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Bacterial Infections in Squirrels

As with people, any number of things can cause a bacterial infection in squirrels, particularly if the immune system is stressed.   Bacterial infections are treated with antibiotics and in most cases, will require a veterinarian to diagnose the infection through tissue, blood or urine samples.  Reference Signs of Bacterial Infection below.


In the rehabilitation setting, many infections we see result from an injury braking the skin barrier, such as a bite wound from another animal or insect, or from internal bacterial infections.   



Anytime there is an open wound on a squirrel, gently flush the wound with saline solution to remove loose debris and disinfect with a non-stinging solution like Betadyne.   If the wound is fresh, a topical antibiotic can help ward off an infection (Reference the section on Topical Treatments below). However, if the wound is red, swollen and oozing viscous,  yellowish-white fluid or has a bad smell, then an infection is definitely a possibility and the squirrel likely requires antibiotics to recover. Since oral antibiotics require a prescription, a visit to the veterinarian is warranted.

Top 7 Bacterial Infections & Their Symptoms

The classic symptoms of a bacterial infection are localized redness, heat, swelling and pain. Any time a squirrel is demonstrating localized pain in a specific part of the body it should the examined closely for infection.  Look for signs of licking or chewing, favoring a limb (reluctance to put pressure on a paw for example), shaking of the head or rubbing an ear.  Keep in mind that these may also be signs of parasites or viral infections.   When in doubt, seek out the advice of a veterinarian.

#1 Abscesses

An abscess is a pus filled cavity beneath the surface of the skin formed by the tissue to encapsulate an infected area.  Abscesses can result from punctures, bite wounds, or other trauma.  Abscesses can occur anywhere on the squirrel’s body and are treated with oral  and topical antibiotics.  If the abscess is draining, keep it open and draining with warm compresses. If it’s closed, the vet may want to lance and flush the wound.  Provide good supportive care during healing and treat the wound daily to keep the drainage hole open until healed from the inside out.  Do not ignore an abscess or allow it to go untreated. Abscesses are very uncomfortable and can be fatal to the squirrel.


Untreated abscess   =   Surrounding bone & tissue damage/uncontrolled infection   =   death


Abscesses occurring on the head can obstruct normal breathing.  Squirrels cannot breath well from the mouth.  If a squirrel is mouth breathing, it must receive veterinary care immediately.


#2 Staphylococcal Skin Infections

Staphylococcal skin infections are caused by Staphylococcus sp. Infection when the bacteria normally found in the environment enters the system through a break in the skin.  A staph skin infection is characterized by itchiness, crusty skin, pustules and small, raised lesions. Hair loss may result.  These can also be signs of other skin conditions such as mange (an infection from mites).  

Internal staphylococcal bacterial infections can affect the upper respiratory tract of the squirrel and is transmittable to humans (Zoonotic) through a bite wound from an infected animal.

#3 Pasteurella Bacterium

Another common bite-associated infection is from the Pasteurella bacterium which is a naturally occurring organism in the mouth of most cats and dogs. The first signs of pasteurellosis usually occur within twelve hours of the bite and include pain, reddening, and swelling of the area around the site of the bite. Pasteurellosis can progress quickly, radiating outward from the bite site. Untreated, this infection can lead to severe complications, commonly ending in death for the squirrel.

#4 Streptococcal Infections

Symptoms of Streptococcal infections are similar to those of Pasteurella. Redness and painful swelling occurring at or near the wound and progressing outward. As with pasteurellosis, the squirrel needs to be seen by a vet.

#5 Leptospirosis

Leptospirosis is a zoonotic disease that can affect both humans and animals. It is a highly contagious disease transmitted through infected urine or bites from infected animals. The signs of Leptospirosis are similar to flu, including fever, vomiting, redness of the mucous membrane, lethargy and depression. If left untreated, permanent kidney damage may occur.

#6 Plague

Yersinia pestis enterobacteria, more commonly known as Plague,  is a deadly infectious disease has been reported in many species of wildlife, including ground squirrels.  Plague is zoonotic meaning that it can infect humans; as well as, epizoonotic, infecting  other mammals.  Affected animals exhibit nonspecific signs such as weight loss, lethargy, loss of appetite, and diarrhea.

The bacteria that causes plague survives in a cycle involving rodents and their fleas.   Plague can survive in some  high density rodent populations by failing to kill all of the infected host animals, making them a long-term reservoir for the bacteria.  Once an infected animal dies, the hungry fleas immediately look for a new host animal, which might be any other warm blooded mammal, such as a human being , or domestic pet like a cat or dog who brings the plague infected fleas home.   


It is important to know if plague has been reported in your area and make sure you follow flea prevention protocols such as using a monthly flea drop on all of your pets and wear protective clothing and insect sprays when around populations of potential host animals.


The plague bacteria can also be transmitted through exposure to the bodily fluids of an infected animal.  

Cats are particularly susceptible to plague, and any animal  can be afflicted by eating infected rodents

and then passing the disease off to their owners or treating veterinarian.  

Plague can be transmitted between people through the inhalation of airborne droplets from a coughing host.

#7 Bite Wound Infections

Capnocytophaga bacteria can infect a squirrel that has been bitten by a dog.   If the squirrel has been retrieved by a slobbering pet, a bite wound must be suspected.  As with cat bites, bite wounds are very hard to detect since the tissue closes up quickly around the wound site.   Check the squirrel closely for any signs of bleeding or signs of abscess (puss filled pockets that look like soft lumps).

Early signs of infection a bacterial infection include lack of appetite(stomach upset), pain with movement  and tiny reddened patches on the skin.  A Capnocytophaga Infection left unchecked can evolve into septicemia, or blood poisoning, particularly in a weak or immune-compromised squirrel.

It is VERY difficult to find bite wounds on a squirrel (particularly if it is feeling uncooperative).


If you suspect the squirrel has been bitten, it must be seen by a vet immediately for wound management and antibiotic treatment.  Cat bites that are left untreated are typically fatal to squirrels.  Cats carry a variety of germs in their mouth that can be harmful to squirrels (and people). 

Treating Bacterial Infections

This section is not intended to be a substitute for competent veterinary care.  Please discuss the use of these medications with your veterinarian. Not all veterinarians are familiar with wildlife medicine treatment protocols.


The general rule of thumb is that an antibiotic that is safe for domestic rabbits and rodents will be safe for squirrels at the same dosage.

Oral Antibiotics

A few oral antibiotics that are commonly prescribed for squirrels include Baytril® (generic enrofloxacin) and SMZ (Sulfamethoxazole).    Baytril 10 mg/ml oral suspension. Standard dosage is .1 ml/cc per 100 grams squirrel weight BID (twice per day). Refrigerate. Prescription required.


Note: If you are supplementing the squirrel’s food or formula with beneficial bacteria, such as acidophilus or yogurt, do not feed at the same time as administration of the oral antibiotic as it will negate the affect of the beneficial bacteria.  Wait a few hours after the antibiotic dose to offer beneficial bacteria.


Topical Treatments

Topical antibiotics such as Neosporin® or triple antibiotic ointment are fine for tiny babies that will not lick at the wound site or bandaged areas; however, should be avoided for older infants and adults since ingesting these will upset the normal beneficial bacterial balance in the gut and may result in life threatening diarrhea.  


Do not use over the counter topical antibiotic ointments for treatment of genital injuries caused by genital nursing unless combined with YUK or other anti-licking gel to prevent ingestion by the offending squirrel.  


Neo-Poly-Dex Ophthalmological antibiotic (generic name Neomycin, Polymyxin B sulfates, and Dexamethasone ophthalmic) are generally considered safer alternatives for topical treatments in areas at risk for ingestion through licking or normal grooming. Prescription required.


Animax a generic for Panalog®, is a combination antimicrobial, antifungal, and corticosteroid used in the treatment of skin disorders characterized by inflammation and dermatitis caused by bacteria or candida (yeast) infections. Prescription required.

More Resources

Supportive Care

Get recommendations for caring for ill, injured, and non-release squirrels.

How to Debug

Get step-by-step instructions for debugging squirrels to stop infections.

Zoonotic Diseases

Head to the CDC for a full list of zoonotic diseases and their descriptions.

Squirrel Board

Ask questions and get expert advice from

squirrel rehabbers.

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