Antibiotics: Rabbits and Guinea Pigs


This topic is one that I wonder about all the time, and perplexes many vets when faced with an infection in a rabbit or guinea pig.

The topic is the rational usage of antibiotics in rabbits and guinea pigs.

This can be tricky, especially if your exotics work load is minimal, and your exotics notes are gathering a thick layer of dust on the clinic shelf. For many this is true, and the scene plays out like this:

As you reach for the notes, the dust falls from the folder. You place the forgotten notes on the bench, and blow the dust off the cover, wiping the remaining dust away with your right hand.

A solitary spider runs out of the folder and behind the computer, but don’t worry, you wont be treating him today.

You open the folder, straining to think back to your uni lectures. But all that surfaces are these words;

Enrofloxacin Good.

Penicillin Bad.

So you delve deep into the middle of the ancient tome of notes, hoping to find an answer, before your client begins to wonder why you’ve been gone fifteen minutes…

Or you google it.


Unlike with cats and dogs, there is limited published information about which antibiotics are most effective in each body system, and a lot of evidence is anecdotal or extrapolated from other species.

The other very real concern is giving toxic medications to your rabbit or guinea pig (remember penicillin bad?), so the safe path of the cautious veterinarian begins and ends with enrofloxacin, closely followed by meloxicam.

Bing bam boom! Next consult!

There’s nothing wrong with this, enrofloxacin is a very safe medication in rabbits, guinea pigs and ferrets. Which is why so many people feel comfortable using it.
I will note that this definitely includes myself, and i have happily prescribed enrofloxacin on many occasions. This mentality is very similar to the use of penicillin in cows, it’s not going to hurt, and it just might help, so whats the harm?

The harm is that are doing a disservice to your self and your patients by limiting your knowledge and your tools, or antibiotics.

So what are our options if enrofloxacin is NOT the cure to all ailments?

The aim of this article is to provide you with options and knowledge to use with your rabbit and guinea pig patients. Each problem is different, and as any micobiologist will gleefully state, ideally culture and sensitivity tests should be run. However, it is good to know what your options are to begin with.


If you’d like a dose rates, check out these two helpful links;


Guinea Pigs:

I’ll start with a story about a case I saw a few years ago.



A young three year old male desexed rabbit had come in to the clinic. it had a mass growing below its eye that had started off quite small and kept growing.

The previous vet had performed a fine needle aspirate, finding a small amount of pus, and consequently started the rabbit on the one-two punch combination of enrofloxacin and metacam.

Unfortunately the rabbit returned to the clinic two weeks later to see me, with a now larger abscess which hadn’t resolved with the medications.

Now as you may know with rabbit abscesses, they often do need surgical resection, and long term antibiotic therapy to resolve completely. In addition to (and extra points if you thought of this) not having any involvement with underlying tooth roots or dental disease.

Luckily, this rabbit did not have underlying dental disease (confirmed with radiographs) and so i laid out the plans to the client, who was very committed.

However, i had limited experience with rabbit abscesses and so i called in reinforcements, my exotics teacher from university. Their advice was surgery followed by long term medication with trimethoprim sulphonamides and…penicillin.

Yes, penicillin.

Don’t leave in disgust just yet!

I almost dropped the phone in shock, remember, pencillin bad! Dysbiosis! Death! Bad!

Now going off that information i was shocked, i knew this expert had lots of experience and success in treating exotics over the years, but as you can imagine, this information was a bit much for me.

So i said this, and consequently delved deep into the realm of “safe” penicillin usage in rabbits, a dangerous dark place (behind the folder on the shelf that i mentioned earlier). This is where i learnt that penicillin can be used can be used cautiously via injection, but never orally.

So now my thoughts were;  Penicillin good. Remember though, as with all power, comes great responsibility – to not give penicillin orally.

Use it wisely.

Following surgery, the patient went home with oral trimethoprim sulphonamides and returned for subcutaneous injections of penicillin.

This little bunny recovered fully and despite my concerns absolutely thrived on penicillin!

The reason for mentioning this story is to illustrate the potential safe usage and penicillin and to give you ideas about safe usage of antibiotics in rabbits and guinea pigs.


Now i am definitely not saying penicillin is 100% safe for rabbits, and i wouldn’t use it for everything. Especially not guinea pigs, as some sources quote toxic reactions to the procaine component of penicillin solutions.

However in cases of abscess, and anaerobic infections, where i need a broad spectrum antibiotic, then i would use penicillin.

BUT NEVER ORALLY! As you and I remember from our dusty tomes of notes, oral penicillin can cause dysbiosis of the gastrointestinal flora and cause death.

So once again, never orally!



Armed with this knowledge, the selection of the correct antibiotic depends on:

  • The location of infection
  • Class of antibiotic
  • Route of administration
  • Type of bacteria
  • Dose/chance of toxicity and dysbiosis

So lets assess each class of antibiotic, addressing common “safe” options for rabbits and guinea pigs:


Beta – lactams:

Penicillin being the main player here,
  • Broad spectrum
  • Bacteriocidal
  • Good gram positive, negative and aerobic/anaerobic activity.

Especially good for abscesses. The good news is you now know that penicillin is safe for usage in rabbits, as a subcutaneous injection. However in guinea pigs, be aware of the risk of procaine toxicity.



  • Broad spectrum
  • Bacteriocidal
  • Great gram positive and negative activity (depending on the generation), covering aerobes and anaerobes.

Though cephalosporins are rarely used, cephalexin can be used subcutaneously in rabbits, or via intramuscular injection in guinea pigs.

Personally id start with penicillin first in rabbits, however in guinea pigs cephalexin may be a useful option.



Doxycycline is the primary antibiotic used from this class,

  • Bacteriostatic
  • Broad spectrum
  • Gram positive and negative action, covering aerobes and anerobes.

Doxycycline has a great ability to penetrate into respiratory secretions. Also a go to choice for respiratory infections in rats and mice.
However, as with other species, the potential for disruption of cartilage growth is there, so beware using tetracyclines in immature rabbits and guinea pigs.



The home of enrofloxacin!
  • Bacteriocidal
  • Broad spectrum
  • Gram positive and negative bacteria, with aerobic, with LIMITED ANAEROBIC activity.

Slander! Heresy! Lies!
Enrofloxacin for everything i say!

Seriously though, enrofloxacin is a great medication a large variety of uses, including;
  • Otitis media
  • Pododermatitis
  • Urinary and respiratory infections

Just to name a few, so enrofloxacin has a well earned reputation!

Additionally, some anaerobic activity is present, however if dealing with an overgrowth of anaerobic bacteria, it may be wise to choose penicillin or metronidazole, if applicable.

Enrofloxacin is not a great first choice with:
  • Rabbit abscesses
    • Abscesses often require surgery to remove the entire capsule and possibly the infected tooth in cases of tooth root abscesses, a suitable choice would be oral TMS with injectable penicillin.

  • Gastrointestinal infections
    • As hind gut fermenters dysbiosis is always a concern, however oral trimethoprim sulphonamides or metronidazole would be good choices to overcome anaerobic bacterial overgrowth.



A popular and safe nitroimidazole

  • Antibacterial and antiprotozoal activity
  • Great activity against anaerobes

Metronidazole is one to consider with gastrointestinal overgrowth or diarrhoea, to be used in conjunction with supportive care.


Trimethoprim sulphonamides:

  • Bacteriocidal (if potentiated and used together)
  • Broad spectrum
  • Good gram positive and negative activity with aerobic and anaerobic activity

Very useful antibiotics, handily available in oral solution. Especially handy for urinary and respiratory infections.



Tylosin is the main player here,
  • Bacteriostatic
  • Narrow spectrum
  • Gram positive action, some anaerobic and some gram negative activity

Not great for usage in rabbits and guinea pigs, consider this a reserve option for colitis and mycoplasma infections. But not a first choice.

There are other options (and yes a few unmentioned classes), this is a good fundamental selection on which to treat your patient. Use them wisely!

A few years ago, i attended a cow seminar, the presenter discussed several cases and asked about the recommended therapy for each.

The answer was penicillin for all three!

I always thought it sent the wrong message, isn’t it better to encourage people to use different antibiotics depending on the infection?

Depending on the interpretation of the previous sentence i picture microbiologists screaming somewhere in horror.

My meaning being, use the most effective antibiotic for the infection. If infection is not a concern, don’t reach for the enrofloxacin. However, there are many infections where the broad spectrum activity of enrofloxacin is a great choice, just not when anaerobes are involved.

The main take away point of this article is to consider the antibiotics at your disposal when dealing with infections in exotic mammals.

Some tools are great and safe, but they should not be used for every situation. We do this every day with other small and large animals, though often the barrier in exotics is not knowing what is safe, or in what dose.

Antibiotics deemed safe have minimal risk of anerobic overgrowth, dysbiosis, and death. Which is why they are used frequently.

So when selecting antibiotics in rabbits and guineas, please consider;

  • The location of the infection
    • Will the antibiotic effectively reach and eradicate the bacteria?
    • For example rabbit abscesses are full of thick caseous purulent exudate, which require surgical excision and adjunct antibiotic therapy.

  • Are these antibiotics effective against the bacteria causing the infection?
    • This is the limitation of enrofloxacin, which has limited anaerobic activity.

  • Route of administration

  • Duration of treatment
    • For example – Otitis media may require one month of antibiotic therapy! So stay the course!

I hope this article will help you make educated decisions about which tools to use with your sick rabbits and guinea pigs!


If you’d like to review you knowledge of doses, you can check them out here!


Guinea Pigs:


What do you use in rabbits and guinea pigs? How do you approach antibiotic selection?

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  • Morris, TH. Antibiotic therapeutics in laboratory animals. Lab Anim. 1995, 29, 16-36
  • Melbourne Rabbit Clinic. Rabbit & Guinea Pig Emergency Manual. Melbourne Rabbit Clinic, Ferntree Gully, 2014.
  • Meredith, A, Johnson Delaney, C. BSAVA Manual of Exotic Pets. 5th Edn. APA, Cheltenham, 2010.
  • BSAVA. BSAVA Small Animal Formulary. 8th Edn. BSAVA, Gloucester, 2014.
  • Centre for Veterinary Education: Time Online Course – Rabbits and Rodents 2018