9.2 Basic Concepts

Normal Flora and Microbiome

Microorganisms occur naturally and are present everywhere in our environment. Some microorganisms live on the skin, in the nasopharynx, and in the gastrointestinal tract, but don’t become an infection unless the host becomes susceptible. These microorganisms are called normal flora . Over the past several years, it has been discovered that every human being carries their own individual suite of microorganisms in and on their body referred to as their microbiome. A person’s microbiome is acquired at birth and evolves over their lifetime. It is different across body sites and between individuals. A person’s gut microbiome has recently been found to impact their immune system.^[1],[2]

Pathogens

Microorganisms that cause disease are called pathogens. There are four common types of pathogens, including viruses, bacteria, fungi, and parasites.

Viruses

Viruses are made up of a piece of genetic code, such as DNA or RNA, and are protected by a coating of protein. After a host (i.e., the person) becomes infected by a virus, the virus invades the body’s cells and uses the components of the cell to replicate and produce more viruses. After the virus replication cycle is complete, the new viruses are released into the body, causing damage or destruction of the host’s cells.^[3]

Antiviral medications can be used to treat some viral infections. Antibiotics do not kill viruses and are ineffective as a treatment for viral infections. See Figure 9.1^[4] for an image of a virus.

Bacteria

Bacteria are microorganisms made of a single cell. They are very diverse, have a variety of shapes and features, and have the ability to live in any environment, including your body. However, not all bacteria cause infections. Those that cause infection are called pathogenic bacteria. See Figure 9.2^[5] for an image of a bacterium called Escherichia coli (E. coli).

A patient is susceptible to bacterial infections when their immune system is compromised by chronic diseases or certain types of medications. Antibiotics are used to treat bacterial infections. However, some strains of bacteria have become resistant to antibiotics, making them difficult to treat. For example, infections caused by methicillin-resistant Staphylococcus Aureus (MRSA) are resistant to many types of antibiotics and have the capability of producing severe and life-threatening infections. MRSA infections usually require IV antibiotics and may require treatment for long periods of time.^[6]

Fungi

There are millions of different fungal species on Earth. Fungi can be found everywhere in the environment, including indoors, outdoors, and on human skin, but only about 300 species cause infection when they overgrow. Candida albicans is a type of fungus that can cause oral thrush and vaginal yeast infections, especially in susceptible patients or those taking antibiotics.^[7] See Figure 9.3^[8] for an image of oral thrush.

Fungi cells contain a nucleus and other components protected by a membrane and a thick cell wall. This structure can make them harder to kill. Some new strains of fungal infections are proving to be especially dangerous, such as Candida auris, which is difficult to diagnose and treat, and can cause outbreaks in health care facilities.^[9]

Parasites

Parasites are organisms that behave like tiny animals, living in or on a host, and feeding at the expense of the host. Three main types of parasites can cause disease in humans. These include the following:

• Protozoa: Single-celled organisms that can live and multiply in your body
• Helminths: Multi-celled organisms that can live inside or outside your body and are commonly known as worms
• Ectoparasites: Multi-celled organisms that live on or feed off skin, including ticks and mosquitos

Parasites can be spread several ways, including through contaminated soil, water, food, and blood, as well as through sexual contact and insect bites.^[10] See Figure 9.4^[11] for an image of a helminth infection causing intestinal obstruction in a child.