Stool sample or what is that thing isolated in my child’s stool?

What is a “bacterial stool culture” and what is a “stool ova and parasite test”? (The traditional methods)

In the past, when a child with diarrhea came to the clinic, these were the standard tests the physician would request:

Bacterial stool culture – This test involves attempting to grow specific pathogenic bacteria from the stool sample, usually organisms like Salmonella, Shigella, or Campylobacter. It’s important to remember that our feces contains billions of bacteria—most of them are beneficial and essential for normal gut function—so isolating just three specific harmful strains is quite challenging.

Stool ova and parasite test – Similar in concept to the bacterial culture, this test aims to detect parasites in the stool, most commonly Giardia lamblia in Western countries.

What are the advantages and disadvantages of bacterial stool culture?

This is a traditional, well-established method that has proven its value over many years. Its main advantages include:

• High clinical relevance: When a bacterial pathogen is successfully grown, it is strong evidence that there is an active, live infection in the stool. A positive result typically correlates directly with the symptoms the child is experiencing.

• Antibiotic sensitivity testing: Once the bacteria is isolated, it can be tested for sensitivity to various antibiotics. This enables targeted treatment based on the specific strain and its resistance profile.

• Simplicity of interpretation: The test usually focuses on a limited number of pathogens (typically three main bacteria and one parasite), making results easier to interpret for both physicians and parents.

However, the method also has two major drawbacks:

1. Limited sensitivity: The test is not very sensitive and often misses infections. One requirement was that the stool sample arrive at the lab while still “fresh,” which is logistically challenging. In many cases, doctors would recommend repeating the test up to three times to increase the chances of detecting a pathogen—an exhausting process for families.

2. Slow turnaround time: Because stool contains billions of bacteria, isolating the relevant harmful ones takes time. Results typically took at least three days—often too late to influence treatment decisions. In many situations, treatment had already been initiated based on clinical suspicion alone, and by the time results came back, they were no longer clinically useful.

What is this new method – stool PCR?

PCR (Polymerase Chain Reaction) is a technique used to detect the genetic material (DNA or RNA) of a pathogen in a biological sample. This pathogen may be a virus, bacterium, or parasite. Most of us are already familiar with PCR from COVID-19 nasal tests—this is the same method, but applied to stool samples.

The advantage here is scale: instead of checking for just one bacterium or virus at a time, commercial PCR kits are designed to detect multiple pathogens simultaneously. These panels can include a wide array of viruses, bacteria, and parasites that are relevant in diagnosing the cause of diarrhea in children.

What are the advantages and disadvantages of the stool PCR test?

The main advantage of stool PCR testing is its high sensitivity and accuracy compared to traditional stool cultures. PCR targets only the genetic material of specific pathogens—regardless of whether they are alive or dead—ignoring the billions of other harmless or beneficial bacteria in the stool.

This means that many infections that would previously go undetected by older methods are now correctly identified. That sounds like a great improvement, right?

Another major advantage is turnaround time. While results from traditional cultures can take several days, PCR test results are often available within 24 hours. In theory, results could even be ready within an hour of receiving the sample at the lab. This allows clinicians to base treatment on precise data rather than relying solely on clinical judgment or experience.

However, there are some important disadvantages you should be aware of:

1. Over-sensitivity: Because PCR detects the DNA of pathogens regardless of whether they are still active, it may return a positive result even when the infection has already resolved. For example, a child who had salmonella three weeks ago but has since recovered may still test positive via PCR, leading to confusion about whether treatment is currently needed.

2. Inclusion of less relevant pathogens: As commercial manufacturers compete to offer broader panels, many PCR kits now include uncommon or clinically irrelevant pathogens. These may appear in the test results, even though they rarely require treatment. This can confuse both doctors and parents. In fact, some reports now include disclaimers next to certain pathogens, such as: “mostly irrelevant and does not warrant any treatment.” If that’s the case, one might ask—why include them at all?

So what pathogens can be detected with stool PCR?

Before reviewing the full list, keep the following in mind:

1. Each medical center or country may use a slightly different PCR kit. This means some pathogens listed here might not appear in your child’s report, and others might appear that are not listed here. If that’s the case, feel free to contact me and I’ll be happy to add or update the list.

2. If the stool sample was submitted and a positive result returned after your child has already recovered, then in most cases—treatment is not necessary. Treatment is typically reserved for children who still have symptoms or when a pathogen requiring treatment has been clearly identified.

3. The approach to managing diarrhea in immunocompromised children is different. If a pathogen is found in such a case, a pediatrician should always be consulted to determine whether treatment is necessary.

4. The medical approach can vary significantly across different regions of the world. What is appropriate in one location may not be suitable in another. Therefore, in every case of a positive stool result, it is essential to consult your local pediatrician.

Now, alphabetically (not by order of importance), let’s go over the pathogens commonly detected in stool PCR panels—and how relevant they are.