Submission tips, frequently asked questions, and resources for microbiology samples.

*Temperature requirements indicate how the sample should be stored up to and during shipment. Refrigerated samples should be maintained with an ice pack during shipment. Ship all samples to the NDSU-VDL overnight whenever possible!

Anaerobic Culture


When should an anaerobic culture be performed?

1. Infection is in close proximity to a mucosal surface.

2. Infection is secondary to a bite wound.

3. The specimen contains gas.

4. Sulfur granules present in the sample could indicate actinomycosis.

Which samples are appropriate for anaerobic culture?

Many body sites contain anaerobic bacteria that are considered normal flora and should not be routinely cultured. For example, throat swabs, bronchial washings, feces, voided urine, genital tract cultures, or surface swabs of wounds could be contaminated with anaerobes considered normal flora, making culture interpretation difficult.

As a general rule, tissues and aspirates are the best samples for anaerobic culture. Swabs may be used, but are not ideal. All samples for anaerobic culture must be sent to the laboratory immediately and in anaerobic transport media. Samples received on normal swabs will not be accepted for anaerobic testing. 

Anaerobic transport containers, such as Port-a-Cul vials or specialized liquid Amies that keeps aerobes and anaerobes stable up to 48 hours, are necessary for good culture results. Liquid Amies swabs, such as the EZ swab or Opti-Swab single swab transport kits that work well for aerobic and anaerobic cultures as well as PCR testing.


Samples that are properly collected and are stored and shipped at the appropriate temperature will yield the best results. Use our helpful resources for guidance on collection, storage, and submission of your samples.

AABP Judicious Therapeutic Use of Antimicrobials in Cattle

EXTERNAL LINK: Guidelines for appropriate use of antimicrobial use in cattle.

Anaerobic Culture Collection

Collection and storage tips for anaerobic culture samples.

Antimicrobial Resistance and Stewardship Information

EXTERNAL LINK: University of Minnesota resources for appropriate use of antimicrobials in companion animals

Blood Culture Collection

Collection and submission tips for blood culture samples.

Dermatophyte Submission Guide

Collection and submission tips for dermatophyte culture and PCR testing.

Escherichia coli Interpretation Guide

Guidance on interpretation of E. coli culture results.

FECAVA Recommendations for Appropriate Antimicrobial Therapy

EXTERNAL LINK: Companion animal treatment and diagnostic test guide.

ISCAID management of urinary tract disease in dogs and cats

Clinical practice guidelines for treatment of urinary tract infections in dogs and cats.

Weese JS, et al. International Society for Companion Animal Infectious Diseases (ISCAID) guidelines for the diagnosis and management of bacterial urinary tract infections in dogs and cats. Vet J. 2019 May; 247:8-25.

Microbiology and Molecular Diagnostics Collection Guide

Collection and submission tips for collecting samples for cultures or PCR tests.

Milk Culture Collection Guide

Collection and storage information for milk culture samples.

Frequently Asked Questions

What happens to a sample once it is submitted for culture?

Check out our process: Part 1 and Part 2.

Why is it important to include case history?

Including a brief clinical history on laboratory submissions is critical for a multitude of reasons. One of the most important being that it enables diagnosticians to assemble a complete differential diagnosis list and thus facilitates appropriate test selection up front to ensure rapid turnaround of results.  Safety and rapid diagnosis of zoonotic agents is another reason: For instance, tissues submitted from a cat with acute illness, high fever and history of contact with rabbits would alert the pathologist to request Francisella tularensis (tularemia) PCR testing, a test which would not be routinely ordered in the absence of case history or lesions (if tissues were included for histopathology). If a select agent is suspected (Brucella spp., Bacillus anthracis, F. tularensis, Y. pestis) it is important to contact the laboratory to ensure the sample is handled properly. See our Anthrax, Plague, and Tularemia Submission Guidelines document for more information.

Along with appropriate test selection clinical history is also necessary for interpretation of some results. It is particularly important for bacteriology where the clinical history is used to ensure the specimen is set up on the appropriate type of media(s) and culture condition(s). Many bacteria require special media for growth and unless adequate clinical history is submitted a specimen may not be cultured for specific bacteria. For more examples of how clinical history informs culture setup and interpretation, check out this article from the American Society for Microbiology (ASM).  Thorough clinical case histories help the lab help you make the right diagnosis.

An organism was isolated, but there was a comment stating “Isolate not viable for antimicrobial susceptibility testing (AST)”. What does this mean?

It means that the isolate was able to grow in the culture, well enough that we could identify it, but when we tried to perform AST, the isolate would not grow by our standard methods. It could mean that the bacteria was fastidious or had potentially been damaged by previous treatment or transport.

You isolated a bacteria but did not perform AST. Why wasn’t it performed?

Certain bacteria do not grow well by standard broth dilution methods used for AST or standards for interpretation of results have not been developed by a reputable source, such as the Clinical and Laboratory Standards Institute, meaning we have no way to interpret the growth of the organism.

Alternatively, the organism may have predictable susceptibility patterns to commonly used antimicrobials, such as beta-hemolytic Streptococcus spp. (eg. S. canis, S. equi subsp. equi, S. equi subsp. zooepidemicus, S. felis) to beta-lactam class antibiotics. In other cases, such as Corynebacterium pseudotuberculosis, the causative agent of caseous lymphadenitis, treatment is not effective.

Why didn’t you perform antimicrobial susceptibility testing on the E. coli from an intestinal/fecal source?

E. coli is normal flora in the gastrointestinal tract. Current practice methods recommend supportive therapy for diarrhea in most cases for humans, food animals, and companion animals. This includes diarrhea caused by Salmonella sp. or toxigenic E. coli. Antimicrobial treatment not only wipes out normal gut flora which makes it harder for the animal to recover from illness, but also contributes to antimicrobial resistance in our normal flora which can make later treatment of significant infection more challenging. Additionally, interpretations for AST have not been developed by the Clinical and Laboratory Standards Institute (due to lack of clinical efficacy), meaning we have no way to interpret the growth of the organism so the results have little value and cannot be used for treatment planning.

My report says “2 morphotypes”. What does this mean?

When we isolate colonies of bacteria that look distinctly different from each other but are in significant amounts and identify as the same organism, eg., Escherichia coli, we perform AST separately on each colony type. Sometimes the AST results are the same, in which case we only report the one result and do not charge the client for both tests. Often the isolates have different susceptibility results. We cannot accurately mix the colonies for AST and ensure that the isolate does not appear more or less resistant because of differing amounts of each type used for testing. Inaccurate AST results could mean treatment of the infection with a broader spectrum than necessary or treating it with an antimicrobial that is ineffective against that isolate; both possibilities contribute to the ongoing public health issue of antimicrobial resistance.


Antibiograms are cumulative antimicrobial susceptibility test (AST) reports of select bacterial isolates to show resistance trends over time. They are useful for monitoring antimicrobial resistance in a population over time and help clinicians choose empiric therapy until an AST report is available from the laboratory for a particular isolate.

Antibiograms do not represent isolates from all patient populations and may vary greatly by geographic region or species. Antibiograms are intended for use in conjunction with traditional culture an susceptibility testing; samples must still be sent to the laboratory for testing. To obtain reliable results, samples should always be collected prior to administering antimicrobial therapy.