Poop, Pus and Positive Results: Cultural Oddities From the Clinical Microbiology Lab

Aug. 19, 2019

Clinical microbiologists diagnose infections caused by all microbial types, using samples of almost every imaginable kind. While we can laugh about the unusual things that occur during specimen collection or result interpretation, the proper execution of both of these components of the diagnostic process is critical to quality patient care, and it is the job of a clinical microbiologist to ensure they happen correctly. What are the most unique microbiological samples, and what should you do if you get one of these? How should difficult questions and requests regarding specimen collection and results be communicated between the clinical staff and the laboratory?

Laboratory Phone Calls: Important and Uncomfortable

Nearly 11 years ago as a newly minted medical technologist, I observed eagerly as my trainer called a nurse to give an update on the identification of an organism from a positive blood culture. “This organism is a Bacillus species, but it is not cereus” she said, to which the nurse replied, “EXCUSE ME?! This is very very serious!” I learned something that day: calling results to the clinical team would be more challenging than it seems. Laboratory-related phone calls range from the notification of specimen rejection to the notification of a critical result that requires immediate follow up. 

Tests are clinically relevant only when they are used correctly, as Dr. Michael Wilson describes in his article on clinically relevant and cost effective microbiology, Although microbiologists are often met with angst when they ask for specimen recollection, it is an important part of the job. Laboratories should use explicit specimen rejection criteria, which should be rigorously enforced. In addition to specimen collection clarification, relaying microbiology results to the medical team via a phone call remains a useful way to effectively communicate critical results. Although electronic communication methods are becoming available, phone calls are fast and direct, and can give providers information that can be acted on quickly. 

Multi-source Sampling: Start From the Top and Work Your Way Down

One day I received a phone call from a nurse who wanted to collect a “multi-source” specimen on a child with a suspected enteroviral infection. Non-polio enteroviruses can cause a variety of syndromes ranging from hand, foot and mouth disease to acute flaccid paralysis and meningitis. 

The virus can be detected in respiratory tract samples, stool/rectum, blood and CSF. At the time, it was not uncommon for multiple areas of the body to be sampled using one swab. This type of collection method is referred to as a “multi-source” swab. The nurse was getting ready to swab the throat and the rectum of the patient on a single swab and called to ask if she should sample the throat or the rectum first. After a short silence, I suggested that she avoid placing the swab from the rectum into the patient’s throat—and that it might be best to start from the top and work her way down. 

The development of tools like the nasopharyngeal swab used for enterovirus (and other viral testing) has helped reduce patient discomfort during sampling compared with traditional nasal washes or larger swabs, and if used appropriately, can reduce unnecessary pain and suffering. It is important to think through sampling techniques before executing them! Additional collection methods for the testing and/or isolation of Enterovirus can be found here.

A typical viral transport swab used to sample areas of the body for viral testing.
A typical viral transport swab used to sample areas of the body for viral testing.

Culture Sampling: Less is Often More

Every once in a while, members of the medical community need reminders that the word microbiology actually means the science of extremely small things. Most of the powerful microbiological testing that happens in the laboratory can be accomplished with a very small amount of specimen (but not too small). Regardless of this fact, it seems that most clinical microbiologists have received an enormous specimen for culture at least once. When I asked microbiologists from across the U.S. about these types of specimens, the responses were impressive:
There is truly a science to processing tissue for culture in the laboratory. When a tissue is received, the most purulent (or infected looking area) is selected and then manually ground, most often by hand, in order to homogenize the material and release trapped pathogens. While the histology department might have use for entire body part, the microbiology department does not.
An example of manual tissue grinders.
An example of manual tissue grinders.

In summary, consider the following before sending tissue to the lab for culture:
  • Let the lab know which pathogen is suspected. Even if an organism is low on the differential, telling a microbiologist what is suspected can improve yield (they can apply special growth techniques for many organisms) and helps keep them safe (in case the specimen grows a pathogen like Francisella tularensis, Brucella or Yersinia pestis that can be acquired by working with cultures in the laboratory). 
  • Surgical specimens should be an appropriate size. Specimens should be sent to the lab in sterile containers that are big enough to hold the specimen and that have a lid. On the contrary, minimum specimen requirements should be followed to allow for all requested testing.
  • Samples should be suspicious for infection. In the case of a large specimen, the surgeon should select the area most likely to be infected and send that piece to the laboratory. 
It is important that the clinician who orders the test knows what they are suspecting and why they are ordering the test, as this guides the microbiology lab’s workup.

Animal Sampling: Best Left to Veterinarians 

Every day across the world, humans and animals interact in a variety of ways. Because of this, humans are at risk of acquiring pathogenic organisms from colonized or infected animals. What types of animal specimens do clinical microbiologists see? While veterinary and state laboratories can perform testing on specimens from animals, it is not unusual to receive these specimens in the clinical “human” lab as well. Oftentimes the medical team will want to culture a pet or suspected vector to determine where the patient acquired their infection. While the clinical laboratory has strict operating procedures for the management and culture of human specimens, they often don’t have procedures for environmental and animal culturing procedures, and those protocols should be left to veterinary and public health laboratories. 

In summary, consider the following when submitting animal samples for testing:
  • Inform the lab staff about the suspected pathogen.
  • Appropriate samples for rabies testing typically includes the brain and brainstem of the infected animal, except in cases of small animals like bats (when the entire animal can be sent). 
  • Whole animals submitted to the laboratory should be deceased and not wriggling around in a pair of women’s underwear. 

Inanimate Objects: Causation is Difficult to Demonstrate

In the 1960’s, hospitals regularly cultured all sorts of environmental items such as floors, counters and hospital supplies. This use of this practice declined after 1970 because meaningful standards for permissible levels of microbial contamination of environmental surfaces or air did not exist. While it is possible to isolate pathogens from inanimate objects, it is nearly impossible to prove that they are the cause of human infection without knowing the series of events that lead to human contact and subsequent infection. It’s also difficult to ensure that the object is not grossly contaminated with environmental organisms that make the pathogen of interest difficult to isolate. In addition to these limitations, the act of culturing an inanimate object can be cumbersome and challenging, as in a case shared by Dr. Rodney Rohde:

Diarrhea Obsession

If you ask any clinical microbiologist, they will tell you the same thing: they want to receive diarrhea. Are they crazy? No, there is a very sane reason for this obsession with liquid stool: with respect to C. difficile testing, liquid, loose, or lightly-formed stool is a must. 

Patients with solid stools (lovingly termed “rattlers” by many microbiologists) are unlikely to have a true C. difficile infection, and unnecessary testing can lead to unjustified costs and clinically misleading positive results. Giving a patient a false-positive C. difficile result can have very serious consequences like increasing the risk of inappropriate antibiotic use and the length of stay in the hospital. Every day, microbiologists are given the difficult task of rejecting formed stools and frustrating the medical staff.  As in most of the specimen requests microbiologists make, there is a valid scientific rationale for this request.

The Importance of Specimen Collection

Microbiologists work with some of the strangest specimens imaginable. But no matter how strange the specimen is, special attention should be paid to specimen collection. The quality of the specimen collected will always dictate the quality of the answers the microbiology lab is able to give. 

To increase chances of proper diagnosis, submitted samples must:
  • Contain the infecting organism.
  • Be collected under appropriately clean, preferably sterile, conditions.
  • Come with information about the suspected pathogens, particularly if unusual, fastidious, or dangerous organisms are suspected. 
  • Be properly labeled.
  • Be appropriate for the test that is ordered.
Microbiologists are not miracle workers, but if given a relevant patient history and quality specimen, they can get answers and solve problems. Clinicians should worry most about proper sample submission;  never underestimate the mind-or stomach- of a clinical microbiologist. 

Continue to share your personal experiences in the clinical laboratory using the comments section below!

Special thanks to
all of the microbiologists who shared their experiences on Twitter and contributed greatly to the development of this article.

The above represent the views of the author and does not necessarily reflect the opinion of the American Society for Microbiology.

Author: Andrea Prinzi, Ph.D., MPH, SM(ASCP)

Andrea Prinzi, Ph.D., MPH, SM(ASCP)
Andrea Prinzi, Ph.D., MPH, SM(ASCP) is a field medical director of U.S. medical affairs and works to bridge the gap between clinical diagnostics and clinical practice.