Infectious Disease Genetic Testing
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Some microbes, including bacteria, fungi, parasites and viruses, cause infections in humans. These are known as infectious agents or pathogens. Traditional testing techniques for detection of such pathogens includes, for example, growing microbes in cultures followed by identification of the microbe, or testing blood samples for antibodies that people develop in response to an infection by a particular microbe.
Because microbes contain genetic material, also called nucleic acids (DNA and RNA), that is different from the genetic material in human cells, genetic testing techniques can also be used to detect microbes. Samples that might contain these microbes include urine, blood, sputum, cerebrospinal fluid and stool. In addition to detecting microbes directly in specimens like these, genetic testing techniques may also be used to identify microbes after they have been grown in culture.
Genetic testing may be more sensitive and specific than traditional methods of testing, and provide results faster than other techniques, such as cultures. One particular type of genetic testing is called “NAAT”, which stands for nucleic acid amplification test. This technique makes numerous copies (amplification) of any genetic material from the microbes present in a sample so that it can be more easily detected. One type of NAAT is polymerase chain reaction (PCR).
In addition to identifying the microbes causing an infection, genetic testing may also be used to determine the type (e.g. sub-type, strain or species) of microbe present. This information may help guide treatment of an infection and link multiple cases to a common source of the infection. Some genetic tests identify specific genes that enable a microbe to grow in the presence of an antimicrobial drug or identify a genotype of a virus that will respond to specific treatment.
Some newer infectious disease genetic testing techniques can simultaneously test for several different microbes in a single sample to help diagnose the pathogen causing an infection. These are usually referred to as “panels” and are often used for identifying infections that have similar signs and symptoms but can be caused by a wide variety of microbes. For example, you may have symptoms such as stomach pain and diarrhea, which can be caused by a virus (e.g. norovirus), bacteria (e.g. Salmonella) or a parasite (e.g. Giardia). Panels of genetic tests can identify the cause of your infection more quickly, allowing more timely treatment decisions. Some examples of these panels include:
- A panel of molecular genetic tests that can identify the most common viruses or bacteria causing a respiratory infection by testing a sample collected from the back of the nose and throat.
- A panel of molecular genetic tests that can identify the most common bacteria, parasites, or viruses causing infectious diarrhea by testing a single stool sample.
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Identifying disease-causing microbes by genetic techniques
Bacteria are one-celled, ever-present organisms that in some cases can cause serious disease. By isolating and testing the nucleic acids from bacteria, the bacteria can be identified rapidly. Some examples include:
- Chlamydia trachomatis, which causes the sexually-transmitted disease chlamydia
- Neisseria gonorrhoeae, which causes gonorrhea
- Streptococcus pyogenes (Group A strep) which causes “strep throat”
- Borrelia burgdorferi, which causes Lyme disease
- Legionella pneumophila, which causes Legionnaire disease
- Mycoplasma pneumoniae, which leads to “walking pneumonia”
- Mycobacterium tuberculosis, which causes tuberculosis
- Bordetella pertussis, which causes whooping cough
Viruses are the smallest of all microbes. They are unusual pathogens in that they exist and multiply inside the cells of other living things (host cells). Viruses cause infections ranging from relatively mild to life-threatening. Examples of genetic tests for viruses include those for:
- Coronavirus, SARS-CoV-2
- Influenza virus (flu)
- Hepatitis C virus (HCV)
- Hepatitis B virus (HBV)
- Human Immunodeficiency Virus (HIV)
- Herpes simplex virus
- Cytomegalovirus (CMV)
- Epstein-Barr virus (EBV), which causes “mono,” a.k.a. “kissing disease”)
- Varicella-zoster virus (VZV), which causes chickenpox and shingles
- BK virus
Fungi are microbes that exist in nature as one-celled yeasts or as long, thread-like, branching molds. Only about 20 to 25 species of fungi have been identified as common causes of infection. Some fungi can cause meningitis or deep tissue and lung infections that have the potential to spread to the blood, or the rest of the body. Genetic techniques such as PCR may be used to detect the genetic material of the fungus causing an infection and may be performed on blood, cerebrospinal fluid (CSF) or other body fluids, or on a sample of the microbe grown in culture. Some examples of these fungi include:
Parasites are one-celled or complex multi-cellular organisms. Parasites can infect an individual through the saliva of a biting insect, such as a mosquito, or through ingesting contaminated material. Examples of a parasites that can be identified using genetic tests include:
- Toxoplasma gondii, which can cause encephalitis or infections during pregnancy in which the mother passes the infection to her baby (congenital), potentially causing serious complications.
- Blood parasites that cause infections such as malaria and babesiosis
- Parasites that can infect the digestive tract and cause diarrhea, such as:
- Giardia lamblia
- Entamoeba histolytica
- Cryptosporidium parvum
Viral load testing
Determining how many copies of a virus are present in an individual’s blood is another use of an infectious disease genetic testing technique. The number of virus copies present is typically referred to as the “viral load” or “viral burden.” This testing is usually done initially when first diagnosed and then after a drug therapy is initiated to assess whether the drug is effectively decreasing the viral load. Some common viral load tests are for hepatitis C, hepatitis B, cytomegalovirus (CMV), HIV, and BK virus (in kidney transplant patients).
Guiding treatment: Antimicrobial resistance testing and viral genotyping
Antimicrobials are medications that stop the growth of or kill microbes. Antivirals and antibiotics are examples of types of antimicrobials. In general, antimicrobial resistance describes the condition in which a microbe is able to survive, grow and/or multiply in the presence of one or more antimicrobial drugs. Resistance can develop when antimicrobials are used to treat an infection and a mutation or change occurs in one of the microbe’s genes. This change leads to a mixed population of microbes in the infected person’s body – some microbes do not have the mutation and are drug-sensitive (are killed by the antimicrobial agent) and some have the mutation and are drug-resistant (are not killed and can quickly multiply). When this occurs, the antimicrobial is no longer effective in treating the infection.
Bacteria can also acquire resistance to antibiotics when they pass genetic material back and forth from one type of bacteria to another. When this occurs, antibiotic resistance can spread easily and quickly among bacteria and among the people infected.
As mentioned earlier, some genetic tests can detect the genes that give microbes resistance to antimicrobials. Other tests may determine the type (genotype) of virus present to select an appropriate drug for treatment.
Some examples include:
- Methicillin-resistant Staphylococcus aureus (MRSA) are strains of Staphylococcus aureus, or “staph,” bacteria that are resistant to the antibiotic methicillin, as well as to related antibiotics, such as oxacillin, penicillin, amoxicillin, and cephalosporins, that are used to treat common staph infections. Genetic tests for MRSA can detect within hours the genetic markers to identify S. aureus and the mecA gene that confers resistance to the antibiotics listed above.
- Carbapenem-resistant Enterobacteriaceae (CRE) are bacteria that can cause hard-to-treat urinary tract infections, blood infections, wound infections, and pneumonia. Some of these bacteria are resistant to nearly all antibiotics, including carbapenems, which are often considered the antibiotics of last resort. Molecular testing can be used to test for the most common genes associated with resistance to carbapenem antibiotics.
- An individual may be initially infected with a drug-resistant human immunodeficiency virus (HIV) strain or drug resistance may develop during treatment. HIV genotypic antiretroviral drug resistance testing analyzes the genes of the HIV strain infecting a person to evaluate the likelihood that the strain is resistant or has developed resistance to one or more antiretroviral therapy (ART) drugs.
- There are 6 major types of hepatitis C virus (HCV) and more than 50 subtypes identified; the most common, genotype 1, accounts for about 70% of cases in the U.S. The drugs selected for treatment depend in part on the genotype of HCV infecting a person. Viral genotyping may be used to determine the genotype of the HCV present to help guide treatment.
- Some malarial parasites have become resistant to the drugs commonly used to treat the infections. Some specialized laboratories can test the parasites from an infected person to determine their drug susceptibility. This can be done by testing the DNA of the parasite to detect genes that indicate resistance.
Public health genetic testing of infectious diseases
Knowing the identity of a specific microbe, types or subtypes through genetic testing can be important for public health. Below are a few examples:
- Foodborne illnesses—When there are suspected cases or outbreaks of foodborne illnesses (food poisoning), local or state public health officials investigate to identify the likely source of the illnesses. Food samples and stool samples from the people who become sick and/or samples of the microbe causing the illnesses are often sent to public health laboratories so that special testing can be done. If bacteria are suspected to be the cause, these labs can perform genetic tests that can determine a “DNA fingerprint” of the pathogen that is present. This information is entered into PulseNet, a database used by local and state public health agencies, federal food safety regulatory labs, and the Centers for Disease Control and Prevention (CDC) to track illnesses. It allows for rapid comparison of DNA fingerprints in order to determine if illnesses and groups of illnesses are related. PulseNet also has an international component that allows for tracking of illnesses that may cross borders, an important activity given the increasing globalization of the food supply.
- Healthcare-associated and hospital-acquired infections—Infections can be spread by contaminated hands, medical equipment, and surfaces in healthcare settings such as hospitals, clinics, or nursing homes. Most institutions have implemented measures to control the spread of healthcare-associated infections. Genetic tests can help identify infections that are related and patients who test positive for a specific microbe may be isolated to prevent the spread to others. When an outbreak is under investigation, screening of healthcare workers, family members, and close contacts may be performed to identify the source of the infection and to help devise a plan to contain these infections. In some settings, such as nursing homes, a large number of people may be screened to evaluate the spread in a specific population.
- Influenza testing— Influenza testing helps local and state health departments and the CDC track influenza in communities. One of the most useful pieces of information provided by molecular tests is the identification of the subtype of influenza viruses circulating during the flu season. Since the flu viruses change every year, testing helps the CDC to monitor the subtypes and strains of flu that are circulating that year and determine if the current vaccine provides coverage for those strains. In addition, this information is used to develop next year’s flu vaccine and to monitor strains for resistance to anti-viral drugs.
Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. Nader Rifai. 6th edition, Elsevier Health Sciences; 2018, Chap. 48, Molecular Microbiology.
Clarke, W. Editor (2016). Contemporary Practice in Clinical Chemistry, 3rd edition, AACC Press, Washington, DC.
Henry’s Clinical Diagnosis and Management by Laboratory Methods. 23nd ed. McPherson R, Pincus M, eds. Philadelphia, PA: Saunders Elsevier: 2017. Chap. 65, Chap. 67.
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(February 8, 2019) Centers for Disease Control and Prevention. Influenza (Flu). Available online at https://www.cdc.gov/flu/index.htm. Accessed February 2019.
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