Diagnose well to treat better

Why not everything is a parasite in dogs and cats

In everyday veterinary medicine, there is a widespread belief that if a dog or cat has diarrhoea, it must be caused by parasites. Recurrent loose stools, mucus, occasional blood, gas, weight loss or irregular appetite almost automatically lead to this suspicion. However, clinical experience and scientific evidence agree on one fundamental point: this direct association is, in many cases, erroneous. Correctly diagnosing parasitic infections—and knowing when they are not present—is key to protecting the digestive and overall health of our pets, as well as avoiding repeated treatments that, although well-intentioned, are not always harmless to the intestine, as demonstrated by evidence accumulated in retrospective studies on chronic diarrhoea in dogs and cats.

Invisible parasites: why they are not always detected

The big misunderstanding: digestive symptoms and parasites

Several clinical studies published in leading veterinary journals have shown that up to 40% of chronic diarrhoea in dogs and cats is not caused by parasites, but is related to food intolerances or allergies, imbalances in the gut microbiota (dysbiosis), inflammatory bowel disease or pancreatic disorders. Simply put, many animals with diarrhoea do not have parasites, and treating them as if they did can delay the actual diagnosis. Therefore, when a digestive problem recurs for weeks or reappears after each treatment, it is important not to automatically assume that “the parasite has returned,” but to rethink the origin of the problem with a broader view, as recommended by the WSAVA international clinical guidelines on chronic gastrointestinal diseases.

In large retrospective studies on chronic diarrhoea in dogs, most cases are grouped under so-called primary enteropathies (problems specific to the intestine), while infectious causes, including parasites, account for a significantly smaller proportion. In practice, this means that closely observing the animal’s progress at home — frequency of bowel movements, actual stool consistency, relationship to diet changes or stressful situations — provides valuable information that complements diagnostic tests and helps to guide the clinical process correctly.

Intermittent excretion: when the parasite ‘hides’

Intestinal parasitic infections do not behave consistently. Many parasites do not shed eggs, larvae or cysts every day, but intermittently, depending on their biological cycle, the number of parasites present and the state of the animal’s immune system, a phenomenon well documented in studies on the dynamics of parasite excretion. This means something very important:

👉 A negative faecal analysis does not automatically rule out parasitic infection, especially if clinical symptoms persist.

For this reason, when the vet requests that the test be repeated or that several samples be collected on different days, it is not a matter of “insisting as a matter of routine”, but rather of adapting to the actual biological behaviour of the parasite, as indicated in the diagnostic recommendations of the CAPC and ESCCAP. From a practical point of view, storing the sample correctly (in a clean, tightly closed container and refrigerated if not delivered immediately) and avoiding long delays before analysis significantly improves the reliability of the result, as demonstrated in studies on faecal sample storage.

Clinical integration: diagnose judiciously, not out of habit

The most common mistake in veterinary parasitology is to swing between two extremes:

• ruling out a parasitic infection based on a single negative analysis, or
• systematically treating without confirming the diagnosis.

Both approaches can make the disease chronic, cause relapses and give a false sense of improvement. Responsible clinical practice is based on combining a detailed medical history, clinical examination, repeated tests and complementary techniques when indicated, together with real monitoring of the patient’s progress, as agreed by the ESCCAP and WSAVA recommendations. For the guardian, this means trusting the diagnostic process, following the instructions for collecting samples and communicating any changes observed at home.

A good diagnosis not only allows for better treatment. It allows for less treatment, avoids unnecessary treatments, protects long-term intestinal health and reinforces truly preventive and evidence-based veterinary medicine. In parasitology, as in all medicine, the correct diagnosis is always the first treatment.

Faecal examination: essential, but not infallible

What is a coprological examination and what can it detect?

A coprological examination is the analysis of faeces and forms the basis for the diagnosis of intestinal parasites. It allows the identification of:

• Nematodes (roundworms) such as Toxocara, Ancylostoma or Trichuris
• Cestodes (flatworms) such as Dipylidium, Taenia or Echinococcus
• Protozoa such as Giardia, Cystoisospora or Cryptosporidium

It is an essential tool, but its performance depends greatly on the technique used and how the sample is collected, as emphasised in the ESCCAP official guidelines on intestinal parasites. At home, collecting a small amount of recent faeces, avoiding contact with soil or sand, can make the difference between a reliable and a dubious result.

Medical fact: “It’s not all about ‘deworming’: it’s also about ‘testing’.”

CAPC guidelines recommend faecal diagnosis 2–4 times a year and treating adults 4 times a year with effective antiparasitic drugs, depending on lifestyle. This fits perfectly with reinforcing risk-based prevention.

Source: https://capcvet.org/guidelines/general-guidelines/

Faecal flotation: useful, but with clear limitations

Faecal flotation is the most commonly used technique in clinics. It consists of making the eggs or oocysts ‘float’ so that they can be observed under a microscope. Although very useful, it has a well-known limitation:

📉 a single coprological test may fail to detect parasites in up to 30% of cases, especially when the parasite load is low or excretion is intermittent.

Therefore, when an animal has persistent digestive signs, it should come as no surprise that the vet recommends repeating the test even if the first one was negative. In daily practice, this repetition avoids unnecessary “blind” treatments and reduces the frustration of not understanding why the problem is not being resolved.

DID YOU KNOW: “There are worms that do not appear in faeces… even though they are ‘intestinal’ in nature.”

Trichuris vulpis (whipworm) has a temporary trick: its prepatent period is long, 74–90 days. This means that a dog may have compatible clinical symptoms and still not shed eggs for weeks, especially after life changes (moving house, adoption, stays in the countryside). 

Serial samples: a key change in diagnosis

Collecting stool samples every other day (ideally three days) increases diagnostic sensitivity to over 85–90%, as shown by comparative studies on serial coprological techniques. In simple terms: repeating the test increases the chances of detecting the parasite and allows for a more confident decision on whether treatment is necessary or other causes should be sought. For guardians, this small logistical effort often saves weeks of repeated treatments and unnecessary visits.

Faecal sedimentation: when flotation is not enough

Faecal sedimentation complements flotation and is especially useful for detecting heavier eggs, such as those of some cestodes. In practice, this explains why a ‘normal’ coprological test does not rule out cestodosis, especially if there are compatible data such as anal pruritus, the presence of fleas or occasional visualisation of segments in the faeces, a limitation well described in reviews on the diagnosis of Dipylidium caninum. In these cases, effective flea control in the animal’s environment is as important as the antiparasitic treatment itself.

Intestinal protozoa: when looking through a microscope is not enough

Giardia: the clearest example

Giardia duodenalis is one of the most common intestinal protozoa and also one of the most difficult to confirm. European epidemiological studies show prevalences ranging from 15% to 30% in young animals or in groups, and its cysts are shed very irregularly, so they may not be visible under the microscope, especially if the sample is not recent or the load is low. This explains why some animals have recurrent diarrhoea that partially improves and then reappears.

In a practical comparison, passive flotation (as often done in clinics) only matched centrifugation with ZnSO₄ in 62.4% of samples; and in Giardia, detection by passive flotation fell to 14.7%. Translation: sometimes “it’s not that there are no parasites,” it’s that the technique doesn’t see them. A study comparing methods showed that a rapid antigen test for Giardia achieved 86.2% sensitivity, while microscopy remained at 58.6%. This is a perfect anecdote to explain why sometimes the test “comes back negative” and yet the vet insists on repeating or changing the technique.

From a practical point of view, simple measures such as thoroughly cleaning drinking troughs, preventing the animal from drinking stagnant water and regularly washing blankets and beds help to reduce reinfection while the diagnosis is being completed, as recommended by health and veterinary authorities.

Faecal antigen test: detecting the parasite without seeing it

Faecal antigen detection tests identify specific proteins of the parasite. In simple terms, they do not look for the parasite itself, but rather its biological ‘footprint’. They are particularly useful in young animals, in groups (breeding facilities, shelters) or in cases of recurrent diarrhoea with inconsistent coprological results, and have a sensitivity of 85-95% according to comparative studies, allowing for safer therapeutic decisions without resorting to repeated empirical treatments.

Faecal PCR: the most sensitive technique

Faecal PCR detects the genetic material of the parasite and is currently the most sensitive and specific technique, with detection rates that can exceed 95–97% for certain protozoa. It is particularly indicated in chronic, refractory cases or when it is essential to confirm or rule out a parasitic infection before starting exclusion diets, anti-inflammatory treatments or more invasive tests, thus avoiding unnecessary dietary changes or medications.

In a comparison of tests for Giardia, qPCR showed a sensitivity of 97.0%, compared to classical techniques with much lower sensitivities. Useful for introducing the concept of “intermittent parasites” and why diagnostic technology is a game changer.

Parasite diagnosis beyond the gut

When stools are normal… but the problem persists

Not all worms live in the intestine. There are cardiac, pulmonary, subcutaneous and ocular parasites that are not detected in faeces, so a normal coprological test can coexist with severe parasitosis. In Dirofilaria immitis, for example, up to 30% of dogs may be infected without showing obvious signs in the early stages, making a specific diagnostic approach essential.

Heartworms and lungworms

Parasites such as filariae or lungworms can cause coughing, breathing difficulties, exercise intolerance or even collapse. Their diagnosis requires specific blood tests, techniques such as Baermann or imaging tests, not conventional faecal analyses. As a preventive measure, international guidelines recommend periodic testing even in asymptomatic animals.

HISTORICAL FACT: “The Baermann method is over a century old.”

The Baermann technique, used to recover larvae (e.g., in suspected cases of lungworms), is a classic “low-tech” method with a long history: it is described as the Baermann method (1917) and is still in use today because it takes advantage of the natural movement of the larvae to separate them from faeces/tissues. 

Skin and eye parasites

Some worms are found under the skin or in the eyes, causing nodules, inflammation, secretions or persistent discomfort. In these cases, targeted clinical examination and specific techniques are key to diagnosis, and seeking prompt medical attention for any visible changes prevents further complications, as indicated by European studies on ocular nematodes.

Scientific sources and recommended reading

Hall, E. J., Simpson, J. W., Williams, D. A. (2015) – Chronic enteropathies in dogs: classification, diagnosis, and management – Journal of the American Veterinary Medical Association (JAVMA) – Clinical review showing that a significant proportion of chronic canine diarrhoea is not caused by infection or parasites.

https://pubmed.ncbi.nlm.nih.gov/26041519/

Allenspach, K., Wieland, B., Gröne, A., Gaschen, F. (2007) – Chronic enteropathies in dogs: evaluation of risk factors for negative outcome – Journal of Veterinary Internal Medicine – Retrospective study identifying primary enteropathies as the main cause compared to parasitic infections.

https://avmajournals.avma.org/view/journals/javma/246/6/javma.246.6.640.xml

WSAVA Gastrointestinal Standardisation Group (2010) – Guidelines for the evaluation of chronic gastrointestinal disease in dogs and cats – World Small Animal Veterinary Association – International consensus document recommending a structured diagnostic approach before empirical treatment.

https://wsava.org/wp-content/uploads/2020/01/WSAVA-GI-Standardization-Group-Guidelines.pdf

Zajac, A. M., Johnson, J., King, S. E. (2022) – Evaluation of faecal diagnostic techniques for detection of Giardia and other intestinal parasites in dogs – Parasitology Research – Comparative study demonstrating intermittent excretion and the limitations of single faecal examination.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9508988/

Companion Animal Parasite Council (CAPC) (2023) – Recommendations for faecal testing and parasite diagnosis in dogs and cats – CAPC Guidelines – Official recommendations endorsing the use of serial samples to increase diagnostic sensitivity.

https://capcvet.org/guidelines/testing-guidelines/

Dryden, M. W., Payne, P. A., Smith, V. (2017) – Effect of faecal sample storage on parasite detection in dogs and cats – Veterinary Parasitology – Study demonstrating the loss of diagnostic sensitivity when faecal samples are not analysed under optimal conditions.

https://pubmed.ncbi.nlm.nih.gov/28517325/

ESCCAP (European Scientific Counsel Companion Animal Parasites) (2021) – Guidelines for the diagnosis and control of endoparasites in dogs and cats – ESCCAP Guidelines – European reference document on parasitological diagnosis and rational control.

https://www.esccap.org/guidelines/

Scare, J. A., Slusser, J., Leutenegger, C. M. (2023) – Comparison of faecal flotation, antigen testing and qPCR for detection of intestinal parasites in dogs – Veterinary Parasitology – Study showing sensitivities close to 97% for qPCR compared to classical techniques.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10650246/

Beugnet, F., Labuschagne, M. (2018) – Diagnosis of Dipylidium caninum infection: limits of coprological methods – Parasites & Vectors – Review explaining the high false negative rate in cestodosis using conventional coprology.

https://pubmed.ncbi.nlm.nih.gov/31473268/

Centres for Disease Control and Prevention (CDC) (2022) – Giardia: diagnosis and laboratory testing – CDC Parasitic Diseases – Official document describing the limitations of microscopy and the value of antigen tests.

https://www.cdc.gov/parasites/giardia/diagnosis.html

Rishniw, M., Liotta, J., Bellosa, M. (2010) – Comparison of Giardia antigen tests and faecal flotation in dogs – Journal of Veterinary Internal Medicine – Comparative study demonstrating sensitivities of 85–95% for faecal antigen tests.

https://pubmed.ncbi.nlm.nih.gov/21697035/

American Heartworm Society (2023) – Heartworm disease: epidemiology and diagnosis – AHS Guidelines – Document indicating that up to 30% of infected dogs may be asymptomatic in the early stages.

https://www.heartwormsociety.org/pet-owner-resources/heartworm-basics

American Heartworm Society (2023) – Guidelines for the diagnosis, prevention, and management of heartworm disease – AHS Veterinary Guidelines – International recommendations on periodic screening even in animals without symptoms.

https://www.heartwormsociety.org/veterinary-resources/american-heartworm-society-guidelines

Otranto, D., Traversa, D. (2005) – Thelazia spp. and other ocular nematodes in Europe – Parasitology Research – European review on ocular nematodes and the importance of early diagnosis.

https://pubmed.ncbi.nlm.nih.gov/30318220/