Conducting avian fecal assessments

dvm360dvm360 June 2023
Volume 54
Issue 6
Pages: 40

Primary and secondary cytologic abnormalities, the species, and how the sample is collected are among the foundational considerations

Content submitted by Moichor, a dvm360® Strategic Alliance Partner

The fecal assessment has long been an integral part of an avian examination in both sickness and in health, but are we getting the most out of this diagnostic? What are we really trying to understand when we peer at the voluminous bacteria under the microscope?

When we think about disease states that present with fecal sample cytologic abnormalities, there are a few foundational considerations to keep in mind. The first to consider is that abnormalities can be primary or secondary. The second is that not every disease state is found in all avian species. Finally, depending on the organism in question, the timing of sample assessment and the manner in which it is assessed are critical to making a diagnosis.

Green-lighting the root cause with green wing macaws

A great example of the importance of differentiating primary vs secondary fecal abnormalities can be seen using an all-too-common scenario we are presented with in practice. Your patient is a 7-year-old, female, green wing macaw that presents for malodorous and voluminous droppings. During your examination, she is bright, alert, and displaying reproductive behaviors. She is moderately overweight based on palpation of adipose along the lateral aspects of her body and chest. In further conversation with the owner, you learn that she is eating an all-seed diet and loves to cuddle. Cytologic examination of her feces is performed at your veterinary reference lab via light microscopy and Diff Quik staining, where a prevalence of budding rods consistent with clostridial organisms is identified.

Patient sample of clostridial organism in green wing macaw. Contributed by Moichor using the pathology viewer.

Patient sample of clostridial organism in green wing macaw. Contributed by Moichor using the pathology viewer.

You theorize that due to the overstimulation of the hypothalamic- pituitary-gonadal (HPG) axis with associated reproductive behaviors and overconditioning, this bird is likely retaining feces, leading to an overgrowth of this organism. We could go 1 step further and theorize that cloacitis may be present at some level, adding to abnormal elimination patterns. Therapeutically, metronidazole plus or minus meloxicam seems fair, but long-term diet and husbandry improvements focused on reducing HPG stimulation are necessary for this bird to, likely, fully resolve this issue.

Now, what if this were a slightly underweight, reproductively quiescent 38-year-old green wing macaw? The presenting history is the same, but your examination identifies an uneven wear pattern on the feet. Fecal cytology supports a diagnosis of Clostridium overgrowth, and you start questioning whether this is primary or secondary. In this bird, based on the uneven wear pattern on the plantar surfaces of the feet, osteoarthritis is added to the differential list. Radiographs confirm your suspicion of osteoarthritis. Based on the patient’s history, physical examination, and diagnostics, you conclude that this patient is experiencing clostridial overgrowth due to fecal retention, secondary to unmanaged arthritis. Essentially, this bird is in much pain to posture and pass its dropping, so it holds them. Although we may use the same therapy we did with our young bird, adjustments in the environment and unimodal to trimodal analgesia should be implemented to truly address this issue.

In both of these cases, answering why this organism is here and whether it is primary or secondary directly affects the treatment plan. Although metronidazole therapy would have helped in the short term, both patients would not have been provided a complete therapeutic plan in the long term, which could ultimately increase the likelihood of recurrence and/or pathologic sequelae of the primary issue.

Budgeting for age with budgerigar

In our previous example, we highlighted the importance of differentiating primary vs secondary disease processes and how this can directly affect the overall outcome for your patients. Here, let’s change up the species to showcase how not every disease state is found in all species. Instead of a macaw, what if you were working with a budgerigar (also known as budgie)? It’s not to say that budgies and macaws do not have the potential to have similar fecal cytology findings and definitive diagnoses, but there are certain diseases identified on fecal cytology that are more prevalent based on the species.

Patient sample of Macrorhabdus ornithogaster in a budgie. Contributed by Moichor using the pathology viewer.

Patient sample of Macrorhabdus ornithogaster in a budgie. Contributed by Moichor using the pathology viewer.

The patient is a 6-month-old budgie presenting for regurgitation and hyporexia. Based on the species of this patient and its presenting clinical signs, you choose to do an in-house fecal wet mount using a fresh dropping. You identify Macrorhabdus organisms and achieve your diagnosis.

You start administering amphotericin B to the patient, knowing that this is one of the more effective therapies for this diagnosis.1 In this case, the species of the patient, along with the physical examination and history, prompted the consideration of specific diseases more commonly seen in small birds.

Hopefully, as you were going through this case, you started to question whether this could be primary or secondary. Although primary macrorhabdosis happens, it is more often seen in young, small psittacines and passerines. In older birds, this could very well be a secondary process. How so? Budgies, specifically as they age, have an increased prevalence of proventricular and ventricular carcinoma.2 Because Macrorhabdus organisms live in the proventriculus, neoplasia sets the stage perfectly for this organism to move in. Therefore, in addition to implementing amphotericin B and possibly a short course of analgesia, it is not unreasonable to pursue imaging when Macrorhabdus organisms are identified in small older parrots.

Two avian fecal assays to use

Along with considering primary vs secondary disease states and interspecies differences, veterinarians should be mindful of when and how a sample is collected and assessed. In the examples with our budgie and macaw patients, the timing of the evaluation and different techniques for fecal assessment were employed. Why? Because your diagnosis directly depends on the consideration of these factors. For example, let’s say a fecal wet mount is performed on an old fecal sample or is assessed too late from the time of collection; you may have picked the right test, but you will still miss your diagnosis.

How do we avoid wrong assays and bad timing? Consider the 2 main ways to assess avian feces, and because the details of these 2 methods are important, let’s dig into them more.

Fecal wet mount

Common pathogens identified in fecal wet mounts are Macrorhabdus, Spironucleus, and Giardia. Wet mounts are helpful in diagnosing these organisms, as size and movement patterns are common criteria that assist in identification. In our young budgie, this method was successfully employed to achieve a diagnosis; however, this was pretty lucky, as these organisms are generally motile for a short period of time and are not always excreted in every dropping equally. A fecal wet mount is great to do in clinic if both a fresh fecal sample and an experienced person exists to read the slide, but what if you have neither? What about scenarios where the fecal wet mount doesn’t identify any organisms?

This is where polymerase chain reaction (PCR) testing can help. PCRs identify a pathogen by using a confirmed section of DNA like a name tag. This is a more sensitive form of identification (ID) and is helpful if you have a boring wet mount or see something but are not totally sure what it is. Because most of these pathogens affect small parrots, finches, and canaries, keep both fecal wet mounts and PCRs in mind when working with these patients.

Direct fecal smear

A Diff Quik stained fecal smear is another excellent way to assess feces. As we saw in our macaw patients, this methodology allowed us to ID an organism that wouldn’t necessarily grow in an aerobic fecal culture and would have been missed by bacteria-specific PCR and fecal wet mount. Parrots should have a variety of rod and cocci bacteria, and regardless of their gram-positive or -negative characteristics, overrepresentation of either should spark the question: Why?

Other things that can be identified on a direct fecal assessment include the presence of blood and/or abnormal cells possibly exfoliated by the cloaca upon elimination.3 There may even be evidence of foreign material, such as sand or small grit particles, to take note of as you smear the sample on the slide. Although less common to observe, the pathogens that don’t stain with standard stains, such as mycobacterium, are just as (if not even more) important than what does stain. If there is suspicion of mycobacterium in a sample, acid-fast staining will help make these more apparent.4

At this point, the question that should be swirling in your mind is: What about the good ol’ fecal Gram stain? Many practitioners use this assessment as part of a way to evaluate their patient’s health. In this case, our expectation is that we find a heterogeneous population of bacteria of various characteristics. But when we don’t, what does that mean?

Let’s think through this based on the foundation we have built. What is our patient signalment? Is the methodology we used likely to ID pathogens of concern? Could this be a primary or secondary issue? Maybe this abnormal fecal Gram stain makes us repeat our physical examination or gather more history regarding husbandry and diet. We might even possibly consider furthering our workup.

But as we know in medicine, it all depends. The reality is that examination of the feces has the potential to be highly informative. However, if the wrong method is used at the wrong time, a fecal assessment also has the potential to be highly misleading.


When used thoughtfully, fecal assessments are a great tool to noninvasively investigate the potential source of a patient’s clinical signs. Differentiating primary and secondary disease states, accounting for species differences, and considering the timing and manner of assessment are all variables of importance. If we set our thought processes up correctly, fecal cytology has the potential to directly and positively affect veteri- nary therapeutic plans and case outcomes.

Bianca Murphy, DVM, Diplomate ABVP (Avian Practice), is the director of clinical medicine at Moichor, a veterinary reference laboratory devoted to enhancing animal diagnostics using artificial intelligence and data. She is a 2014 graduate of the University of Florida and is a diplomate in Avian Practice through the American Board of Veterinary Practitioners. In addition to her work at Moichor, she practices veterinary medicine and actively provides avian consultation services and mentorship to veterinarians throughout the country. When she is not working, she enjoys surfing, climbing, and spending time with family and friends.


  1. Phalen DN. Update on the diagnosis and management of Macrorhabdus ornithogaster (formerly megabacteria) in avian patients. Vet Clin North Am Exot Anim Pract. 2014;17(2):203-210. doi:10.1016/j.cvex.2014.01.005
  2. Powers LV, Mitchell MA, Garner MM. Macrorhabdus ornithogaster infection and spontaneous proventricular adenocarcinoma in budgerigars (Melopsittacus undulatus). Vet Pathol. 2019;56(3):486-493. doi:10.1177/0300985818823773
  3. Murphy B, et al. Four cases of lymphoma in unrelated lineolated parakeets. Presented at: ExoticsCon 2017; July 29-August 2, 2017; Washington, DC.
  4. Speer BL. Current Therapy in Avian Medicine and Surgery. Elsevier; 2016.
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