Yersinia Infections – Testing & Natural Treatments


Yersinia enterocolitica is a bacterial infection that I have seen in patients with chronic digestive health issues. With a Yersinia infection common symptoms include diarrhoea and cramping but this bug can cause a range of other digestive issues. When approaching this bacterial pathogen the goal is complete eradication rather than rebalancing or reducing its numbers in the gut. 

Today we will be covering what this bug is, some common symptoms associated with a yersinia infection, testing options and some natural treatment approaches I use for eradication.

Yersinia Overview 

\Yersinia is a gram negative genus of bacteria from the Enterobacteriaceae family. If you have been following along for a while here this family will be quite familiar to you. Many members of this family, like Citrobacter and Klebsiella, are considered less friendly bugs while some are outright pathogens like enterotoxic Escherichia coli and Shigella. 

Both Yersinia enterocolitica and Yersinia pseudotuberculosis can cause gastrointestinal disease. Yersinia pestis stands alone as an extremely deadly bacterial infection causing pneumonic, bubonic, and septicemic plague (1).

Focusing on the gut bugs, both Yersinia enterocolitica and Yersinia pseudotuberculosis can cause a range of symptoms starting with mild diarrhoea and working up to enterocolitis. 

Yersinia enterocolitica in particular is a well studied urease producer. Urease is an enzyme that certain bacteria produce which hydrolyses (cuts) urea, producing carbonic acid and ammonia. This enables urease producing bacteria kike Yersinia to survive acidic environments like the stomach. Researchers have compared the urease production of Yersinia enterocolitica to Helicobacter pylori, a notorious and well studied urease producing bacteria (2).

Testing for Yersinia in the gut 

Thankfully Yersinia is quite easy to test for in the gut. 

Simple stool tests including a PCR stool test from the doctor will give you a yes or no answer. 

Quantitative PCR testing including the GI-MAP and the Complete Microbiome Mapping tests are both available in Australia. While they incur an out of pocket expense they can be well worth the investment. 

These tests will tell you if you have a Yersinia infection and also how much. 

16S rRNA testing, like Ombre (formerly Thryve), can help to give a more complete picture of the gut and will tell you how much of the genus Yersinia you have in the gut. I don’t like to rely on 16s rRNA testing down to the species and have phased this out of my test recommendations in my practice. 

Finally shotgun metagenomic testing can be helpful and has taken the place of tests like Ombre (16S rRNA) in my practice when I want to see what is happening around bacterial balance in the large bowel. 

There is a great test here in Australia available to the general public called Microba, but a word of caution. It takes a keen eye to unpack what this test reveals PLUS I don’t recommend it to everyone for every gut related condition. It is very specialised and patient specific. 

So there you have it. Four different options to choose from depending on the patient’s presentation.

How Did I Catch Yersinia?

If you have tested positive on one of the testing options above for a yersinia infection in your gut I am sure you are wondering where it came from. 

Ingesting contaminated food tends to be the primary source of infection for Yersinia enterocolitica, especially contaminated or undercooked pork (3), although there have been cases of infection from untreated water (think tank water here in Australia!) contaminated tofu and even pasteurised milk (4).

Image taken from: Pathogens and toxins in foods challenges and interventions – chapter 11

Yersiniosis, the acute or chronic symptoms caused by Yersinia enterocolitica infection, is the third leading cause of food poisoning in Europe (5).

Symptoms of Yersinia infection in the gut

There have been a few cases of Yersinia pseudotuberculosis outbreaks around the world but from the two gut related infections Yersinia enterocolitica is more common. 

Upon ingestion Yersinia enterocolitica or Yersinia pseudotuberculosis travels to the end of the small intestine (the terminal ileum). Here these bacteria attack the M cells along the gut mucosa. From here pathogenic Yersinia can replicate in the Peyer’s patch, a part of the gut associated lymphatic tissue – aka the gut immune system. Enteropathogenic Yersinia can then travel through the lymphatic system to the spleen, liver and lungs. This migration to other immune organs is less common due to the inflammatory response mounted by the body (6).

All in all an unpleasant process for the body. 

As such it shouldn’t be a surprise that you are experiencing symptoms with a Yersinia positive stool test. 

The most common three symptoms of a Yersinia infection are 

  1. Fever
  2. Abdominal pain 
  3. Diarrhoea 

If we are getting granular diarrhoea seems to be more common with Yersinia enterocolitica and abdominal pain and fever more so with Yersinia pseudotuberculosis (6).

Image taken from: Symptoms and sources of Yersinia enterocolitica-infection: a case-control study

Herbal Medicine for Yersinia infections 

The literature is pretty darn sparse when it comes to herbal treatments for Yersinia infections. 

My approach is to treat with a combination of science backed and traditionally backed herbal medicine. In every case treating the patient in front of you is the most important when formulating a herbal protocol. 

I will trial a month’s worth of herbs, check in with the patient to see how they are tracking and then either repeat the same formula if they are progressing well or make adjustments if needed. 

Herbs I would consider to treat Yersinia would include 

  • Oregano leaf or oil (7, 8)
  • Clove – eugenol, the phenol oil found in abundance in cloves has shown some strong antimicrobial effects against Yersinia in vitro (8).
  • Cinnamon (8).
  • Pomegranate husk (9, 10).
  • Guava leaf (11).
  • Berberine containing plants (12). Here they investigated barberry root but herbs like Coptis chinensis, Oregon grape root and even Goldenseal if you can get your hands on it may help.

Probiotics for yersinia infection treatment

Some probiotics have been studied for Yersinia infections. When working with patients with this bacterial infection I would consider a range of probiotics.

Saccharomyces boulardii, a well known probiotic yeast, has one study showing inhibition of Yersinia enterocolitica growth as well as an inhibition of its ability to invade cells (13).

I often trial patients on a moderate dose of this particular probiotic, especially if they are experiencing diarrhoea. If there is minimal response there is room to increase the dose short term. 

Image taken from: Inhibition of Saccharomyces boulardii (nom. inval.) on cell invasion of Salmonella typhimurium and Yersinia enterocolitica showing an inhibition of bacterial invasion into cells by S. boulardii. 

Many different Lactobacilli and Bifidobacteria species have been shown to inhibit Yersinia growth (test tube and animal studies mainly) (14, 15, 16).

There are a few mechanisms to explain this process that many common probiotics share, mainly displacement and exclusion. The science is more complex but to keep it simple these studies look at a probiotics ability to either displace a less friendly bug post infection (adding probiotics after infection) or to exclude the less friendly bug when the enteropathogen is added after the probiotic (17).

Lactic acid and the lowering of the gut pH is another proposed mechanism (18) which makes sense as both Lactobacillus and Bifidobacterium produce lactic acid as a byproduct of the fermentation of carbohydrates (19).

E. coli Nissle 1917 is one that has some science behind using it for Yersinia infections. Clinically I have found this probiotic very hit or miss from patient to patient (20).

Prebiotics for yersinia infection treatment

While I haven’t been able to track down a specific paper supporting the use of prebiotic fibres in Yersinia infections specifically, the concept is solid. If we can increase the native lactic acid producers like Bifidobacteria and Lactobacillus (as well as the butyrate producers) we can gain similar benefits as with oral probiotics (plus prebiotics are more affordable and can beneficially shift the gut for a longer period). 

For a good primer check out one of my favourite authors Gibson unpack how prebiotics can improve our resistance to gut infections here Prebiotics and resistance to gastrointestinal infections

Treating Yersinia infections naturally

If you are experiencing ongoing loose, possibly urgent bowel movements combined with recurring abdominal pain it is definitely wise to test your gut using a functional stool test. There is a bit of an upfront cost but for any patient that has been unwell for longer than 6-12 months it is 100% worth the investment. 

When a patient’s test comes back positive for Yersinia I will combine many of the above herbs in a liquid herbal tincture, recommend selective and targeted probiotics and frequently support their gut with prebiotic fibres and demulcent herbs.

If you are living in Australia or New Zealand and are looking for gut health support consider booking in at Byron Herbalist below. 

Now over to you. Have you experienced any of the symptoms above? What helped you rebalance your digestion?  

References & Resources

  1. Yersinia infection tools—characterization of structure and function of adhesins 
  2. A novel mechanism of urease regulation in Yersinia enterocolitica 
  3. Yersinia infection tools—characterization of structure and function of adhesins 
  4. Symptoms and sources of Yersinia enterocolitica-infection: a case-control study
  5. Urease Expression in Pathogenic Yersinia enterocolitica Strains of Bio-Serotypes 2/O:9 and 1B/O:8 Is Differentially Regulated by the OmpR Regulator
  6. Pathogens and toxins in foods challenges and interventions – chapter 11
  7. Effects of Essential Oils of Oregano and Nutmeg on Growth and Survival of Yersinia enterocolitica and Listeria monocytogenes in Barbecued Chicken
  8. Antimicrobial Effect of Spices on the Growth of Yersinia enterocolitica
  9. Antimicrobial activity of pomegranate (Punica granatum L.) fruit peels
  10. Pomegranate (Punica granatum L.) Peel Extract Inhibits Quorum Sensing and Biofilm Formation Potential in Yersinia enterocolitica
  11. Effects of Psidium guajava leaf extract on secretion systems of gram-negative enteropathogenic bacteria
  12. Study of antibacterial effects of barberry root (Berberis vulgaris) and fennel seed (Foeniculum vulgare) extracts individually and combined with nisin and sodium diacetate on Yersinia enterocolitica
  13. Inhibition of Saccharomyces boulardii (nom. inval.) on cell invasion of Salmonella typhimurium and Yersinia enterocolitica
  14. Antagonistic Activity of Potential Probiotic Lactobacilli Against the Ureolytic Pathogen Yersinia enterocolitica
  15. Real-time PCR quantification of bacterial adhesion to Caco-2 cells: Competition between bifidobacteria and enteropathogens
  16. Plasmacytoid Dendritic Cells Are Crucial in Bifidobacterium adolescentis-Mediated Inhibition of Yersinia enterocoliticaInfection
  17. Real-time PCR quantification of bacterial adhesion to Caco-2 cells: Competition between bifidobacteria and enteropathogens
  18. Antagonistic Activity of Potential Probiotic Lactobacilli Against the Ureolytic Pathogen Yersinia enterocolitica
  19. The Role of Probiotic Lactic Acid Bacteria and Bifidobacteria in the Prevention and Treatment of Inflammatory Bowel Disease and Other Related Diseases: A Systematic Review of Randomized Human Clinical Trial
  20. The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens 
  21. Prebiotics and resistance to gastrointestinal infections

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  1. Thank you for this helpful article! I was diagnosed with crohns desease 2012. After 3 years of contraproductive Treatment with azathioprin (immunsupressiva), i was tested positive on Yersinia by my Doctor, because of the unusual process of crohns desease. It Turned out – high ampunt of antibodies against yersinia entercolitica. The Doctor Decided to stop medication after the result and clinical remission of my gut inflammation. The yersiniosis then turned in an low but chronic Infection with diverse Symptoms and was Never treatet with antibiotics. Is there a Long Term Natural or medical treatment for this persistent yersinia traveling around my lymphnodes, tissues and other Organs? What would you suggest?

    Best regards from Germany

    1. Bastian, I wish you well with this frustrating issue. I will soon be 66 and my doctor thinks that my Yersinia was misdiagnosed as appendicitis when I was 16. I was diagnosed 7 years ago with chronic yersinia infection and have been treated with antibiotics (currently rifampin and clarithromycin), all of the herbs and probiotics listed in this article, and ozone therapy. My symptoms have gotten better over the years and my blood test numbers have come down but have not disappeared. I suggest you have your blood tested for iron, as the disease feeds on it. You can take calcium with meals to limit iron absorption, and alpha liopic acid and turmeric to help remove iron from your blood. I also urge you to get your thyroid tested and take whatever means possible to protect it. Mine was destroyed by the long term infection. Good luck. Chuck

  2. Bastian, Louis Klein wrote an important book with a chapter on Yersinia. It’s “The Miasms and Nosodes, Origins of Disease.” He treated his patients (I believe he is retired now) with the homeopathic nosode of Yersinia, often Yersinia enterocolitica. There are other homeopathic medicines for curing Yersinia, too. Homeopathic medicines cure us at our deepest level, the level of energy. Remedia Homeopathic Pharmacy in Germany sells the nosode of Yersinia ⏤ but they won’t send it to the U.S. so I just ordered some for my family and myself from Ainsworth’s Pharmacy in London. Best of luck to you – Linda

  3. Sorry, I should have addressed my comments to you, too, Chuck. Sounds like Yersinia has really been a horrible experience in your life. I’ve been studying and using homeopathy for all kinds of disorders for about 12 years. It has worked miracles. Homeopathic arsenic (“Arsenicum”) cured my food poisoning in about 2 hours. Another remedy mostly cured my really bad cough (may have been whooping cough) within a few seconds. Another remedy cured one family member’s “incurable bipolar with psychosis” in 10 minutes, although he needed more doses over the next several weeks. I’m just about to self-publish a book on Amazon about my family’s experiences with psychosis and meth addiction. It’s about the quackery that passes for mental health care in the U.S. Warm regards, Linda 🙂

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