori early in life, with most maintaining it as part of the normal microbiota for the rest of their life without ever developing disease.

Koch’s second faulty assumption was that all healthy test subjects are equally susceptible to disease. We now know that individuals are not equally susceptible to disease. Individuals are unique in terms of their microbiota and the state of their immune system at any given time. The makeup of the resident microbiota can influence an individual’s susceptibility to an infection. Members of the normal microbiota play an important role in immunity by inhibiting the growth of transient pathogens. In some cases, the microbiota may prevent a pathogen from establishing an infection; in others, it may not prevent an infection altogether but may influence the severity or type of signs and symptoms. As a result, two individuals with the same disease may not always present with the same signs and symptoms. In addition, some individuals have stronger immune systems than others. Individuals with immune systems weakened by age or an unrelated illness are much more susceptible to certain infections than individuals with strong immune systems.

Koch also assumed that all pathogens are microorganisms that can be grown in pure culture (postulate 2) and that animals could serve as reliable models for human disease. However, we now know that not all pathogens can be grown in pure culture, and many human diseases cannot be reliably replicated in animal hosts. Viruses and certain bacteria, including Rickettsia and Chlamydia, are obligate intracellular pathogens that can grow only when inside a host cell. If a microbe cannot be cultured, a researcher cannot move past postulate 2. Likewise, without a suitable nonhuman host, a researcher cannot evaluate postulate 3 without deliberately infecting humans, which presents obvious ethical concerns. AIDS is an example of such a disease because the human immunodeficiency virus (HIV) only causes disease in humans.

Molecular Koch’s Postulates

In 1988, Stanley Falkow (1934–) proposed a revised form of Koch’s postulates known as molecular Koch’s postulates. These are listed in the left column of Table 15.4. The premise for molecular Koch’s postulates is not in the ability to isolate a particular pathogen but rather to identify a gene that may cause the organism to be pathogenic.


Molecular Koch’s Postulates Applied to EHEC
Molecular Koch’s Postulates Application to EHEC

(1) The phenotype (sign or symptom of disease) should be associated only with pathogenic strains of a species.

EHEC causes intestinal inflammation and diarrhea, whereas nonpathogenic strains of E. coli do not.
(2) Inactivation of the suspected gene(s) associated with pathogenicity should result in a measurable loss of pathogenicity. One of the genes in EHEC encodes for Shiga toxin, a bacterial toxin (poison) that inhibits protein synthesis. Inactivating this gene reduces the bacteria’s ability to cause disease.
(3) Reversion of the inactive gene should restore the disease phenotype. By adding the gene that encodes the toxin back into the genome (e.g., with a phage or plasmid), EHEC’s ability to cause disease is restored.
Microbiology book's Table 15.4 Molecular Koch’s Postulates Applied to EHEC

As with Koch’s original postulates, the molecular Koch’s postulates have limitations. For example, genetic manipulation of some pathogens is not possible using current methods of molecular genetics. In a similar vein, some diseases do not have suitable animal models, which limits the utility of both the original and molecular postulates.

Pathogenicity and Virulence

The ability of a microbial agent to cause disease is called pathogenicity, and the degree to which an organism is pathogenic is called virulence. Virulence is a continuum. On one end of the spectrum are organisms that are avirulent (not harmful) and on the other are organisms that are highly virulent. Highly virulent pathogens will almost always lead to a disease state when introduced to the body, and some may even cause multi-organ and body system failure in healthy individuals. Less virulent pathogens may cause an initial infection, but may not always cause severe illness. Pathogens with low virulence would more likely result in mild signs and symptoms of disease, such as low-grade fever, headache, or muscle aches. Some individuals might even be asymptomatic.

Virulence of a pathogen can be quantified using controlled experiments with laboratory animals. Two important indicators of virulence are the median infectious dose (ID50) and the median lethal dose (LD50), both of which are typically determined experimentally using animal models. The ID50 is the number of pathogen cells or virions required to cause active infection in 50% of inoculated animals. The LD50 is the number of pathogenic cells, virions, or amount of toxin required to kill 50% of infected animals. To calculate these values, each group of animals is inoculated with one of a range of known numbers of pathogen cells or virions. In graphs like the one shown in Figure 15.5, the percentage of animals that have been infected (for ID50) or killed (for LD50) is plotted against the concentration of pathogen inoculated. Figure 15.5 represents data graphed from a hypothetical experiment measuring the LD50 of a pathogen. Interpretation of the data from this graph indicates that the LD50 of the pathogen for the test animals is 104 pathogen cells or virions (depending upon the pathogen studied).

figure 15.5

Microbiology book's Figure 15.5 A graph like this is used to determine LD50 by plotting pathogen concentration against the percent of infected test animals that have died. In this example, the LD50 = 104 pathogenic particles.

Primary Pathogens and Opportunistic Pathogens

Primary pathogens are capable of causing pathological changes associated with disease in a healthy individual, whereas opportunistic pathogens can only cause disease when the individual is compromised by a break in protective barriers or immunosuppression. Individuals susceptible to opportunistic infections include the very young, the elderly, women who are pregnant, patients undergoing chemotherapy, people with immunodeficiencies (such as acquired immunodeficiency syndrome [AIDS]), patients who are recovering from surgery, and those who have had a breach of protective barriers (such as a severe wound or burn).

Stages of Pathogenesis

To cause disease, a pathogen must successfully achieve four steps or stages of pathogenesis: exposure (contact), adhesion (colonization), invasion, and infection. The pathogen must be able to gain entry to the host, travel to the location where it can establish an infection, evade or overcome the host’s immune response, and cause damage (i.e., disease) to the host. In many cases, the cycle is completed when the pathogen exits the host and is transmitted to a new host.


An encounter with a potential pathogen is known as exposure or contact. The food we eat and the objects we handle are all ways that we can come into contact with potential pathogens. Yet, not all contacts result in infection and disease. For a pathogen to cause disease, it needs to be able to gain access into host tissue. An anatomic site through which pathogens can pass into host tissue is called a portal of entry. These are locations where the host cells are in direct contact with the external environment. Major portals of entry are identified in Figure 15.6 and include the skin, mucous membranes, and parenteral routes.

Microbiology book's Figure 15.6 Shown are different portals of entry where pathogens can gain access into the body. With the exception of the placenta, which is only present during pregnancy, many of these locations are directly exposed to external environments.

Mucosal surfaces are the most important portals of entry for microbes; these include the mucous membranes of the respiratory tract, the gastrointestinal tract, and the genitourinary tract. Although most mucosal surfaces are in the interior of the body, some are contiguous with the external skin at various body openings, including the eyes, nose, mouth, urethra, and anus.

Most pathogens are suited to a particular portal of entry. A pathogen’s portal specificity is determined by the organism’s environmental adaptions and by the enzymes and toxins they secrete. The respiratory and gastrointestinal tracts are particularly vulnerable portals of entry because particles that include microorganisms are constantly inhaled or ingested, respectively.

Pathogens can also enter through a breach in the protective barriers of the skin and mucous membranes. Pathogens that enter the body in this way are said to enter by the parenteral route. For example, the skin is a good natural barrier to pathogens, but breaks in the skin (e.g., wounds, insect bites, animal bites, needle pricks) can provide a parenteral portal of entry for microorganisms. In pregnant women, the placenta normally prevents microorganisms from passing from the mother to the fetus. However, a few pathogens are capable of crossing the blood-placental barrier. The gram-positive bacterium Listeria monocytogenes, which causes the foodborne disease listeriosis, is one example that poses a serious risk to the fetus and can sometimes lead to spontaneous abortion. Other pathogens that can pass the placental barrier to infect the fetus are known collectively by the acronym TORCH (Table 15.6).

Transmission of infectious diseases from mother to baby is also a concern at the time of birth when the baby passes through the birth canal. Babies whose mothers have active chlamydia or gonorrhea infections may be exposed to the causative pathogens in the vagina, which can result in eye infections that lead to blindness. To prevent this, it is standard practice to administer antibiotic drops to infants’ eyes shortly after birth.

Pathogens Capable of Crossing the Placental Barrier (TORCH Infections)
Disease Pathogen




Toxoplasma gondii (protozoan)


Hepatitis B
Fifth disease (erythema infectiosum)


Treponema pallidum (bacterium)
Varicella-zoster virus (human herpesvirus 3)
Hepatitis B virus (hepadnavirus)
Parvovirus B19


Rubella (German measles)






Human herpesvirus 5




Herpes simplex viruses (HSV) 1 and 2

Microbiology book's Table 15.6

Following the initial exposure, the pathogen adheres at the portal of entry. The term adhesion refers to the capability of pathogenic microbes to attach to the cells of the body using adhesion factors, and different pathogens use various mechanisms to adhere to the cells of host tissues.


Once adhesion is successful, invasion can proceed. Invasion involves the dissemination of a pathogen throughout local tissues or the body. Pathogens may produce exoenzymes or toxins, which serve as virulence factors that allow them to colonize and damage host tissues as they spread deeper into the body. Pathogens may also produce virulence factors that protect them against immune system defenses. A pathogen’s specific virulence factors determine the degree of tissue damage that occurs. Figure 15.8 shows the invasion of H. pylori into the tissues of the stomach, causing damage as it progresses.

figure 15.8

Microbiology book's Figure 15.8 H. pylori is able to invade the lining of the stomach by producing virulence factors that enable it pass through the mucin layer covering epithelial cells. (credit: modification of work by Zina Deretsky, National Science Foundation)

Intracellular pathogens achieve invasion by entering the host’s cells and reproducing. Some are obligate intracellular pathogens (meaning they can only reproduce inside of host cells) and others are facultative intracellular pathogens (meaning they can reproduce either inside or outside of host cells). By entering the host cells, intracellular pathogens are able to evade some mechanisms of the immune system while also exploiting the nutrients in the host cell.


Following invasion, successful multiplication of the pathogen leads to infection. Infections can be described as local, focal, or systemic, depending on the extent of the infection.

  • Infections and disease can be caused by pathogens in the environment or microbes in an individual’s resident microbiota.
  • secondary infection can sometimes occur after the host’s defenses or normal microbiota are compromised by a primary infection or antibiotic treatment.
Transmission of Disease

For a pathogen to persist, it must put itself in a position to be transmitted to a new host, leaving the infected host through a portal of exit (Figure 15.9). As with portals of entry, many pathogens are adapted to use a particular portal of exit. Similar to portals of entry, the most common portals of exit include the skin and the respiratory, urogenital, and gastrointestinal tracts. Coughing and sneezing can expel pathogens from the respiratory tract. A single sneeze can send thousands of virus particles into the air. Secretions and excretions can transport pathogens out of other portals of exit. Feces, urine, semen, vaginal secretions, tears, sweat, and shed skin cells can all serve as vehicles for a pathogen to leave the body. Pathogens that rely on insect vectors for transmission exit the body in the blood extracted by a biting insect. Similarly, some pathogens exit the body in blood extracted by needles.

figure 15.9

Microbiology book's Figure 15.9 Pathogens leave the body of an infected host through various portals of exit to infect new hosts.)

Knowledge Check

Topic 4: Modes of Disease Transmission

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • describe the different types of disease reservoirs.
  • compare contact, vector, and vehicle modes of transmission.
  • define nosocomial infections.


Understanding how infectious pathogens spread is critical to preventing infectious disease. Many pathogens require a living host to survive, while others may be able to persist in a dormant state outside of a living host. But having infected one host, all pathogens must also have a mechanism of transfer from one host to another or they will die when their host dies. Pathogens often have elaborate adaptations to exploit host biology, behavior, and ecology to live in and move between hosts. Hosts have evolved defenses against pathogens, but because their rates of evolution are typically slower than their pathogens (because their generation times are longer), hosts are usually at an evolutionary disadvantage.

Reservoirs and Carriers

For pathogens to persist over long periods of time they require reservoirs where they normally reside. Reservoirs can be living organisms or nonliving sites. Reservoirs of human disease can include the human and animal populations, soil, water, and inanimate objects or materials.

An individual capable of transmitting a pathogen without displaying symptoms is referred to as a carrier. A passive carrier is contaminated with the pathogen and can mechanically transmit it to another host; however, a passive carrier is not infected. For example, a health-care professional who fails to wash his hands after seeing a patient harboring an infectious agent could become a passive carrier, transmitting the pathogen to another patient who becomes infected.

By contrast, an active carrier is an infected individual who can transmit the disease to others. An active carrier may or may not exhibit signs or symptoms of infection. For example, active carriers may transmit the disease during the incubation period (before they show signs and symptoms) or the period of convalescence (after symptoms have subsided). Active carriers who do not present signs or symptoms of disease despite infection are called asymptomatic carriers. Pathogens such as hepatitis B virus, herpes simplex virus, and HIV are frequently transmitted by asymptomatic carriers. 


Regardless of the reservoir, transmission must occur for an infection to spread. First, transmission from the reservoir to the individual must occur. Then, the individual must transmit the infectious agent to other susceptible individuals, either directly or indirectly. Pathogenic microorganisms employ diverse transmission mechanisms.

Contact Transmission

Contact transmission includes direct contact or indirect contact. Person-to-person transmission is a form of direct contact transmission. Here the agent is transmitted by physical contact between two individuals (Figure 16.9) through actions such as touching, kissing, sexual intercourse, or droplet sprays. Direct contact can be categorized as vertical, horizontal, or droplet transmission. Vertical direct contact transmission occurs when pathogens are transmitted from mother to child during pregnancy, birth, or breastfeeding. Other kinds of direct contact transmission are called horizontal direct contact transmission. Often, contact between mucous membranes is required for entry of the pathogen into the new host, although skin-to-skin contact can lead to mucous membrane contact if the new host subsequently touches a mucous membrane. Contact transmission may also be site-specific; for example, some diseases can be transmitted by sexual contact but not by other forms of contact.

When an individual coughs or sneezes, small droplets of mucus that may contain pathogens are ejected. This leads to direct droplet transmission, which refers to droplet transmission of a pathogen to a new host over distances of one meter or less. A wide variety of diseases are transmitted by droplets, including influenza and many forms of pneumonia. Transmission over distances greater than one meter is called airborne transmission.

Indirect contact transmission involves inanimate objects called fomites that become contaminated by pathogens from an infected individual or reservoir (Figure 16.10). For example, an individual with the common cold may sneeze, causing droplets to land on a fomite such as a tablecloth or carpet, or the individual may wipe her nose and then transfer mucus to a fomite such as a doorknob or towel. Transmission occurs indirectly when a new susceptible host later touches the fomite and transfers the contaminated material to a susceptible portal of entry. Fomites can also include objects used in clinical settings that are not properly sterilized, such as syringes, needles, catheters, and surgical equipment. Pathogens transmitted indirectly via such fomites are a major cause of healthcare-associated infections (see Controlling Microbial Growth).

figure 16.9

Microbiology book's Figure 16.9 Direct contact transmission of pathogens can occur through physical contact. Many pathogens require contact with a mucous membrane to enter the body, but the host may transfer the pathogen from another point of contact (e.g., hand) to a mucous membrane (e.g., mouth or eye). (credit left: modification of work by Lisa Doehnert)


figure 16.10.

Microbiology book's Figure 16.10 Fomites are nonliving objects that facilitate the indirect transmission of pathogens. Contaminated doorknobs, towels, and syringes are all common examples of fomites. (credit left: modification of work by Kate Ter Haar; credit middle: modification of work by Vernon Swanepoel; credit right: modification of work by “Zaldylmg”/Flickr)

Vehicle Transmission

The term vehicle transmission refers to the transmission of pathogens through vehicles such as water, food, and air. Water contamination through poor sanitation methods leads to waterborne transmission of disease. Waterborne disease remains a serious problem in many regions throughout the world. The World Health Organization (WHO) estimates that contaminated drinking water is responsible for more than 500,000 deaths each year.10 Similarly, food contaminated through poor handling or storage can lead to foodborne transmission of disease (Figure 16.11).

figure 16.11.

Microbiology book's Figure 16.11 Food is an important vehicle of transmission for pathogens, especially of the gastrointestinal and upper respiratory systems. Notice the glass shield above the food trays, designed to prevent pathogens ejected in coughs and sneezes from entering the food. (credit: Fort George G. Meade Public Affairs Office)

Dust and fine particles known as aerosols, which can float in the air, can carry pathogens and facilitate the airborne transmission of disease. For example, dust particles are the dominant mode of transmission of hantavirus to humans. Hantavirus is found in mouse feces, urine, and saliva, but when these substances dry, they can disintegrate into fine particles that can become airborne when disturbed; inhalation of these particles can lead to a serious and sometimes fatal respiratory infection.

Although droplet transmission over short distances is considered contact transmission as discussed above, longer distance transmission of droplets through the air is considered vehicle transmission. Unlike larger particles that drop quickly out of the air column, fine mucus droplets produced by coughs or sneezes can remain suspended for long periods of time, traveling considerable distances. In certain conditions, droplets desiccate quickly to produce a droplet nucleus that is capable of transmitting pathogens; air temperature and humidity can have an impact on effectiveness of airborne transmission.

Tuberculosis is often transmitted via airborne transmission when the causative agent, Mycobacterium tuberculosis, is released in small particles with coughs. Because tuberculosis requires as few as 10 microbes to initiate a new infection, patients with tuberculosis must be treated in rooms equipped with special ventilation, and anyone entering the room should wear a mask.

Vector Transmission

Diseases can also be transmitted by a mechanical or biological vector, an animal (typically an arthropod) that carries the disease from one host to another. Mechanical transmission is facilitated by a mechanical vector, an animal that carries a pathogen from one host to another without being infected itself. For example, a fly may land on fecal matter and later transmit bacteria from the feces to food that it lands on; a human eating the food may then become infected by the bacteria, resulting in a case of diarrhea or dysentery (Figure 16.12).

figure 16.12.

Microbiology book's Figure 16.12 (a) A mechanical vector carries a pathogen on its body from one host to another, not as an infection. (b) A biological vector carries a pathogen from one host to another after becoming infected itself.

Biological transmission occurs when the pathogen reproduces within a biological vector that transmits the pathogen from one host to another (Figure 16.12). Arthropods are the main vectors responsible for biological transmission. Most arthropod vectors transmit the pathogen by biting the host, creating a wound that serves as a portal of entry. The pathogen may go through part of its reproductive cycle in the gut or salivary glands of the arthropod to facilitate its transmission through the bite. For example, hemipterans (called “kissing bugs” or “assassin bugs”) transmit Chagas disease to humans by defecating when they bite, after which the human scratches or rubs the infected feces into a mucous membrane or break in the skin.

Biological insect vectors include mosquitoes, which transmit malaria and other diseases, and lice, which transmit typhus. Other arthropod vectors can include arachnids, primarily ticks, which transmit Lyme disease and other diseases, and mites, which transmit scrub typhus and rickettsial pox. Biological transmission, because it involves survival and reproduction within a parasitized vector, complicates the biology of the pathogen and its transmission. There are also important non-arthropod vectors of disease, including mammals and birds. Various species of mammals can transmit rabies to humans, usually by means of a bite that transmits the rabies virus. Chickens and other domestic poultry can transmit avian influenza to humans through direct or indirect contact with avian influenza virus A shed in the birds’ saliva, mucous, and feces.

Healthcare-associated infections (HAI), or nosocomial infections, are acquired in a clinical setting. Transmission is facilitated by medical interventions and the high concentration of susceptible, immunocompromised individuals in clinical settings.

Global Public Health external link.

  • The World Health Organization (WHO) is an agency of the United Nations that collects and analyzes data on disease occurrence from member nations. WHO also coordinates public health programs and responses to international health emergencies.
  • Emerging diseases are those that are new to human populations or that have been increasing in the past two decades. Emerging diseases are found in all countries, both developed and developing, such as AIDS, Chikungunya fever, Ebola virus disease, H1N1 influenza, Lyme disease and West Nile disease. Reemerging diseases are those that are making a resurgence in susceptible populations after previously having been controlled in some geographic areas. Examples of such diseases are drug-resistant forms of tuberculosis, bacterial pneumonia, and malaria. Drug-resistant strains of the bacteria causing gonorrhea and syphilis are also becoming more widespread, raising concerns of untreatable infections.

Knowledge Check

Topic 5: The Global Spread of Infectious Disease

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • summarizes recent global changes and their impacts on disease emergence, local-scale dynamics and global spread
  • interpret charts that reflect “A historical outlook of global spread of infectious diseases”


The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013–2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society.

The table summarizes select recent global changes (rows) and their impacts on disease emergence, local-scale dynamics and global spread (columns). An example susceptible (S), infected (I), recovered (R) model is shown, where β represents the transmission rate and γ is the recovery rate.

fig 3

"Infectious disease in an era of global change" article's Figure 3 The table summarizes select recent global changes (rows) and their impacts on disease emergence, local-scale dynamics and global spread (columns). An example susceptible (S), infected (I), recovered (R) model is shown, where β represents the transmission rate and γ is the recovery rate.

Citation: Baker, R.E., Mahmud, A.S., Miller, I.F. et al. Infectious disease in an era of global change. Nat Rev Microbiol 20, 193–205 (2022).

A historical outlook of global spread of infectious diseases

In premodern times, colonization, slavery and war led to the global spread of infectious diseases, with devastating consequences (Fig. 1a). Human diseases such as tuberculosis, polio, smallpox and diphtheria circulated widely, and before the advent of vaccines, these diseases caused substantial morbidity and mortality. At the same time, animal diseases such as rinderpest spread along trade routes and with travelling armies, with devastating impacts on livestock and dependent human populations1. However, in the past two decades, medical advances, access to health care and improved sanitation have reduced the overall mortality and morbidity linked to infectious diseases, particularly for lower respiratory tract infections and diarrhoeal disease (Fig. 1d). The swift development of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine speaks to the efficacy of modern science in rapidly countering threats from emerging pathogens. Nevertheless, infectious disease burden remains substantial in countries with low and lower-middle incomes, while mortality and morbidity associated with neglected tropical diseases, HIV infection, tuberculosis and malaria remain high. Moreover, deaths from emerging and re-emerging infections, in comparison with seasonal and endemic infections, have persisted throughout the twenty-first century (Fig. 1c). This points to a possible new era of infectious disease, defined by outbreaks of emerging, re-emerging and endemic pathogens that spread quickly, aided by global connectivity and shifted ranges owing to climate change (Fig. 1d).

fig 1.

"Infectious disease in an era of global change" article's Figure 1 a | Examples of epidemic periods associated with different eras of human transportation (land, maritime and air travel) are shown. Overland trade networks and war campaigns are thought to have contributed to multiple epidemics in the Mediterranean in late classical antiquity (green), beginning with the Antonine plague, which reportedly claimed the life of the Roman emperor Lucius Verus125,126,127,128. Maritime transportation (red and grey) leading to European contact with the Americas and the subsequent Atlantic slave trade resulted in the importation of Plasmodium falciparum malaria and novel viral pathogens129. In modern times, air travel (purple) resulted in the importation of severe acute respiratory syndrome (SARS) coronavirus to 27 countries before transmission was halted130. b | In recent years, increases in air travel, trade and urbanization at global (left) and regional (right) scales have accelerated, indicating ever more frequent transport of people and goods between growing urban areas (source World Bank). c | Log deaths from major epidemics in the twenty-first century (source World Health Organization). d | Disability-adjusted life years lost from infectious diseases (source Our World in Data). MERS, Middle East respiratory syndrome; NTD, neglected tropical disease.

Citation: Baker, R.E., Mahmud, A.S., Miller, I.F. et al. Infectious disease in an era of global change. Nat Rev Microbiol 20, 193–205 (2022).

Knowledge Check

Topic 6: Selected Infectious Diseases - Influenza

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • summarize the symptoms, testing, treatment options and prevention of influenza.
  • summarize the infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of influenza.
  • summarize how flu viruses adapt to evade the immune system.



Flu is a contagious respiratory illness caused by influenza viruses that infect the nose, throat, and sometimes the lungs. Most people with the flu get better on their own. But sometimes, influenza and its complications can cause severe illness, and at times can lead to death.



There are two main types of human flu viruses: types A and B. The flu A and B viruses that routinely spread in people are responsible for seasonal flu epidemics each year. Flu A viruses can be broken down into sub-types depending on the genes that make up the surface proteins. Over the course of a flu season, different types (A & B) and subtypes (only for flu A) of flu circulate and cause illness.


People who have flu often feel some or all of these symptoms:

  • fever* or feeling feverish/chills
  • cough
  • sore throat
  • runny or stuffy nose
  • muscle or body aches
  • headaches
  • fatigue (tiredness)
  • some people may have vomiting and diarrhea, though this is more common in children than adults.

*It’s important to note that not everyone with flu will have a fever.

Risk Factors (Mayo Clinic) external link.

Factors that may increase your risk of developing the flu or its complications include:

  • Age. Seasonal influenza tends to have worse outcomes in children under age 2, and adults older than age 65.
  • Living or working conditions. People who live or work in facilities with many other residents, such as nursing homes or military barracks, are more likely to develop the flu. People who are staying in the hospital also are at higher risk.
  • Weakened immune system. Cancer treatments, anti-rejection medications, long-term use of steroids, organ transplant, blood cancer or HIV/AIDS can weaken the immune system. This can make it easier to catch the flu and may increase the risk of developing complications.
  • Chronic illnesses. Chronic conditions may increase the risk of influenza complications. Examples include asthma and other lung diseases, diabetes, heart disease, nervous system diseases, metabolic disorders, problems with an airway, and kidney, liver or blood disease.
  • Race. American Indians or Alaska Natives people may have an increased risk of influenza complications.
  • Aspirin use under age 19. People who are younger than 19 years of age and receiving long-term aspirin therapy are at risk of developing Reye's syndrome if infected with influenza.
  • Pregnancy. Pregnant people are more likely to develop influenza complications, particularly in the second and third trimesters. This risk continues up to two weeks after the baby is born.
  • Obesity. People with a body mass index (BMI) of 40 or higher have an increased risk of flu complications.


Most experts believe that flu viruses spread mainly by tiny droplets made when people with flu cough, sneeze, or talk. These droplets can land in the mouths or noses of people who are nearby. Less often, a person might get flu by touching a surface or object that has flu virus on it and then touching their own mouth, nose or possibly their eyes.

Complications (Mayo Clinic) external link.

The flu is not serious for young and healthy adult. Although it may make produce miserable symptoms, the flu usually goes away in a week or two with no lasting effects. But children and adults at high risk may develop complications that may include:

  • Pneumonia
  • Bronchitis
  • Asthma flare-ups
  • Heart problems
  • Ear infections
  • Acute respiratory distress syndrome

Pneumonia is one of the most serious complications. For older adults and people with a chronic illness, pneumonia can be deadly.


A number of tests are available to detect flu viruses in respiratory specimens. The most common are called “rapid influenza diagnostic tests (RIDTs).” RIDTs work by detecting the parts of the virus (antigens) that stimulate an immune response. These tests can provide results within approximately 10-15 minutes but may not be as accurate as other flu tests. Therefore, you could still have flu, even though your rapid test result is negative. Other flu tests called “rapid molecular assays” detect genetic material of the flu virus. Rapid molecular assays produce results in 15-20 minutes and are more accurate than RIDTs.

In addition to RIDTs and rapid molecular assays, there are several more accurate flu tests available that must be performed in specialized laboratories, such as hospital and public health laboratories. These tests include reverse transcription polymerase chain reaction (RT-PCR), viral culture, and immunofluorescence assays. All of these tests require that a health care provider swipe the inside of your nose or the back of your throat with a swab and then send the swab for testing. Results may take one to several hours.

After an evaluation, a doctor may choose to diagnose the patient with flu based on the symptoms and their clinical judgement and may not perform any testing.


Usually, people will need nothing more than rest and plenty of fluids to treat the flu. But if one has a severe infection or are at higher risk of complications, the health care provider may prescribe an antiviral medication to treat the flu. These drugs can include oseltamivir (Tamiflu), zanamivir (Relenza), peramivir (Rapivab) or baloxavir (Xofluza). These medications may shorten your illness by a day or so and help prevent serious complications.

Prevention/ Controlling the spread of infection

The U.S. Centers for Disease Control and Prevention (CDC) recommends annual flu vaccination for everyone age 6 months or older. The flu vaccine can lower your risk of getting the flu. It also can lower the risk of having serious illness from the flu and needing to stay in the hospital.

The influenza vaccine isn't 100% effective, so it's also important to take several measures to reduce the spread of infection, including:

  • Wash your hands. Washing your hands often with soap and water for at least 20 seconds is an effective way to prevent many common infections. Or use alcohol-based hand sanitizers if soap and water aren't available.
  • Avoid touching your face. Avoid touching your eyes, nose and mouth.
  • Cover your coughs and sneezes. Cough or sneeze into a tissue or your elbow. Then wash your hands.
  • Clean surfaces. Regularly clean often-touched surfaces to prevent spread of infection from touching a surface with the virus on it and then your face.
  • Avoid crowds. The flu spreads easily wherever people gather — in child care centers, schools, office buildings, auditoriums and public transportation. By avoiding crowds during peak flu season, you reduce your chances of infection.

Also avoid anyone who is sick. And if you're sick, stay home for at least 24 hours after your fever is gone so that you lessen your chance of infecting others.


Each year CDC estimates the burden of influenza in the U.S. CDC uses modeling to estimate the number of flu illnesses, medical visits, hospitalizations, and deaths related to flu that occurred in a given season. The methods used to calculate these estimates are described on CDC’s webpage, How CDC Estimates the Burden of Seasonal Flu in the U.S.

CDC uses the estimates of the burden of flu in the population and the impact of flu vaccination to inform policy and communications related to flu.

Estimated rates of influenza disease outcomes, per 100,000 by age group — United States, 2010-2011 influenza season
Illness rate
Age Group Estimate 95% Cr I
0-4 yrs 13,743.2 (11,319.6, 17,432.0)
5-17 yrs 8,216.6 (6,686.1, 10,832.1)
18-49 yrs 5,468.1 (4,537.7, 7,030.2)
50-64 yrs 8,240.5 (6,858.4, 11,046.5)
65+ yrs 4,521.1 (3,951.1, 5,948.4)
Medical visit rate
Age Group Estimate 95% Cr I
0-4 yrs 9,207.9 (7,411.9, 11,935.4)
5-17 yrs 4,272.6 (3,423.3, 5,712.9)
18-49 yrs 2,023.2 (1,626.2, 2,684.8)
50-64 yrs 3,543.4 (2,827.8, 4,881.0)
65+ yrs 2,531.8 (2,114.9, 3,436.3)
Hospitalization rate
Age Group Estimate 95% Cr I
0-4 yrs 95.8 (78.9, 121.5)
5-17 yrs 22.5 (18.3, 29.7)
18-49 yrs 30.7 (25.5, 39.5)
50-64 yrs 87.4 (72.7, 117.1)
65+ yrs 411.0 (359.2, 540.8)
Mortality rate
Age Group Estimate 95% Cr I
0-4 yrs 1.0 (0.0, 2.5)
5-17 yrs 0.3 (0.0, 1.2)
18-49 yrs 3.9 (2.7, 6.2)
50-64 yrs 10.1 (6.8, 17.8)
65+ yrs 62.4 (50.5, 95.2)

Knowledge Check:

Topic 7: Selected Infectious Diseases - COVID-19 (CDC)

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • summarize the symptoms, testing, treatment options and prevention of COVID-19.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of COVID-19


Overview (Mayo Clinic) external link.

Coronaviruses are a family of viruses that can cause illnesses such as the common cold, severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). In 2019, a new coronavirus was identified as the cause of a disease outbreak that originated in China.

In March 2020, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemic.

Public health groups, including the U.S. Centers for Disease Control and Prevention (CDC) and WHO, are monitoring the COVID-19 pandemic and posting updates on their websites. These groups also have issued recommendations for preventing and treating the virus that causes COVID-19.


The virus is known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It contain a single-stranded RNA. The disease it causes is called coronavirus disease 2019 (COVID-19).


People with COVID-19 have had a wide range of symptoms reported – ranging from mild symptoms to severe illness. Symptoms may appear 2-14 days after exposure to the virus. Anyone can have mild to severe symptoms.

Possible symptoms include:

  • Fever or chills
  • Cough
  • Shortness of breath or difficulty breathing
  • Fatigue
  • Muscle or body aches
  • Headache
  • New loss of taste or smell
  • Sore throat
  • Congestion or runny nose
  • Nausea or vomiting
  • Diarrhea

This list does not include all possible symptoms. Symptoms may change with new COVID-19 variants and can vary depending on vaccination status. CDC will continue to update this list as we learn more about COVID-19. Older adults and people who have underlying medical conditions like heart or lung disease or diabetes are at higher risk for getting very sick from COVID-19.

Risk Factors (Mayo Clinic) external link.

Risk factors for COVID-19 appear to include:

  • Close contact with someone who has COVID-19, especially someone with symptoms.
  • Being coughed or sneezed on by an infected person.
  • Being near an infected person when in an indoor space with poor airflow.

Risk factors for serious COVID-19 illness

Some people are at a higher risk of serious COVID-19 illness than others. This includes people who are older, and the risk increases with age.

People with existing medical conditions also may have a higher risk of serious illness. This includes people who have:

  • Sickle cell disease or thalassemia.
  • Serious heart diseases, such as heart failure, coronary artery disease or cardiomyopathy, and possibly high blood pressure.
  • Chronic kidney, liver or lung diseases.

People with dementia or Alzheimer's are also at higher risk, as are people with brain and nervous system conditions such as stroke. Smoking increases the risk of serious COVID-19 illness. And people with body mass index in the overweight category or obese category may have an increased risk as well.

Other medical conditions that may increase the risk of serious illness from COVID-19 include:

  • Cancer.
  • Type 1 or type 2 diabetes.
  • Weakened immune system from solid organ transplants or bone marrow transplants, some medicines, or HIV.
  • Pregnancy.
  • Down syndrome.
  • Substance use disorders.

This list is not complete. Other medical conditions may increase your risk of serious illness from COVID-19.


COVID-19 spreads when an infected person breathes out droplets and very small particles that contain the virus. These droplets and particles can be breathed in by other people or land on their eyes, noses, or mouth. In some circumstances, they may contaminate surfaces they touch.

Anyone infected with COVID-19 can spread it, even if they do NOT have symptoms.


Although most people with COVID-19 have mild to moderate symptoms, the disease can cause severe medical complications and lead to death in some people.

Older adults or people with existing medical conditions are at greater risk of becoming seriously ill with COVID-19.

Complications can include:

  • Pneumonia and trouble breathing.
  • Organ failure in several organs.
  • Heart problems.
  • A severe lung condition that causes a low amount of oxygen to go through your bloodstream to your organs, called acute respiratory distress syndrome.
  • Blood clots.
  • Acute kidney injury.
  • Additional viral and bacterial infections.

People with Long COVID can have a wide range of symptoms that can last weeks, months, or even years after infection. Sometimes the symptoms can even go away and come back again. For some people, Long COVID can last weeks, months, or years after COVID-19 illness and can sometimes result in disability.


various at home covid tests.

Viral tests

Llook for a current infection with SARS-CoV-2, the virus that causes COVID-19, by testing specimens from your nose or mouth. All tests should be performed following FDA’s requirements.

There are two main types of viral tests:

  • Polymerase Chain Reaction (PCR) tests
  • Antigen tests
PCR Tests

PCR tests are the “gold standard” for COVID-19 tests. They are a type of nucleic acid amplification test (NAAT), which are more likely to detect the virus than antigen tests. Your sample will usually be taken by a healthcare provider and transported to a laboratory for testing. It may take up to 3 days to receive results.

Antigen Tests

Antigen tests* are rapid tests that usually produce results in 15-30 minutes. Positive results are very accurate and reliable. However, in general, antigen tests are less likely to detect the virus than PCR tests, especially when symptoms are not present. Therefore, a single negative antigen test cannot rule out infection. To be confident you do not have COVID-19, FDA recommends 2 negative antigen tests for individuals with symptoms or 3 antigen tests for those without symptoms, performed 48 hours apart. A single PCR test can be used to confirm an antigen test result.

*Self-tests, or at-home tests, are antigen tests that can be taken anywhere without having to go to a specific testing site. Read self-test package inserts thoroughly and follow the instructions closely when performing the test.


Most people with COVID-19 have mild illness and can recover at home. You can treat symptoms with rest, fluid and over-the-counter medicines, such as acetaminophen (Tylenol) or ibuprofen (Motrin, Advil), to help you feel better.

There are several FDA-authorized or approved antiviral medications used to treat mild to moderate COVID-19 in people who are more likely to get very sick. Medications to treat COVID-19 must be prescribed by a healthcare provider and started as soon as possible after diagnosis to be effective.

  • Antiviral treatments target specific parts of the virus to stop it from multiplying in the body, helping to prevent severe illness and death.

Prevention/control of the spread

COVID-19 vaccines available in the United States effectively protect people from getting seriously ill, being hospitalized, and even dying.

People who have COVID-19 can spread the virus to others. Precautions such as isolation, masking, and avoiding contact with people who are at high risk of getting very sick can limit the spread of the disease. Isolation is used to separate people with confirmed or suspected COVID-19 from those without COVID-19.

Knowledge Check

Topic 8: Selected Infectious Diseases – MPox (CDC)

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • summarize the symptoms, testing, treatment options and prevention of MPox.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of MPox


Overview external link.

Mpox is a rare disease caused by infection with the mpox virus. Mpox virus is part of the same family of viruses as variola virus, the virus that causes smallpox. Mpox symptoms are similar to smallpox symptoms, but milder, and mpox is rarely fatal. Mpox is not related to chickenpox.

The first human case of mpox was recorded in 1970. Prior to the 2022 outbreak, mpox had been reported in people in several central and western African countries. Previously, almost all mpox cases in people outside of Africa were linked to international travel to countries where the disease commonly occurs or through imported animals. These cases occurred on multiple continents.

In the most recent mpox outbreak, the virus is spreading primarily through sexual contact; however, infections have occurred through other exposures, including non-sexual contact with infectious lesions and from contaminated instruments in clinic settings.


Monkey Pox (Mpox), an enveloped double - stranded DNA virus , belongs to the Orthopoxvirus genus.


People with mpoxoften get a rash that may be located on hands, feet, chest, face, or mouth or near the genitals, including penis, testicles, labia, and vagina, and anus. The incubation period is 3-17 days. During this time, a person does not have symptoms and may feel fine.

  • The rash will go through several stages, including scabs, before healing.
  • The rash can initially look like pimples or blisters and may be painful or itchy.

Other symptoms of mpox can include:

  • Fever
  • Chills
  • Swollen lymph nodes
  • Exhaustion
  • Muscle aches and backache
  • Headache
  • Respiratory symptoms (e.g., sore throat, nasal congestion, or cough)

Risk factors/Transmission (WHO) external link.

Anyone can get mpox. It spreads from contact with infected:

  • persons, through touch, kissing, or sex
  • animals, when hunting, skinning, or cooking them
  • materials, such as contaminated sheets, clothes or needles
  • pregnant persons, who may pass the virus on to their unborn baby.


People with mpoxcan become very sick. Persons with immune suppression due to medication or medical conditions are at higher risk of serious illness and death due to mpox. People with advanced HIV (immunocompromised) are at increased risk of severe mpox and death if they get the mpox virus.


Identifying mpox can be difficult as other infections and conditions can look similar. It is important to distinguish mpox from chickenpox, measles, bacterial skin infections, scabies, herpes, syphilis, other sexually transmissible infections, and medication-associated allergies.Detection of viral DNA by polymerase chain reaction (PCR) is the preferred laboratory test for mpox. The best diagnostic specimens are taken directly from the rash –skin, fluid or crusts –collected by vigorous swabbing. Testing blood is not recommended. Antibody detection methods may not be useful as they do not distinguish between different orthopoxviruses.

Treatment (CDC & WHO)

There are no treatments approved by the Food and Drug Administration (FDA) specifically for mpox. Antiviral drugs approved for treatment of smallpox may help to treat mpox because the viruses that cause mpox and smallpox are similar. The goal of treating mpox is to take care of the rash, manage pain and prevent complications. Early and supportive care is important to help manage symptoms and avoid further problems.

Prevention/control of the spread

  • Avoid close, skin-to-skin contact with people who have a rash that looks like mpox.
  • Avoid contact with objects and materials that a person with mpox has used.
  • Wash your hands often.
  • Get vaccinated. The JYNNEOS vaccine is approved for prevention of smallpoxand mpox. It is the primary vaccine being used in the U.S. during this outbreak.

Knowledge Check

Topic 9: Selected Infectious Diseases - Viral Hepatitis (CDC)

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • describe the functions of the liver.
  • summarize the symptoms, testing, treatment options and prevention of Hepatitis A, B, C.
  • summarize the complication of viral hepatitis.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of Hepatitis A, B, C.


Overview (John Hopkin’s Medicine) external link.

The liver regulates most chemical levels in the blood and excretes a product called bile. This helps carry away waste products from the liver. All the blood leaving the stomach and intestines passes through the liver. The liver processes this blood and breaks down, balances, and creates the nutrients and also metabolizes drugs into forms that are easier to use for the rest of the body or that are nontoxic. More than 500 vital functions have been identified with the liver. Some of the more well-known functions include the following:

  • Production of bile, which helps carry away waste and break down fats in the small intestine during digestion
  • Production of certain proteins for blood plasma
  • Production of cholesterol and special proteins to help carry fats through the body
  • Conversion of excess glucose into glycogen for storage (glycogen can later be converted back to glucose for energy) and to balance and make glucose as needed 
  • Regulation of blood levels of amino acids, which form the building blocks of proteins
  • Processing of hemoglobin for use of its iron content (the liver stores iron)
  • Conversion of poisonous ammonia to urea (urea is an end product of protein metabolism and is excreted in the urine)
  • Clearing the blood of drugs and other poisonous substances
  • Regulating blood clotting
  • Resisting infections by making immune factors and removing bacteria from the bloodstream
  • Clearance of bilirubin, also from red blood cells. If there is an accumulation of bilirubin, the skin and eyes turn yellow. 

When the liver has broken down harmful substances, its by-products are excreted into the bile or blood. Bile by-products enter the intestine and leave the body in the form of feces. Blood by-products are filtered out by the kidneys, and leave the body in the form of urine.

Hepatitis means inflammation of the liver. When the liver is inflamed or damaged, its function can be affected.

In the United States, the most common types of viral hepatitis:

  • hepatitis A, caused by Hepatitis A virus
  • hepatitis B, caused by Hepatitis B virus
  • hepatitis C, caused by Hepatitis C virus

Symptoms (Practical Management of Chronic Viral Hepatitis) external link.

Hepatitis A (15-150 days)/ Hepatitis B (1-6 months)/ Hepatitis C (The latent course: 2 to 26 weeks)
  • Most do not have any symptoms and their disease is diagnosed by doing medical tests.
  • The acute symptoms of disease exist in some patients.
  • Following the contact with the virus causing hepatitis and going through a period, which varies from a week to a few months (latent period), the acute symptoms of suffering from viral hepatitis would emerge: lack of appetite, excessive fatigue, exhaustion and vomit, abdominal pain, darkening of urine, paling of stool and turning of skin into yellow .
  • The symptoms usually last for days or weeks and  would be eradicated automatically.
  • Symptoms resembling influenza could be seen as muscular pain, exhaustion, and slight fever days or weeks before the emergence of the disease acute symptoms .

Course of the Disease:

Hepatitis A
  • Does not become a chronic, long-term, infection.
  • Not likely become re-infected.
  • Antibodies to the hepatitis A virus, which appear early in the course of infection, provide lifelong protection against the disease
Hepatitis B
  • Approximately 90% of infants and 25%–50% of children aged 1–5 years will remain chronically infected with HBV.
  • By contrast, approximately 95% of adults recover completely from HBV infection and do not become chronically infected
Hepatitis C
  • Many people eventually develop chronic liver disease, which can range from mild to severe and include cirrhosis and liver cancer.
  • Chronic liver disease in people with hepatitis C usually happens slowly, without any signs or symptoms, over several decades.
  • Chronic hepatitis C virus infection is often not recognized until people are screened for blood donation or from an abnormal blood test found during a routine doctor’s visit.

Risk factors

Hepatitis A
  • International travelers
  • Anal or oral sex
  • People who use illegal drugs
  • People with occupational risk for exposure
  • People who anticipate close personal contact with an international adoptee
  • People experiencing homelessness
Hepatitis B
  • Infants born to mothers with hepatitis B
  • People who inject drugs or share needles, syringes, and other types of drug equipment
  • Sex partners of people with hepatitis B
  • Oral and anal sex
  • People who live with someone who has hepatitis B
  • Health care and public safety workers exposed to blood on the job
  • People on dialysis
Hepatitis C
  • People who use injection drugs or did so in the past, even those who injected only once many years ago
  • People with HIV infection
  • People who have received transfusions or organ transplants concentrates produced before 1987
  • received a transfusion of blood or blood components, organ transplant before July 1992
  • Health care, emergency medical, and public safety personnel who have been exposed to the blood of someone who has hepatitis C Children born to mothers who have hepatitis C


Hepatitis A
  • Close person-to-person contact with an infected person
  • Sexual contact with an infected person
  • Ingestion of contaminated food or water
Hepatitis B
  • sex with a partner who has HBV infection;
  • injection drug use that involves sharing needles, syringes, or drug-preparation equipment
  • birth to a person who has HBV infection;
  • contact with blood from or open sores on a person who has HBV infection;
  • sharing certain items with a person who has HBV infection that can break the skin or mucous membranes (e.g., razors, toothbrushes, and glucose monitoring equipment), potentially resulting in exposure to blood
Hepatitis C
  • Contact with blood from an infected person

Complications: (Practical Management of Chronic Viral Hepatitis) external link.

  • A chronic disease that is identified by the replacement of fibrosis and consequently the deformation of liver's structure and performance.
  • Hepatitis B and C are the most important causes.
  • The symptoms at initial stages are fatigue, lethargy, loss of appetite, vomit, weight loss, reduction in sexual desire and potency in men, irritation and bloody vomit.


Hepatitis A
  • Hepatitis A cannot be distinguished from other types of viral hepatitis on the basis of clinical or epidemiologic features alone.
  • Serologic testing is required to confirm the diagnosis. Virtually all patients with acute hepatitis A have detectable IgM anti-HAV.
  • IgM generally becomes detectable 5 to 10 days before the onset of symptoms and can persist for up to 6 months.
Hepatitis B

CDC recommends use of the triple panel test which includes:

  • hepatitis B surface antigen (HBsAg)
  • antibody to hepatitis B surface antigen (anti-HBs)
  • total antibody to hepatitis B core antigen (total anti-HBc).
Hepatitis C
  • A blood test, called an HCV antibody test, is used to find out if someone has ever been infected with the hepatitis C virus. The HCV antibody test, sometimes called the anti-HCV test, looks for antibodies to the hepatitis C virus in blood.

Treatment (Mayo & CDC) external link.

Hepatitis A

No specific treatment exists for hepatitis A. Your body will clear the hepatitis A virus on its own. In most cases of hepatitis A, the liver heals within six months with no lasting damage.

Hepatitis B
  • acute: rest, proper nutrition, plenty of fluids and close monitoring while your body fights the infection
  • chronic: need treatment for the rest of their lives. The decision to start treatment depends on many factors, including: if cirrhosis is present; if you have other infections, such as hepatitis C or HIV
  • anti-viral meds, interferon injections
Hepatitis C
  • Antiviral medications (such as Direct Acting Antivirals (DAAs)
  • The goal of treatment is to have no hepatitis C virus detected in your body at least 12 weeks after one completes treatment.
  • Over 90% of people infected with hepatitis C virus (HCV) can be cured of their infection, regardless of HCV genotype, with 8–12 weeks of oral therapy
  • Supportive care following a healthy diet

prevention/control of the spread

Hepatitis A
  • full, two-dose series of hepatitis A vaccine
  • good hand hygiene
Hepatitis B
  • Full, three-dose Hepatitis B Vaccination
  • Avoid sharing items with an infected person (see transmission route)
Hepatitis C
  • There is no vaccine for hepatitis C
  • Observe the personal hygienic points (See transmission route)

Knowledge Check

Topic 10: Selected Infectious Diseases – STIs (NIH/HIV Info)

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • list the pathogens for listed STIs.
  • summarize the symptoms, diagnosis, treatment options and prevention of STIs.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of all STIs.



  1. Human Papilloma Virus (HPV)
  2. Human Simplex Virus (HSV)
  3. Trichomoniasis
  4. Chlamydia
  5. Gonorrhea
  6. Syphilis


  1. Human Papilloma Virus (HPV) pathogens:
    • Human Papillomavirus
    • the most common STI
  2. Human Simplex Virus (HSV) pathogens:
    • herpes simplex virus type 1 (HSV-1)
    • herpes simplex virus type 2 (HSV-2).
  3. Trichomoniasis pathogens:
    • Trichomonas vaginalis, a protozoan parasite
  4. Chlamydia pathogens:
    • Chlamydia trachomatis bacterium
  5. Gonorrhea pathogens:
    • Neisseria gonorrhoeae bacterium
  6. Syphilis pathogens:
    • Treponema pallidum bacterium


  1. Human Papilloma Virus (HPV) diagnosis:
    • Pap smear
    • DNA test (PCR, Southern Blot Hybridization, In Situ Hybridization)
  2. Human Simplex Virus (HSV) diagnosis:
    • By looking at any sores that are present
    • Take a sample from the sore(s) and test it.
    • A blood test may be used to look for HSV antibodies.
  3. Trichomoniasis diagnosis:
    • Examination and laboratory test.
  4. Chlamydia diagnosis:
    • Nucleic acid amplification tests (NAATs), cell culture, and other types of tests.
    • NAATs are the most sensitive tests to use on easy-to-obtain specimens. This includes vaginal swabs (either clinician- or patient-collected) or urine.
  5. Gonorrhea diagnosis:
    • Testing urine, urethral (for men), or endocervical or vaginal (for women) specimens using nucleic acid amplification testing (NAAT)
  6. Syphilis diagnosis:
    • Treponemal tests detect antibodies that are specific for syphilis.

Prevention/control of spread

  1. Human Papilloma Virus (HPV) prevention/control of spread:
    • *Get vaccinated for HPV
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)
  2. Human Simplex Virus (HSV) prevention/control of spread:
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)
  3. Trichomoniasis prevention/control of spread:
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)
  4. Chlamydia prevention/control of spread:
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)
  5. Gonorrhea prevention/control of spread:
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)
  6. Syphilis prevention/control of spread:
    • Abstinence
    • Use condom during sex to lower the risk. (Transmission can occur with lesions not covered by a condom.)


  1. Human Papilloma Virus (HPV) treatment:
    • Genital warts:  prescription medicine. If left untreated, genital warts may go away, stay the same, or grow in size or number.
    • Cervical precancer treatment is available.
    • Other HPV-related cancers are also more treatable when found and treated early.
  2. Human Simplex Virus (HSV) treatment:
    • There is no cure for genital herpes.
    • There are medicines that can prevent or shorten outbreaks.
  3. Trichomoniasis treatment:
    • Curable with antibiotics
  4. Chlamydia treatment:
    • Curable with antibiotics
  5. Gonorrhea treatment:
    • Curable with the right treatment of antibiotics
  6. Syphilis treatment:
    • Curable with the right antibiotics from your healthcare provider.
    • However, treatment might not undo any damage the infection can cause.

Knowledge Check

Topic 11: Selected Infectious Diseases – HIV/AIDS

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • differentiate between HIV and AIDS.
  • summarize the symptoms, testing, treatment options and prevention of HIV.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of HIV.


Overview external link.

HIV stands for human immunodeficiency virus, which is the virus that causes HIV infection. The abbreviation “HIV” can refer to the virus or to HIV infection.

AIDS stands for acquired immunodeficiency syndrome. AIDS is the most advanced stage of HIV infection.

HIV attacks and destroys the infection-fighting CD4 cells (CD4 T lymphocyte) of the immune system. The loss of CD4 cells makes it difficult for the body to fight off infections and certain cancers. Without treatment, HIV can gradually destroy the immune system and HIV infection advances to AIDS.


The HIV genome consists of two identical single-stranded RNA molecules that are enclosed within the core of the virus particle.

  • HIV attacks and destroys the CD4 cells (CD4 T lymphocyte) of the immune system. CD4 cells play a major role in protecting the body from infection.
  • HIV uses the machinery of the CD4 cells to multiply and spread throughout the body. This process, which is carried out in seven steps or stages, is called the HIV life cycle. HIV medicines protect the immune system by blocking HIV at different stages of the HIV life cycle.

Schematic of adaptive and humoral immunity from Bárcena, Juan & Blanco, Esther. (2013). Design of Novel Vaccines Based on Virus-Like Particles or Chimeric Virions. Sub-cellular biochemistry. 68. 631-65. 10.1007/978-94-007-6552-8_21.

The seven stages of the HIV life cycle are: 1) binding, 2) fusion, 3) reverse transcription, 4) integration, 5) replication, 6) assembly, and 7) budding


Within 2 to 4 weeks after infection with HIV, some people may have flu-like symptoms, such as fever, chills, or rash. The symptoms may last for a few days to several weeks. Other possible symptoms of HIV include night sweats, muscle aches, sore throat, fatigue, swollen lymph nodes, and mouth ulcers. Having these symptoms do not mean you have HIV. Other illnesses can cause the same symptoms. Some people may not feel sick during early HIV infection (called acute HIV infection). During this earliest stage of HIV infection, the virus multiplies rapidly. After the initial stage of infection, HIV continues to multiply but at very low levels.

More severe symptoms of HIV infection, such as a badly damaged immune system and signs of opportunistic infections, generally do not appear for many years until HIV has advanced to AIDS. People with AIDS have badly damaged immune systems that make them prone to opportunistic infections. (Opportunistic infections are infections and infection-related cancers that occur more frequently or are more severe in people with weakened immune systems than in people with healthy immune systems.)

Without treatment with HIV medicines, HIV infection usually advances to AIDS in 10 years or longer, though it may advance faster in some people.

HIV transmission is possible at any stage of HIV infection—even if a person with HIV has no symptoms of HIV.

Risk factors

In the United States, HIV is mainly spread by having sex or sharing syringes and other injection equipment with someone who is infected with HIV. Substance use can contribute to these risks indirectly because alcohol and other drugs can lower people’s inhibitions and make them less likely to use condoms. Factors that increase the risk of HIV include:

  • Having vaginal or anal sex with someone who is HIV positive or whose HIV status you do not know
  • Injecting drugs and sharing needles, syringes, or other drug equipment with others
  • Exchanging sex for money or drugs
  • Having a sexually transmitted disease (STD), such as syphilis
  • Having sex with anyone who has any of the HIV risk factors listed above


HIV is spread only through certain body fluids from a person who has HIV. These body fluids include:

  • Blood
  • Semen
  • Pre-seminal fluid
  • Vaginal fluids
  • Rectal fluids
  • Breast milk

HIV transmission is only possible through contact with HIV-infected body fluids. In the United States, HIV is spread mainly by:

  • Having anal or vaginal sex with someone who has HIV without using a condom or taking medicines to prevent or treat HIV
  • Sharing injection drug equipment (works), such as needles or syringes, with someone who has HIV

The spread of HIV from a woman with HIV to her child during pregnancy, childbirth, or breastfeeding is called perinatal transmission of HIV.

Complications (NIH neurological disorders and stroke) external link.

The Human Immunodeficiency Virus (HIV), which causes the disorder Acquired Immunodeficiency Syndrome (AIDS), primarily affects the immune system but also can lead to a wide range of severe neurological disorders, particularly if HIV goes untreated and progresses to AIDS.

HIV does not directly invade nerve cells (neurons) but puts their function at risk by infecting cells called glia that support and protect neurons. HIV also triggers inflammation that may damage the brain and spinal cord (central nervous system) and cause symptoms such as:

  • Confusion and forgetfulness
  • Inability to concentrate
  • Behavioral changes
  • Headaches
  • Mood disorders (anxiety disorder and depression)
  • Movement problems (loss of movement control) including a lack of coordination and difficulty walking

Damage to the peripheral nerves can cause progressive weakness and loss of sensation in the arms and legs. Research has shown that HIV infection can cause shrinking of brain structures involved in learning and information processing.


There are three types of HIV tests: antibody tests, antigen/antibody tests, and nucleic acid tests (NAT). Antibodies are produced by your immune system when you’re exposed to viruses like HIV. Antigens are foreign substances that cause your immune system to activate. If you have HIV, an antigen called p24 is produced even before antibodies develop.

Symptoms such as fever, weakness, and weight loss may be a sign that a person’s HIV has advanced to AIDS. However, a diagnosis of AIDS is based on the following criteria:

  • A drop in CD4 count to less than 200 cells/mm3. A CD4 count measures the number of CD4 cells in a sample of blood. 
  • The presence of certain opportunistic infections.

Although an AIDS diagnosis indicates severe damage to the immune system, HIV medicines can still help people at this stage of HIV infection.


Antiretroviral therapy (ART) is the use of HIV medicines to treat HIV infection. People on ART take a combination of HIV medicines (called an HIV treatment regimen) every day.

ART is recommended for everyone who has HIV. ART prevents HIV from multiplying, which reduces the amount of HIV in the body (called the viral load). Having less HIV in the body protects the immune system and prevents HIV infection from advancing to AIDS. ART cannot cure HIV, but HIV medicines help people with HIV live longer, healthier lives.

ART also reduces the risk of HIV transmission. A main goal of ART is to reduce a person’s viral load to an undetectable level. An undetectable viral load means that the level of HIV in the blood is too low to be detected by a viral load test. People with HIV who maintain an undetectable viral load have effectively no risk of transmitting HIV to their HIV-negative partner through sex.

Prevention/control of the spread

  • Use condoms correctly every time you have sex
  • Limit your number of sexual partners
  • Never share injection drug equipment.
  • Also talk to your health care provider about pre-exposure prophylaxis (PrEP). PrEP is an HIV prevention option for people who do not have HIV but who are at high risk of becoming infected with HIV. PrEP involves taking a specific HIV medicine every day.
  • HIV medicines, given to people with HIV during pregnancy and childbirth and to their babies after birth, reduce the risk of perinatal transmission of HIV. 

Knowledge Check

Topic 12: Selected Infectious Diseases – TB

Learning Objectives:

learning outcomes icon.

By the end of this section, you will be able to:

  • summarize the symptoms, testing, treatment options and prevention of TB.
  • summarize how the pathogenesis of TB.
  • summarize infectious agent, reservoir, portal of exit, mode of transmission, portal of entry, and susceptible host of TB.


Overview external link.

Tuberculosis (TB) is caused by a bacterium called Mycobacterium tuberculosis. The bacteria usually attack the lungs, but TB bacteria can attack any part of the body such as the kidney, spine, and brain. Not everyone infected with TB bacteria becomes sick. As a result, two TB-related conditions exist: latent TB infection (LTBI) and TB disease. If not treated properly, TB disease can be fatal.

Citation: [CDC] (May 26, 2020) CDC Tuberculosis (TB) Transmission and Pathogenesis (1:41) [Video].


Mycobacterium tuberculosis, a bacterium 


Symptoms of TB disease depend on where in the body the TB bacteria are growing. TB bacteria usually grow in the lungs (pulmonary TB). TB disease in the lungs may cause symptoms such as

  • a bad cough that lasts 3 weeks or longer
  • pain in the chest
  • coughing up blood or sputum (phlegm from deep inside the lungs)

Other symptoms of TB disease are

  • weakness or fatigue
  • weight loss
  • no appetite
  • chills
  • fever
  • sweating at night

Symptoms of TB disease in other parts of the body depend on the area affected.

People who have latent TB infection

  • do not feel sick,
  • do not have any symptoms, and
  • cannot spread TB to others

Risk factors

Generally, persons at high risk for developing TB disease fall into two categories:

  • Persons who have been recently infected with TB bacteria
  • Persons with medical conditions that weaken the immune system

Persons who have been Recently Infected with TB Bacteria

This includes:

  • Close contacts of a person with infectious TB disease
  • Persons who have immigrated from areas of the world with high rates of TB
  • Children less than 5 years of age who have a positive TB test
  • Groups with high rates of TB transmission, such as homeless persons, injection drug users, and persons with HIV infection
  • Persons who work or reside with people who are at high risk for TB in facilities or institutions such as hospitals, homeless shelters, correctional facilities, nursing homes, and residential homes for those with HIV

Persons with Medical Conditions that Weaken the Immune System

Babies and young children often have weak immune systems. Other people can have weak immune systems, too, especially people with any of these conditions:

  • HIV infection (the virus that causes AIDS)
  • Substance abuse
  • Silicosis
  • Diabetes mellitus
  • Severe kidney disease
  • Low body weight
  • Organ transplants
  • Head and neck cancer
  • Medical treatments such as corticosteroids or organ transplant
  • Specialized treatment for rheumatoid arthritis or Crohn’s disease


TB bacteria spread through the air from one person to another. When a person with TB disease of the lungs or throat coughs, speaks, or sings, TB bacteria can get into the air. People nearby may breathe in these bacteria and become infected

Complications (NIH) external link.

Most patients have a relatively benign course. Complications are more frequently seen in patients with the risk factors mentioned above. Some of the complications associated with tuberculosis are:

  • Extensive lung destruction
  • Damage to cervical sympathetic ganglia leading to Horner's syndrome.
  • Acute respiratory distress syndrome
  • Milliary spread (disseminated tuberculosis)including TB meningitis.
  • Empyema
  • Pneumothorax
  • Systemic amyloidosis

Diagnosis (John Hopkins Medicine) external link.

TB is often diagnosed with a skin test. In this test, a small amount of testing material is injected into the top layer of the skin. If a certain size bump develops within 2 or 3 days, the test may be positive for tuberculosis infection. Other tests include X-rays and sputum tests. A blood test can be done in place of the TB skin test.

Treatment (American Lung Association) external link.

For active TB:
  • A combination of antibacterial medications for a period of six to 12 months.
  • The most common treatment for active TB is isoniazid INH in combination with three other drugs—rifampin, pyrazinamide and ethambutol.
  • Treating TB takes much longer than other bacterial infections. You must continue taking your medication as prescribed for the entire time your doctor indicates or you could get sick again, have a harder time fighting the disease in the future and spread the disease to others.
  • Not completing your entire course of medication could also contribute to drug-resistant TB.
For latent TB:
  • Preventive therapy. This treatment kills germs that could cause problems if the disease becomes active.
  • The most common preventive therapy is a daily dose of the antibiotic isoniazid (INH) taken as a single daily pill for six to nine months. You are not contagious if you have latent TB.
Drug-Resistant TB:
  • Drug-resistant TB means that some drugs initially used to treat TB will no longer be able to fight the TB germs in your body. TB that is resistant to more than one drug, called multidrug-resistant TB (MDR TB) is very dangerous.
  • The treatment for this type of TB takes much longer, 20 to 30 months to complete, and you may experience more side effects.

Prevention/control of the spread (American Lung Association)

  • If you will be spending time with a person or people with active TB, wear a face mask and try not to stay in a small enclosed space with poor ventilation.
  • People who work in situations where there is a high risk for encountering people infected with TB, such as healthcare workers, should be tested for TB on a routine basis.
  • In countries outside the U.S. where TB is more common, a childhood vaccine is often given.

Knowledge Check

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