Introduction

Infectious diseases caused by microorganisms and infectious agents have gotten a lot of publicity. We have heard news stories about COVID-19, influenza, Zika, and more. With news of foodborne illnesses, contaminated water supplies, tick-borne diseases, and communicable infections, it appears all microorganisms are harmful and can cause disease. Healthcare-associated infections (HAIs) are making it increasingly difficult to control Infectious diseases caused by microorganisms and infectious agents have gotten a lot of publicity. We have heard news stories about COVID-19, influenza, Zika, and more. With news of foodborne illnesses, contaminated water supplies, tick-borne diseases, and communicable infections, it appears all microorganisms are harmful and can cause disease. Healthcare-associated infections (HAIs) are making it increasingly difficult to control methicillin-resistant Staphylococcus aureus (MRSA) and Clostridium difficile infections.
      New strains of drug-resistant microorganisms are difficult to treat with existing antibiotics. Bioterrorism has become a real concern worldwide. Antimicrobial products line the pharmacy and supermarket shelves and are going to keep us “germ-free.” It is no wonder many people have the impression that all microorganisms are harmful. In reality, less than 1% of known microorganisms are pathogens.

Normal Flora
Most microorganisms are good. For example, saprophytes are beneficial microorganisms that are responsible for breaking down organic matter, such as plants and organic waste in farming, water purification, composting, and gardening. Without microorganisms, we could not survive. The normal flora in and on our bodies is needed for the following processes:
            • Digesting food and making nutrients available to the body.
            • Forming blood clots. Vitamin K is used in the clotting process and is made by bacteria in our intestines.
            • Preventing pathogens from invading our skin, mucous membranes, and gastrointestinal and genitourinary tracts.

      Normal flora takes up space, requires nutrients, and excretes waste. When pathogens try to populate the skin or areas of the body that have normal flora, they must compete with the existing organisms. This makes it harder for pathogens to cause disease. Normal flora discourages pathogen populations.
      When the body’s normal flora is weakened (e.g., by antibiotic overuse or hormonal changes), certain opportunistic organisms that are normally present in low numbers can overgrow. An example is Candida albicans, which is a yeast that is normally found in mucous membranes in the body. When a patient has been on broad-spectrum antibiotics for an infection, the antibiotics kill pathogens, along with some of the normal flora. For example, Candida albicans is not normally a problem in the vagina. If enough normal flora in the vagina is killed off, Candida albicans can increase in numbers, which causes a vaginal yeast infection.

Medical Assistant’s Role
As a medical assistant, you need to understand basic microbiology and the role of microorganisms in both health and disease. The main objective of medical microbiology is to identify the organisms responsible for illness so that the provider can properly treat the patient. Your responsibilities will also include preventing HAIs by following infection control policies. Microbiology testing procedures may be performed in the physician’s office laboratory (POL) or in the microbiology department of a medical referral laboratory.

Immunology
Immunology is the study of the immune system, which is closely tied to microbiology. Invasive microorganisms stimulate an immune response, leading to the production of antibodies that come to our defense. Often a bacterial or viral infection is diagnosed by testing for a specific antibody that is produced to fight the infectious agent.
This chapter covers the following topics related to microbiology and immunology:
             • Major categories of infectious agents
            • Quality control issues regarding the collection and handling of microbiological specimens
            • Common CLIA-waived microbiology and immunology testing
The chapter concludes with an overview of the more complex microbiology procedures and tests performed in hospitals and reference laboratories. and Clostridium difficile infections.
      New strains of drug-resistant microorganisms are difficult to treat with existing antibiotics. Bioterrorism has become a real concern worldwide. Antimicrobial products line the pharmacy and supermarket shelves and are going to keep us “germ-free.” It is no wonder many people have the impression that all microorganisms are harmful. In reality, less than 1% of known microorganisms are pathogens.