Stool sample or what is that thing isolated in my child’s stool?
Recently, most medical centers transferred to a new method for inspecting stools in children (and adults). From the old method of “stool culture” to a new one called PCR.
This new method has significant advantages, which will be specified later on, but also disadvantages that you need to be familiar with.
So in this post, I’ll try to do 2 things:
1- Specify a bit on the different methods.
2- Give the confused parents, receiving a positive result in the PCR stool test, a little knowledge on how to interpret the results, understanding whether their child need treatment or not.
This is a complementary post to another post on diarrhea in children. In that other post I don’t talk about specific pathogens, just about what to do when your child has diarrhea (read more here).
Remember that this is a relatively “professional” post, designed to calm parents looking at their child’s stool sample (and wondering if it’s OK or treatment is needed).
What is a “bacterial stool culture” and what is “stool ova and parasite test”? (The old methods)
In the past, when a child with diarrhea came to the clinic, these were the type of tests the doctor would ask for.
Bacterial stool culture – the lab would try to grow virulent bacteria from the stool sample, usually pathogens like Salmonella, Shigella or Campylobacter. I remind you that our feces contains about a billion bacteria, most of them are friendly and important to the activity of our bowels, so growing 3 specific strains of bacteria is not an easy task.
Stool ova and parasite test – the same as bacterial stool culture, only here we are talking about isolating parasites (on most western countries – giardia lambelia).
What are the advantages and disadvantages of bacterial stool culture?
This is a traditional method, which has been proved effective throughout the years. The main advantage is that growing bacteria in a stool sample would indicate almost unambiguously that there is an active bacteria in the sample. It would make the positive answer to very relevant, since if there is an active, live bacteria in the stool of the child, it is probably the cause for symptoms.
An isolation of any bacteria can also led to a antibiotic sensitivity test. So now, not only we can have the name of the bacteria, but also its sensitivity to any given antibiotic.
In addition, the results were limited (about 3 bacteria and one parasite in most cases), which made everybody’s life pretty easy.
However, there are two major disadvantages:
1– Sensitivity: the test wasn’t sensitive enough, and missed quite a few cases. We would ask the stool to arrive to the lab “fresh”, which is technically hard to do. So in many cases we would repeat the test 3 times, to increase the chances for growing bacteria. Not an easy task for parents.
2– Time for a positive result: in our feces there are a billion bacteria, so the process of isolating these specific virulent bacteria takes time. Time for a result would be at least 3 days, most of the time – long after the child needed to start treatment. This is why there were many times we would made the decision of starting treatment without waiting for the results, and when it would finally arrive – it would not be relevant.
What is this new method – stool PCR?
PCR is a method for detecting the presence of a pathogen’s DNA in a sample containing biologic substance. This pathogen can be a virus, bacteria or parasite. We are all familiar with the COVID-19 PCR samples from our nose – so this is the same, only with a stool sample.
But! Instead of checking just one bacteria or virus at a time, we can manufacture a specific kit to include all of the pathogen we think can be relevant when investigating a child’s diarrhea.
So the commercial manufacturers are making kits that check unlimited amount (theoretically) of pathogens relevant for diarrhea in children. Parasite, bacteria and viruses in the same test.
What are the advantages and disadvantages of stool PCR test?
The main advantage is its high sensitivity and accuracy, compared to a stool culture. A PCR test searches only for genetic material of a specific pathogen (dead or alive, as you will see ahead), and it is not at all interested in the other million friendly bacteria present in our stool.
This means that lots of stool samples that in the old method would pass as negative, are now discovered as positive. Which is a good thing, right?
The second advantage is the time it takes for results to arrive. Theoretically, analysis could be done within 1 hour after receiving the stool sample to the lab. Practically, results are in after about 24 hours, and this is a massive advantage. Here, a doctor doesn’t need to make a decision on a clinical base, his sharp instincts and the daily horoscope, but can get a stool test within a day, and give the child a more precise treatment.
But – there is a disadvantage, which you must understand. The test has high specificity.
Imagine that I had salmonella 3 weeks ago, but got better (thank god). At present times, I took a stool sample for a whole different reason. In the old method, the chance for the test to spot the 3 weeks old salmonella is slim to none. This is a good thing. In this new method, the genetic substance of the salmonella can still be present in the stool sample, and the PCR test would identify it as positive. This will confuse everybody involved.
Another disadvantage – the commercial manufacturers are competing on which kit will have more pathogens, so they’ve added lots of bacteria and viruses most of us never heard of before, and in most cases are not relevant. So in this new method we will find some strange pathogens, most of them do not require treatment. They are only leaving doctors and parents confused.
Recently I even saw an answer of a PCR test with a comment on a specific pathogen – “mostly irrelevant and do not warrant any treatment”. If this is the case, then why take a test with irrelevant results?
So what pathogens can be found when using the PCR test?
Before we go on to the full list, remember a few things –
1- Each medical center, in each country, uses a slightly different kit, so there could be pathogens not mentioned in this post, but are listed in your child’s PCR stool test (and vice-versa). If this is the case, you are more than welcome to write to me, and I will add the relevant pathogens.
2- If from this reason or another, you delivered the stool sample to the laboratory, but by the time a positive results arrive your child has stopped having diarrhea, then in most cases – there is no need for treatment. We give treatment only to a child who still has symptoms, or if a specific pathogen that require treatment was isolated.
3- Remember that the approach for diarrhea in immunocompromised children is different, and if there is a pathogen found in a test, there is need to see your physician, and think whether to treat the child or not.
4- Remember that the world Is big, and what’s’ good for one part of it does not fit the other part. So, in any chance, go see you local pediatrician in any case of stool isolation.
So – alphabetically (and not by importance), who are these pathogens found in a stool PCR test and how relevant are they?
Aeromonas species
Who is this pathogen? A family of bacteria, which rarely causes diarrhea in children.
Is this a real infection? In most cases – no.
Should you treat the child? In most cases – no.
If choosing to treat, what is the drug of choice? Sulfamethoxazole and trimethoprim.
Blastocystis hominis
Who is the pathogen? A Eukaryotic cell that can cause diarrhea.
Is this a real infection? Isolating this pathogen in a stool sample mostly means a carrier state, and not a real infection.
Should you treat the child? Mostly no, since this is an asymptomatic carrier state. The decision on treatment should be considered heavily and based on a prolonged duration of symptoms.
If choosing to treat, what is the drug of choice? Metronidazole.
Campylobacter
Who is the pathogen? A very common family of bacteria that causes bacterial diarrhea (dysentery).
Is this a real infection? Yes. Isolation of this bacterium is a stool sample is probably the cause for the diarrhea the child has.
Should you treat the child? Is he still has symptoms – absolutely.
If choosing to treat, what is the drug of choice? Azithromycin, for 3 days.
Cryptosporidium species
Who is the pathogen? A family of parasite that can cause diarrhea, mostly in form of outbrakes.
Is this a real infection? Yes. Though it is not common. Identifying it in a stool sample is probably the reason for the child’s symptoms.
Should you treat the child? Healthy children do not need treatment. Immunocompromised patients most certainly due.
If choosing to treat the child, what is the drug of choice? Nitazoxanide. The duration of treatment will be determined after considering the child’s background illness.
Cyclospora cayetanensis
Who is this pathogen? A parasite causing watery diarrhea
Is this a real infection? Unlikely, but can be a real pathogen, depending on the country.
Should you treat the child? In most cases the positive results is due to the high sensitivity of the PCR test and not a real infection. You should treat severe cases, or when the physician is convinced this is the cause for symptoms.
If choosing to treat, what is the drug of choice? Sulfamethoxazole and trimethoprim, for 7-10 days.
Dientamoeba fragilis
Who is the pathogen? A parasite that can cause diarrhea in children.
Is this a real infection? Isolating this parasite mostly indicate an asymptomatic carrier state, and not a real infection. Although in a child with prolonged symptoms, who lost some weight, this could be the reason.
Should you treat the child? Isolation in a stool sample mostly indicates an asymptomatic carrier state and not a real infection. In cases of a child with prolonged symptoms, you should begin treatment.
If choosing to treat, what is the drug of choice? Metronidazole, for about 10 days. There is a need for repeating the test after a few weeks to prove eradication.
Entamoeba histolytica
Who is this pathogen? A parasite that dwells in our bowels, and can sometimes cause diarrhea in children. It is more common in immigrants and travelers.
Is this a real infection? Yes. A positive result can mean an asymptomatic carrier state in a child, or it could be the cause for diarrhea. Having said that, since it is a rare infection, it may require additional stool samples, to better identify the pathogen before deciding on treatment.
Should you treat the child? Unfortunately, if it is indeed a real infection, textbooks says you must treat the child to prevent the spreading of the disease and transferring it to other family members.
If choosing to treat, what is the drug of choice? This is a bit complex. This is the place to consult with a pediatrician with a subspecialty in infectious disease.
Giardia intestinalis / Giardia lamblia / Giardia duodenalis
Who is the pathogen? The most common parasite to cause diarrhea. Could cause out brakes, mainly in kindergartens.
Is this a real infection? Yes. Most of the time, isolating of the parasite is the cause for a watery diarrhea (which can sometimes be prolonged).
Should you treat the child? Most of the times yes, though there is a state of asymptomatic carrier. Remember that the reason for taking the test is because the child has symptoms, so if a pathogen is found, it is worth treating.
If choosing to treat, what is the drug of choice? Metronidazole, for about 5-7 days. In cases of recurrence, consult with your pediatrician.
Yersinia enterocolitica
Who is the pathogen? Bacteria that can cause, among other things, diarrhea.
Is this a real infection? It can be a real infection, depending on the country.
Should you treat the child? In most cases a positive result is due to the high sensitivity of the test, and not a real infection. In cases of a real infection, if the symptoms are mild – there is no need for treatment. We treat only severe cases, or when the doctor is convinced this is the cause for symptoms.
If choosing to treat, what is the drug of choice? This is complicated and depends on the patient’s age and disease severity. When given oral treatment, you can use Sulfamethoxazole and trimethoprim.
Salmonella species
Who is the pathogen? A notorious family of bacteria which causes dysentery, meaning watery diarrhea with mucus and blood.
Is this a real infection? Yes.
Should you treat the child? A complex question. The textbooks say that allegedly, antibiotic treatment does not always shorten disease duration, and can even prolong the carrier state. But notice – in children younger than 6 months of age or immunocompromised patients, treatment is always warranted. In my opinion, you should also consider treating children who still has symptoms when the test results are back, mainly the younger ones (younger than 1 year). Read more on Salmonella management in this dedicated chapter.
If choosing to treat, what is the drug of choice? Depending on the sensitivity of the bacteria to antibiotics. Mostly one of these antibiotics – Azithromycin, Sulfamethoxazole and trimethoprim or even Amoxicillin.
Shigella species
Who is the pathogen? A dubious family of bacteria causing dysentery, meaning watery diarrhea with mucus and blood.
Is this a real infection? Mostly yes.
Should you treat the child? If the child still has symptoms, most certainly yes.
If choosing to treat the child, what is the drug of choice? Depending on the bacteria sensitivity to antibiotics. Mostly one of these Azithromycin, Sulfamethoxazole and trimethoprim or even Amoxicillin.
This post was on my mind for a long time, and I’m glad it came out the way it has. I hope this will help nervous parents (with no reason at all!), to understand that whatever was isolated in their child’s stool sample, it is not necessarily a virulent pathogen.
Good luck.
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