Diagnosing enteric disease in backyard chickens

Emily Martin, Marina Brash, Emily Brouwer and Kate Todd

Animal Health Laboratory, University of Guelph, ON

AHL Newsletter 2019;23(4):12-14.

Veterinarians that treat backyard flocks can encounter cases of enteric disease due to a number of different etiologies. Due to the length of the intestinal tract, enteric signs can range from gasping, distended crop (crop stasis, crop impaction, pendulous crop), diarrhea, pasty vents, and emaciation. Morbidity and mortality will be variable. How do you approach diagnosing these flocks?

On physical examination, examine the oral cavity for plaques and the crop for distention and consistency (empty/full, doughy/firm). Examine the vent for evidence of fecal or urate concretions, hemorrhage and trauma (Fig. 1A). Birds have two types of normal droppings: brown and well-formed feces with a cap of white urate material or loose brown cecal droppings. Loose cecal droppings need to be differentiated from diarrhea. Knowing the normal appearance of chicken droppings will help detect diarrhea. The colour of droppings can provide clues to disease; for example: green due to increased bile related to anorexia, brilliant yellow due to histomoniasis, orange associated with sloughing of the intestinal mucosa, and white due to excessive urates from the kidneys. Other changes to look for include the presence of undigested feed (malabsorption), blood or abnormal smell.

If there is no mortality but there are changes in the droppings, consider collecting fecal material for parasitology and bacterial culture. If there are oral plaques, swabs (viral transport media) of the plaques and choanal slit could also be collected to perform PCR tests for specific diseases (e.g. poxvirus, Trichomonas). You can watch a video on how to collect samples with these swabs at: https://oahn.ca/resources/small-flock-poultry-veterinary-resources/ (must be registered and signed in to OAHN.ca to view this page)

If there is mortality present, this is an indication for postmortem examination and more intensive sampling. Postmortem examination could be done at a clinic or birds could be shipped to the Animal Health Laboratory. If birds are shipped, please refer to the AHL website for a PM submission form (https://www.uoguelph.ca/ahl/submissions/submission-forms) and packaging instructions (https://www.uoguelph.ca/ahl/submissions/ahl-labnote-27-submission-instructions).

Clinic postmortem: Cut the commissure of the beak and open the oral cavity to look for oral plaques. Rule outs include wet pox, candidiasis, trichomoniasis, impacted fine feed and vitamin A deficiency. Collect pieces of the oral mucosa, including plaques, for PCR and histology. 

Cut down the esophagus into the crop and examine the crop wall and content. Collect pieces of crop for histology. Open the bird and use the gizzard to reflect organs and cut across the esophagus-proventriculus junction to remove the intestines. Open the proventriculus and gizzard and pull out the content for examination. Birds allowed outside will often eat fibrous material that can impact the gizzard and crop (Fig. 1B) or may ingest toxic plants or foreign items (Fig. 1C) that can block or perforate the intestines. Examine the external surface of the small intestines for petechial hemorrhages (e.g. coccidiosis) then cut open most of the length of the small intestines to examine for the presence of worms and irregular mucosal surfaces; the latter may indicate necrotic enteritis (Fig. 1D). If there is increased fluid or irregular mucosal surfaces, tie off pieces of the intestines and submit for culture. For histology, collect pieces of duodenum (with pancreas), jejunum (mid small intestine), and ceca (cut transversely through the ileum and both ceca). Open the colon and cloaca to examine content. In younger birds, examine the bursa to evaluate size and collect pieces for histology and PCR.

Table 1: List of chicken enteric disease tests available at AHL.

DISEASE (by lab section)





Parasitology Lab





Intestinal parasites (coccidia, nematodes, tapeworms




fecal float, histology

Trichomonas gallinae





Clinical pathology





Crop wash




cytology, histology

Virology Lab





Poxvirus (nodules, crusts)





Newcastle/APMV-1 (Avian Paramyxovirus 1)





Avian Influenza/Influenza A





Infectious Bursal Disease (IBD)





Bacteriology Lab





Bacterial culture (feces, intestines)





Mycology/Fungal culture










Mycotoxin (feed analysis)





Sampling Summary:

NOTE: If screening a flock for disease, up to 5 swabs or tissues can be pooled for PCR testing. PCRs are generally the preferred test as they target specific diseases and can be done quickly.

Live Bird Diagnostics:

  • Choanal slit/tracheal swab (viral transport medium) is the optimal sample for PCR (larger number of tests available).
  • Photos of affected birds can be submitted to AHL along with the case history to ahlinfo@uoguelph.ca.

Dead Bird Diagnostics:

NOTE: If a postmortem is refused by the owner, fecal material and swabs from the choanal slit could still be collected for PCR.

  • Postmortem is the key test for lesion identification and appropriate sample collection.
  • Histology is an option to screen tissues for lesions or determine the etiology of specific lesions such as nodular structures (bacterial, fungal, neoplasm). Collect a wide variety of tissues to place in formalin, including all major organs: lung, liver, spleen, and kidney in addition to intestine.
  • PCR tests can be performed on swabs or tissues. If you are sending tissues, package each tissue type separately and label. Do not mix intestinal tissue with organ tissue.
  • Bacterial/fungal culture can be performed on gel swabs or tissues.

For more information on enteric diseases in chickens, please refer to the OAHN website: https://oahn.ca/resources/enteric-diseases-of-small-flock-poultry/


Reportable diseases in Canada include Salmonella Pullorum, Salmonella Gallinarum, Avian Influenza and Newcastle Disease. If high mortality and/or clinical signs lead you to suspect Avian Influenza or Newcastle Disease – quarantine the flock and phone CFIA!

                    A Vent trauma. B Gizzard impaction with fibrous material. C Foreign body (nail) perforating the gizzard. D Necrotic enteritis (Turkish towel mucosa).           

Figure 1. A Vent trauma. B Gizzard impaction with fibrous material. C Foreign body (nail) perforating the gizzard. D Necrotic enteritis (Turkish towel mucosa).