Causes (Germs) and Treatment of Infections in People With Cancer

Infection is one of the most common life-threatening complications of cancer and cancer treatment. This is because cancer and cancer treatment weaken the immune system. The immune system is a complex system by which the body resists and fights infection by germs, such as bacteria or viruses.

This is one part of a series on information about cancer patients and their risk of infection.

A blood test called a complete blood count (CBC) is used to see how well your immune system is working. It measures your white blood cells (WBCs), the immune system cells that fight infection. There are many types of white blood cells, and each fights infection in a special way. See Understanding Your Lab Test Results to learn more about blood tests and how they’re used to see how strong your immune system is.

Common causes of infection

Germs are tiny organisms (microorganisms) that can cause infections. Examples include:

  • Bacteria
  • Viruses
  • Protozoa
  • Fungi (the plural of fungus)

Most germs (other than viruses) are given scientific names from the genus (first names) and species (last names). These names tell biologists and health care workers which living things are related and may be like each other.

While most germs have first and last names, those that are well known are often called by their first names only. Germs like this include Pneumococcus, Candida, and Aspergillus. And like some people, germs with long names are sometimes more commonly known by their initials or nicknames. These include E. coli (Escherichia coli), Staph (Staphylococcus aureus), and CMV (cytomegalovirus).


Biologists believe that bacteria are a separate type of life form – they’re different from plants and animals. Bacteria are the smallest forms of life. Most infections in people with cancer are caused by bacteria, including:

  • Pseudomonas aeruginosa
  • Klebsiella pneumoniae
  • Escherichia coli (E. coli)
  • Salmonella
  • Clostridium difficile (C. diff)
  • Staphylococcus aureus (Staph aureus)
  • Staphylococcus epidemidis (Staph epi)
  • Streptococcus viridans
  • Pneumococcus
  • Enterococcus


Viruses are the smallest known germs. Unlike bacteria, they’re not really alive because they can’t grow on their own. Viruses can only make new viruses when they are inside living cells, such as human, animal, or plant cells.

Most viral infections in people with very low white blood cell counts are caused by:

  • Varicella zoster virus (VZV), the virus that causes chickenpox and shingles
  • Herpes simplex virus (HSV), the virus that causes cold sores and genital herpes
  • Cytomegalovirus (CMV)

Other viruses, such as respiratory and hepatitis viruses, may cause problems, too.

Varicella zoster virus

Varicella zoster virus (VZV) can cause serious infections in people with cancer. Unlike many other infections, a VZV infection never completely goes away, even in a healthy person. This means when a person recovers from chickenpox, some of the virus stays in their nerve cells. If the person’s immune system is weakened, even many years later, the virus can become active again and cause a problem known as shingles.

People with shingles have groups of tiny, painful blisters on their skin. The blisters form along the nerves. The pain from shingles can last long after the blisters go away. The skin blisters hurt, but the most serious part of VZV infection in people with a weak immune system is that the virus can spread to other organs. This can lead to lung infection (pneumonia) or infection of the brain (encephalitis).

There’s a high risk of serious damage from VZV in people with low white blood cell counts and weak immune systems. Unlike chickenpox and shingles in healthy people, VZV infections can be deadly in people with cancer.

Herpes simplex virus

Herpes simplex virus (HSV) is from the same family of viruses as varicella zoster. Like varicella zoster, HSV causes mild infections in people with healthy immune systems, but it also stays in their nerve cells. It can become active again years later, especially if the immune system is weakened. And like varicella zoster, HSV can also cause pneumonia and encephalitis.

Cytomegalovirus (CMV)

Cytomegalovirus (CMV) infection is common in healthy people and it’s usually not serious. Many people have this virus in their bodies and don’t even know it. But when the immune system is weakened, CMV can cause things like serious pneumonia, intestinal infection (enteritis), liver infection (hepatitis), and a serious eye infection that can lead to blindness if not treated (retinitis).

CMV infection can be very hard to treat in people with low white blood cell (WBC) counts, because the drugs used to fight the virus also lower the number of WBCs. This makes it hard for the body to fight the infection. Often, the best thing to do for patients with weak immune systems is try to prevent the infection from flaring up. This is done by giving patients certain anti-viral drugs before any symptoms begin. (Since most people with CMV don’t know they have it, blood tests are used to check for it.)

Respiratory viruses

Respiratory viruses are those like influenza (the flu), respiratory syncytial virus (RSV), and other seasonal viruses. They can cause illnesses in people with normal immune systems, but these illnesses can be more severe in those with weak immunity.

Respiratory viruses can affect the nose, throat, sinuses, breathing passages, and lungs. Pneumonia, which affects the lungs, is the most serious problem that can be caused by respiratory viruses. Pneumonia is more likely when one of these viruses infects a person whose immune system isn’t working well.

The best way to prevent the flu is to get a flu shot every fall and be sure the people you live with get vaccinated, too. Wash your hands often. If your white blood cell counts are low, you should try to stay away from crowds and people with these kinds of infections.


Protozoa are one-celled creatures thought to be the smallest and simplest form of animals. Some protozoa can infect people who have healthy immune systems. But these infections happen more often in less-developed countries than in the United States. In the US, protozoa mostly cause disease in people with weak immune systems. People who have organ transplants, cancer, AIDS, or other diseases can get life-threatening infections with protozoa. Common protozoa that can cause serious illness in people with cancer include

  • Toxoplasma gondii
  • Cryptosporidium

Toxoplasma gondii

Toxoplasma gondii is found in soil, cat waste, water contaminated with cat waste, and undercooked meats. It can cause fever and lymph node swelling or no symptoms at all in adults with normal immune systems. It usually stays inactive in healthy people, but when the immune system is weak the infection may become active and damage the brain or heart. People with cancer can have old infections become active again, or they can get infected for the first time while their immune system is weak.


Cryptosporidium is a common cause of diarrhea and stomach pain in people with weak immune systems. It’s spread by infected people and animals, often through drinking water and fruits or vegetables contaminated with stool. It can cause very severe diarrhea, leading to malnutrition, weight loss, imbalances in blood chemistry, and severe fluid loss (dehydration).

Fungus (Fungi)

In humans, fungi can live in balance with other germs that normally live on or in the body without causing symptoms or damage. But fungal infections can happen when there are changes in this balanced environment. Things that can change the normal balance include:

  • Damage to the skin or mucous membranes
  • Low white blood cell counts
  • A weak immune system
  • Fewer bacteria than normal on the body’s surfaces or mucous membranes (such as the intestines or vagina), which often happens with antibiotic treatment

Fungal infections can be serious and even deadly. Fungi that commonly infect people with cancer include:

Pneumocystis jirovecii

Pneumocystis jirovecii is an atypical fungus that can cause illness in people with weak immune systems. It causes pneumonia and rarely spreads to other organs, but the pneumonia can make it very hard to breathe. Early treatment improves the chance of survival. Pneumocystis infections are common enough in patients with weak immune systems that sometimes doctors will give an antibiotic to help prevent this infection.


This is the most common fungal infection. Candida can live in a healthy person without causing any problems. Sometimes it may cause a mild skin rash or vaginal discharge (called a yeast infection). In babies, it can cause a mouth infection called thrush. But a person with a weak immune system is at risk for a more serious version of thrush. It can affect the mouth and swallowing tube (esophagus) and may spread to other organs. (Thrush looks like creamy white patches or a white coating on the pink tissues of the mouth.) Candida can also cause bloodstream infections in people with weak immune systems.


Aspergillus is a fungus that’s often found in the air and in our environment. It’s rarely a problem in healthy people, but it can cause a mild lung infection in people with allergies or asthma. In people with cancer, though, it can cause serious infections of the sinuses, lungs, kidneys, brain, and heart valves. This is especially true for those with very low white blood cell counts or those getting cancer treatments that suppress the immune system. This type of infection is often hard to diagnose. Quick, aggressive treatment is needed as soon as it’s suspected.


Cryptococcus is found in the soil and in bird droppings, especially pigeon waste. It’s thought to be spread by breathing in the germ after it’s dried out and gets stirred up into the air. In people with healthy immune systems it may cause a lung infection that goes away without symptoms. But the fungus can remain inactive in the lungs for years. And if the person’s immune system becomes weak, Cryptococcus can begin to grow and spread to other parts of the body. One of the most serious outcomes of this infection is meningitis, an infection of the membranes that cover the brain and spinal cord.


Histoplasma often infects the lungs of healthy people without causing symptoms or tissue damage. Infection with Histoplasma (which is called histoplasmosis) is quite common in the Mississippi and Ohio River Valleys in the United States, although it’s also seen outside these regions and in many other parts of the world. People become infected through contact with soil or breathing the dust from soil that contains bird or bat waste. The fungus may stay inactive for years in the lungs of healthy people. But it can become active if their immune system is weakened. In people with cancer, Histoplasma may cause a serious illness and may spread to the lymph system, liver, spleen, and other organs.


Coccidioides causes a fungal disease called coccidioidomycosis or Valley Fever. The fungus lives in the soil in the southwestern US, parts of Mexico, and Central and South America. People breathe in this fungus when dust containing it is stirred up. Most people with healthy immune systems don’t know they have the disease and it goes away on its own. But Coccidioides can cause serious illness in people with weak immune systems. It can spread outside the lungs to the skin, nerves, brain, bones, and joints.

How does the doctor know what kind of infection a person has?

People with cancer can get many different types of infections. These infections differ in their risk factors, the symptoms they cause, how they are treated, and the chance of curing the infection.

If you have an infection, it’s important for your doctor to know:

  • The part of your body affected
  • The type of germ causing the infection

Parts of the body most likely to get infections

Your signs and symptoms (for instance, where you have pain, redness, and/or swelling) help your doctor know what tests are needed to find the cause of the infection. The results of certain tests (such as x-rays, CT scans, or lab tests done on body fluids) help pinpoint where the infection is.

Common sites of infection in people with cancer include:

  • The skin and mucous membranes (soft linings, like inside the mouth, vagina, and intestines)
  • The digestive system (mouth, esophagus [swallowing tube], stomach, and intestines)
  • The lungs and breathing passages (sinuses and throat)
  • The urinary system (bladder and kidneys)
  • The nervous system (brain and spinal cord)
  • The skin and tissue around a central venous catheter (CVC). A CVC is a tube or catheter put in a vein that is used to draw blood and give IV drugs or fluids.

Identifying germs

Most germs normally live on the skin, in the intestines, or in the environment. These germs usually do not cause problems in people with normal defenses and healthy immune systems. But if the normal barriers and immune system are weak, the germs can get in the body, grow, and cause damage.

These infections are often called opportunistic infections, because the germs use the opportunity of a patient’s weakened defenses to cause illness.

Knowing the exact type of germ that’s causing an infection helps doctors choose the best treatment. Different drugs are used to treat each of the main types of germs – bacteria, viruses, fungi, and parasites. And even among the main types of germs, different types are treated with different drugs. This means an antibiotic that can kill one type of bacteria might have no effect on another type of bacteria.

All of the tests listed below are done on samples or specimens from the patient. Common types of samples include:

  • Blood
  • Urine
  • Spinal fluid
  • Wound drainage or pus
  • Phlegm (sputum)

If you have symptoms that point to a certain area of infection, samples will be taken to check for germs in that area. For example, sputum samples may be taken if you have a cough or are short of breath. Urine samples may be taken if you have blood in your urine or feel pain while passing urine. Sometimes, if a person has a very low white blood cell count and a fever, blood and urine samples will be taken before other symptoms start.

Lab tests to identify germs

Your health care team will do all they can to find out exactly what germ is causing your infection. Here are some of the tests they may use.

Gram stain: Samples from the suspected site of infection can be put on a microscope slide and stained with a series of dyes. This test is called a Gram stain. It changes the colors of the germs and makes them easier to see. It takes only a few minutes to stain the sample and look at it. The colors and shapes of the stained germs often give doctors an idea of which germ is causing the infection. This can help narrow the choice of antibiotics until more precise test results come in. Gram stains are most useful for bacteria; fungi and parasites usually need different stains.

Tests for viruses: Viruses are too small to be seen with most microscopes. Instead, viruses are sometimes identified by lab tests that look for the certain proteins or genes related to the virus. Others are detected by finding their antibodies.

Genetic tests: Some lab tests can quickly identify certain germs by testing their DNA, RNA, or other substances. These tests often help doctors choose the best treatment more quickly than older tests. This means the right treatment can be started before the infection causes serious harm.

Culture: Samples from the suspected site of infection are put in a nutrient broth or gel and kept warm until the germs grow. Bacteria and fungi often take at least a few days to grow in the lab before they can be seen. After enough germs have grown, they are tested and identified. Viruses may also be identified by taking samples and growing them in the lab, but it can take weeks to get results.

Sensitivity tests: Once bacteria (or fungi) have been cultured, an extra test called a sensitivity test may be done on the cultured sample. This is often needed because some germs resist certain antibiotics that kill others of that same type. This test also takes time, but it shows the best antibiotic to kill the germ causing a certain infection.

    Because infections in people with cancer can quickly get worse, treatment is usually started before culture and sensitivity results are back. Treatment may be changed after the lab tests have identified the exact germ and which drug will work best to treat it.

Can doctors treat the infection while they wait for lab test results?

Doctors know which germs tend to infect certain body parts of people with cancer. So they can often make an educated guess at which germs are most likely causing a patient’s infection. Educated guesses are very important because it can take many days to get the results of tests that show the exact type of germ causing an infection and which drug will best stop or kill it.

How are infections treated in people with cancer?

Fever, swelling, pain, and other signs of infection in a person known to have a weak immune system are treated as medical emergencies. Antibiotics are started right away.

After a physical exam, lab tests, cultures, and sometimes even imaging studies or special procedures will be done. This will help the doctor find out exactly where the infection is and help figure out which germ may be causing it. Then antibiotics (which can be anti-bacterial, anti-viral, anti-fungal, or anti-protozoal drugs) are started quickly. (See “Identifying germs” in the section called “How does the doctor know what kind of infection a person has?”) After the exact germ is identified, the same antibiotics may be continued, or new ones may be started if the tests show others would work better.

Where treatment is given

In the past, people with cancer were almost always put in the hospital to treat infections, and some still are. But many patients can take their antibiotics at home as pills or liquids. Those who need intravenous (IV) antibiotics may be able to get them in infusion clinics, doctor’s offices, or even at home.

What treatment may be like

For the first 3 to 5 days, the patient is watched closely and lab results are checked often. Antibiotics may be changed when the final culture or other test results come in. (The culture results should tell the doctor which germ is causing the infection; see “Identifying germs” in the section called “How does the doctor know what kind of infection a person has?”)

If the patient doesn’t get better, an infectious disease specialist may be called in. These are doctors who specialize in treating infections. This doctor may recommend extra testing and different treatments.

In some cases, injections of drugs called CSFs (colony-stimulating factors) may be given to boost the white blood cell (WBC) count so the body can better fight the infection.

Each type of infection is treated with different drugs and for different lengths of time. If you have any questions about the drugs you are given or why you’re taking them, talk with your doctor or nurse.

Bacterial infections

When treating bacterial infections in people with weak immune systems, antibiotics that will treat many different bacteria are often chosen first, especially if doctors aren’t yet sure what’s causing the infection. These are called broad-spectrum antibiotics. Often, 2 or 3 antibiotics are used at the same time.

Drug-resistant germs: Even in serious situations, overuse of antibiotics must be avoided because this can make some bacteria resistant to these drugs. Such germs are called drug resistant because they no longer respond to the antibiotics that killed them in the past.

Germs change and adapt all the time. For example, some strains of Staphylococcus (staph) have become resistant to certain antibiotics. These strains get special names.

    Staph that’s resistant to methicillin is called methicillin-resistant staph aureus, or multi-drug-resistant staph aureus. This is often shortened to the initials MRSA and may be pronounced MER-suh rather than being spelled out.

    Some staph has become resistant to intravenous (IV) vancomycin, which was once used to treat resistant infections. This is called vancomycin-resistant staph aureus or VRSA, and may be pronounced VER-suh.

    Some strains of enterococcus, which normally live in the human intestine, have now become resistant to vancomycin, too. These strains are called VRE, for vancomycin-resistant enterococcus.

The good thing is that now, there are newer drugs that can still work against some of these hard-to-kill germs. To avoid spreading drug-resistant bacteria to other patients, health care workers often wear disposable gowns and gloves when caring for people known to have these infections.

Viral infections

Anti-viral drugs are used to treat some virus infections. Herpes simplex virus (HSV) and varicella zoster are most often treated with anti-viral drugs. These same kinds of drugs are used to treat cytomegalovirus (CMV), and may be used to treat the flu (influenza), too.

Protozoal infections

Protozoa seldom cause problems for healthy people, but they can be hard to treat in people with weak immune systems.

Toxoplasma can be treated with a variety of drugs. But there’s no one treatment for Cryptosporidium infection, which causes severe diarrhea. In this case, treatment is aimed at building up the immune system, treating the diarrhea, and avoiding dehydration.

Fungal infections

People with Candida infections in the mouth, throat, and esophagus might be given anti-fungal drugs to be taken by mouth. For more serious Candida infections (such as infections in the blood), anti-fungal drugs may be given into the blood through a vein (IV).

There are also drugs to treat Aspergillus, Cryptococcus, Histoplasma, and Pneumocystis infections.

The American Cancer Society medical and editorial content team

Our team is made up of doctors and oncology certified nurses with deep knowledge of cancer care as well as journalists, editors, and translators with extensive experience in medical writing.

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Last Medical Review: February 25, 2015 Last Revised: February 10, 2017

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