Poultry Coccidiosis: Diagnosis, Lesion Scoring and Identifying the Eimeria Species Involved

A broiler flock may show poor growth, deteriorating feed efficiency or increased mortality without an immediate obvious cause. When coccidiosis is suspected, simply finding oocysts is not enough. The more useful clinical question is: Which Eimeria species is involved, where is it damaging the intestine, and do the lesions fit the production problem? 

Start With the Intestinal Location^[1] 

Coccidiosis is caused by Eimeria species that infect specific regions of the intestinal tract. The major pathogenic species in broilers include E. acervulina, E. maxima, E. brunetti, E. necatrix, and E. tenella, while other species can also affect production. 

The classical “big three” in broilers are E. acervulina, E. maxima, and E. tenella. Identifying the Eimeria species involved is important because diagnosis should not rely on clinical signs or gross lesions alone. Microscopic examination of mucosal scrapings and, where required, molecular methods can help confirm the species involved. 

The so-called lesser species also deserve attention. E. acervulina, E. hagani, and E. praecox infect the small intestine anterior to the Meckel's diverticulum, while E. mitis and E. mivati can involve the small intestine, ceca and rectum. Some may produce limited or no obvious gross lesions despite affecting growth or production. 

What Confirms the Diagnosis?^[1],[2] 

In chickens, a practical diagnosis combines the characteristic appearance and location of gross lesions with microscopic detection of significant numbers of parasites in mucosal scrapings from affected areas. 

That combination matters. Gross lesions can indicate where to look, while microscopy helps establish that Eimeria is actually present in the damaged tissue. 

Molecular techniques can provide another level of species identification. PCR targeting internal transcribed spacer regions or Sequence-Characterized Amplified Region DNA can help determine the Eimeria species composition in fecal droppings, litter or intestinal samples. 

This is particularly relevant when field findings do not clearly explain poor performance. Species composition may also provide clues when an unexpected Eimeria profile is associated with suspected drug resistance or immunovariability. 

Use Lesion Scoring to Put Findings into Context^[1] 

Lesion scoring provides a structured way to assess intestinal damage rather than relying only on a subjective description of severity. Johnson and Reid established a detailed gross-lesion scoring system in 1970 for the five chicken Eimeria species that produce gross lesions. 

During field investigation, the score should therefore be interpreted alongside the intestinal site, microscopic findings, and flock performance. A visible lesion without appropriate microscopic confirmation may not establish the cause of the production problem. 

A Practical Diagnostic Approach 

When coccidiosis is suspected, a useful sequence is: 

• Examine representative birds by postmortem examination. 
• Identify the intestinal regions showing abnormalities. 
• Characterise the gross lesions and apply lesion scoring where appropriate. 
• Collect mucosal scrapings from affected regions for microscopic examination. 
• Consider species identification when the findings are unclear or when species-specific differences could affect interpretation. 
• Where necessary, use molecular methods to determine the Eimeria species composition. 

Clinical Bottom Line 

Coccidiosis diagnosis is stronger when lesion location, lesion severity, microscopy and Eimeria species identification are considered together. For the practicing veterinarian, the objective is not simply to confirm that coccidia are present, but to determine whether the observed Eimeria infection plausibly explains the intestinal damage and production problem in the flock.

References:

1. Mathis GF, Lumpkins B, Cervantes HM, Fitz-Coy SH, Jenkins MC, Jones MK, Price KR, Dalloul RA. Coccidiosis in poultry: Disease mechanisms, control strategies, and future directions. Poultry Science. 2025 May 1;104(5):104663. https://www.sciencedirect.com/science/article/pii/S0032579124012410
2. Jenkins MC, Miska K, Klopp S. Improved polymerase chain reaction technique for determining the species composition of Eimeria in poultry litter. Avian Diseases. 2006 Dec 1;50(4):632-5. https://avian-diseases.kglmeridian.com/downloadpdf/view/journals/avdi/50/4/article-p632.pdf