NAVLE® poultry questions rarely ask for the “ideal” diagnostic sample. They ask for the most practical and appropriate choice based on clinical signs, transmission route, biosecurity, and real-world practice.
What Each Swab Samples
Choanal Swab (Choanal Slit)
The choanal slit sits on the roof of the oral cavity and connects the nasal passages to the oral cavity and pharynx. A choanal swab targets upper respiratory secretions and organisms that colonize the choana, sinuses, and trachea.
The choanal cleft and trachea are among the most useful sites for confirming respiratory pathogens like Mycoplasma gallisepticum via culture or PCR.
Cloacal Swab
A cloacal swab targets the combined gastrointestinal/urogenital outlet and captures organisms shed in urine, feces, and genital secretions. Many multisystemic pathogens are shed through the GI tract, making this a handy sampling location.
For example, laboratories can isolate enteric pathogens (e.g., Salmonella spp. or E. coli) or pathogens that affect multiple systems (e.g., avian influenza, viruses, Newcastle disease virus) from cloacal swabs from domestic and wild birds.
How NAVLE® Tests this Decision
The NAVLE® often provides a classic flock-level scenario and then asks for the “best sample” for PCR/culture. Use this quick rule:
- Respiratory clinical signs → choanal (or oropharyngeal/tracheal)
- Diarrhea or waterfowl risk → cloacal
- High-consequence outbreaks (e.g., avian influenza, exotic Newcastle disease virus) → collect both (when an option exists)
You do not need to memorize every organism’s shedding pattern to apply this rule.
When to Choose Choanal Swabs
Respiratory Disease Workups
If the vignette emphasizes respiratory effort, nasal/ocular discharge, sinus swelling, or rales, think “upper airway”.
Confirm M. gallisepticum infection using PCR on swabs taken from sites including the choanal cleft and trachea. While culture is also possible, the fastidious nature of Mycoplasma make molecular diagnostics the better choice.
Choose choanal (or choanal + tracheal) over cloacal when the case centers on respiratory disease.
Chlamydiosis-Style “Mixed System” Case
Some agents shed intermittently and affect multiple systems. For avian chlamydiosis in individual birds, the preferred samples for culture or PCR include conjunctival, choanal, and cloacal swabs.
When answer choices include a “collect multiple swabs” option (choanal + cloacal, sometimes with conjunctival), that option often wins.
When to Choose Cloacal Swabs
Waterfowl-Heavy Risk or GI Shedding Emphasis
When the prompt highlights duck, geese, ponds, pasture access, or fecal contamination, you should consider GI shedding.
For example, use of cloacal swab is appropriate for enteric pathogens such as salmonellosis (a.k.a fowl typhoid).
If the question focused on surveillance, waterfowl, or fecal shedding, choose cloacal (or “oropharyngeal + cloacal” if offered).
When “Both” Becomes the Best Answer
Some questions allude to taking more than one sample. You’ll notice this pattern when:
- The block shows high morbidity/mortality
- The differentials include a high-consequence reportable disease
- The prompt mentions PCR, state lab, or regulatory response
- The answer choices include both oropharyngeal/choanal and cloacal swabs
For avian influenza, for example, sample from both respiratory and GI routes (oropharyngeal and cloacal swabs) for virus isolation and/or PCR.
If the question gives you the option to “collect both”, take it, especially when the vignette implies an outbreak.
Practical Swab Tips Overlooked by NAVLE® Candidates
- Match the sample to the question’s test. PCR requires a good organism load. Culture calls for good handling of an easy-to-grow bacteria, the right transport media, and quick submission.
- First, think about where the organism lives. Respiratory pathogens colonize respiratory epithelium, enteric pathogens are shed in feces, and mixed agents may require multiple sites.
- Don’t overthink “choanal vs. oropharyngeal.” Many NAVLE® items treat these as the same idea: a practical upper-respiratory sample.
Think Transmission First, Then Swab
Choosing between choanal and cloacal swabs comes down to one question: Where is the pathogen most likely shedding? When you anchor your decision to transmission route and clinical presentation, poultry diagnostics stop feeling ambiguous.
This simple framework lets you move quickly, avoid second-guessing, and select the answer the NAVLE® is designed to reward—clear, practical, and grounded in real veterinary decision-making.
More from Zuku Learning:
- Master NAVLE® concepts
- Subscribe to the Question of the Day to receive a NAVLE® question delivered to your inbox daily
- View the Study Strategy video series
- Review The Productivity Trap: Why More Studying Can Hurt your NAVLE® Score blog
- Review the Chocolate Toxicosis in Dogs: A Common Valentine’s Day Emergency blog
