Culturing The Avian Patient


Culturing of the avian portals is a common procedure in avian medicine. Some guidelines are necessary to make full use of culturing techniques as a tool in your practice.

Normal vs. Abnormal Flora

It is generally agreed that normal gastrointestinal flora consists primarily of gram positive rods and cocci. More than an occasional gram negative rod or fungal organism is usually abnormal but clinical disease cannot be assumed. Organisms worked up for ID and sensitivity are those judged to be opportunistic pathogens.

Standard microbiological workup

At California Avian Lab, the Standard Avian Culture consists of a bacterial culture/sensitivity and a fungal culture.


Anaerobic Infections

Anaerobic infections may occur in avian and exotic patients. Virtually no clinical studies have been performed to identify normal and abnormal flora or appropriate culture techniques. For this reason, California Avian Laboratory does not currently offer anaerobic cultures.

What should I culture?

Start with any clinical signs exhibited. If the patient has respiratory signs, submit one of the following: 1) pharyngeal (choanae) swab, 2) naso-ocular discharge, 3) sinus flush, 4) tracheal wash, 5) air sac wash, or 6) abdominal or thoracic biopsies. Birds with gastrointestinal signs should be sampled in one or more sites: 1)pharynx (choanae), 2) crop swab or wash, and/or 3) cloaca or feces. It should be noted that fecal cultures are generally of doubtful value in birds suspected of bacterial respiratory disease.

Other sites

Cultures of feather follicles generally fail to provide useful information, unless cytology or histopathology suggests otherwise. Usually, normal skin flora or no growth is the result. Post-mortem cultures should be taken carefully to prevent contamination. Due to the size of avian tissues, the sear method is not usually indicated. Immediately after the carcass is opened, take samples from those areas that are uncontaminated by instrumentation. In addition to obvious lesions, sites of value include respiratory organs, heart blood, liver, and the alimentary tract.

Fungal Infections

Yeast infections are common. Candida will sometimes grow when not visualized on initial cytology. The converse can also occur. Diagnosis of active aspergillosis through microbiological methods can be a challenged. Deep tracheal swab or tracheal wash can sometimes be helpful for recovery of Aspergillus. Cytology is recommended. Some localized cases (sinus, airsac) will require surgery or endoscopic sampling in order to recover the organism.

Gram Stains

Gram Staining is sometimes a useful clinical procedure, but should be considered qualitative at best. When in-house gram stains yield gram-negative rods and none are cultured, the reasons may be one of the following: 1) over-decolorization of prep, 2) the organisms are fastidious aerobes or anaerobes (probably clinically unimportant), or 3) the swab submitted was taken subsequent to the gram stain swab. In cases where other clinical information (physical exam and blood testing) suggests a bacterial infection, despite a normal gram stain, culture anyway. Gram staining lacks sensitivity when screening for organisms such as Pseudomonas. A study published by our lab (Fudge AM, Proc AAV 1992) showed that only 38% of Pseudomonas isolates were detectable by gram stain.

Interpretation of Results

Laboratory results should be interpreted in light of other clinical information, including physical examination and blood testing. The avian patient's health status cannot be revealed from a normal or abnormal culture result alone.

Acid Fast Staining

The acid fast stain is currently the only laboratory method readily available for diagnosis of avian tuberculosis. Hematologic changes can increase suspicion. Since affected birds often have multi-organ involvement, intestinal shedding is common. Hence, a fecal acid fast stain serves as a useful but is a quite insensitive tool, due to intermittent shedding. Endoscopic biopsy/acid fast or bone marrow cytology is more specific. We recommend PCR for screening.