Clostridia Bacterial Concerns Part 1: Pathogenicity Mechanisms

Clostridia are a group of anaerobic bacteria that can inhabit the digestive system of humans. Many types of Clostridia bacteria are non-pathogenic and even normal inhabitants of the intestinal tract, but certain species can be very problematic leading to serious illness and even death. Well-recognized Clostridia bacteria are those that cause tetanus, botulism, and Clostridium difficile (C. diff) associated diarrhea and other illnesses resulting from inflammation of the colon. Pseudomembranous colitis (or C. diff colitis) is another type of inflammatory bowel illness triggered by C. diff. It is estimated that upwards of 29,000 people in the United States die yearly from a problem related to C. diff (1).

However, there are other aspects of C. diff that can be problematic. Various chemicals produced by these bacteria have toxic effects beyond those that trigger C. diff colitis and the intestinal problems often associated with it. Many of these toxins, e.g. HPHPA, 4-Cresol, can adversely affect the brain and nervous system.

This series discusses various aspects of specific Clostridia bacterial infections as they relate to not only influences on digestive system illnesses but also neurological consequences. I will discuss: 

  1. Certain toxins of Clostridia
  2. Mechanisms of pathogenicity
  3. Laboratory testing
  4. Treatment intervention options

In Part 1, we begin with examples of certain Clostridia bacterial toxins and their mechanisms of pathogenicity:

  • Toxins A & B
  • HPHPA (3-(3-hydroxyphenyl)-3-hydroxypropionic acid)
  • 4-Cresol (aka p-Cresol, 4-methylphenol).

Toxins A & B

In 1977, it was established that pseudomembranous colitis was caused by toxins produced from Clostridium difficile. These toxins referred to as toxin A and toxin B are enterotoxins produced by various types of C. diff that cause damage to the intestinal mucosa and initiate other detrimental processes within the digestive system (2).

Toxin A, known specifically as an enterotoxin (a toxin released by microorganisms that target the intestines), functions by changing host cell metabolism, as well as disrupting actin and tight junction function leading to mucosal damage and leaky gut.

Toxin B, known as a cytotoxin (a chemical or antibody that is toxic to other cells, the brain, digestive system), causes major cellular disruption by interfering with signaling pathways, tight junction formation, and derangement of overall gut epithelial cell structure.

These reactions and others like Tumor Necrosis Factor-α and various pro-inflammatory cytokines can also have local gastrointestinal and systemic effects within the body.

HPHPA and 4-Cresol

In 2010, William Shaw, Ph.D., from Great Plains Laboratory in Lenexa, Kansas published an important paper in Nutritional Neuroscience discussing how a toxic compound called HPHPA was found in very high concentrations in urine samples of children with autism compared to age- and sex-appropriate controls, and in adults with recurrent diarrhea due to C. diff infections (3). In fact, the highest value was 7500 mmol/ml creatinine – a value 300 times the median normal value for an adult. It was found in an individual with acute schizophrenia whose psychosis remitted after an antibiotic treatment course of oral vancomycin.

For years, through my private patient consultations and health-professional educational programs, I have been recommending that parents and caregivers of individuals with autism, as well as adults themselves with chronic digestive illnesses and/or brain, neurological, and mental health concerns, perform Organic Acid Testing (OAT) from Dr. Shaw’s Great Plains Laboratory for the evaluation of HPHPA (see image 1 below) and other metabolic toxins.

Image 1:This image is from the Clostridia Bacterial Markers section of the OAT. The elevation of HPHPA is quite high. Notice that one of the strains of Clostridia known to produce this toxin is Clostridium botulinum, the bacteria known to cause botulism.

The role of Clostridial infections in neurological health had been poorly understood until Dr. Shaw’s paper in 2010, but the clinical experience of many integrative medicine doctors working with special needs individuals who recognized digestive pathogens and their role in negative health outcomes dates back many years. The major impact I personally see clinically in patients with elevated HPHPA (and 4-Cresol), particularly in individuals on the autism spectrum, is erratic, aggressive, and self-injurious behavior. Sometimes these behaviors are so severe the person is heavily medicated in attempts to control the problems. In some others without autism, anxiety, depression, poor memory, and sleep disturbances can occur.

In Part 2 of this series, I will cover laboratory testing for Clostridia bacterial infections. More will be discussed with regard to HPHPA, 4-Cresol, and the Organic Acids Test. However, for now I want to focus on another important pathogenicity mechanism of these toxins linked to neurotransmitter imbalances and associated problems.

HPHPA and 4-Cresol Inhibition of Dopamine-Beta Hydroxylase (DBH)

Biochemically, HPHPA and 4-Cresol specifically interfere with a converting dopamine enzyme called Dopamine Beta-Hydroxylase (4). This enzyme is responsible for converting dopamine into the neurotransmitter norepinephrine. Norepinephrine is the neurochemical most responsible for vigilant concentration, whereas one of the roles of dopamine is alertness (5). Image 2 below details the complex biochemical reaction between these two Clostridia bacterial toxins and their relationship in the metabolism of dopamine to norepinephrine.

Image 2: Clostridium difficile and multiple species of Clostridia produce various compounds, including HPHPA and 4-Cresol. These organic acid toxins can inhibit Dopamine Beta-Hydroxylase which interferes with the conversion of dopamine to norepinephrine.

When DBH is inhibited there can be a build-up of dopamine within the nervous system leading to cellular toxicity. A major problem recognized with the accumulation of dopamine and the negative effects it has on brain function has to do with neurodegeneration associated with oxidative stress.

A 2008 research article published in the Journal of Neuroscience (6) discusses the biochemical consequences of excess dopamine: •

  • Dopamine is a reactive molecule compared with other neurotransmitters and dopamine degradation naturally produces oxidative species.
  • More than 90% of dopamine in dopamine neurons is stored in terminal vesicles and is protected from degradation.
  • A small fraction of dopamine is cytosolic, and it is the major source of dopamine metabolism and presumed toxicity.
  • Cytosolic dopamine undergoes degradation to form a compound called 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) as well as hydrogen peroxide via the monoamine oxidase pathway. The HVA and DOPAC are markers measured on the Organic Acids Test (see image 3 below).

Image 3: The elevated HVA is often seen with high HPHPA and/or 4-Cresol. The Dopamine Beta-Hydroxylase enzyme can be inhibited causing excess dopamine to build up leading to the production of HVA and DOPAC.

  • Dopamine also undergoes oxidation to form superoxide, hydrogen peroxide, and o-quinone and reacts with cysteine residues on glutathione, thus rendering glutathione ineffective.
  • Dopamine oxidation can also form cysteinyl-dopamine and cysteinyl-DOPAC conjugates which are neurotoxic.
  • These biochemical abnormalities caused by excess dopamine may cause severe neurodegeneration of neural pathways that utilize dopamine as a neurotransmitter.

Prior to the 2008 article, a research paper published in 2000 in the Journal of Child Neurology discussed various benefits of short-term treatment with oral vancomycin to a group of autistic children (7). The authors summarized: “...although the protocol used is not suggested as useful therapy, these results indicate that a possible gut flora-brain connection warrants further investigation, as it might lead to greater pathophysiologic insight and meaningful prevention or treatment in a subset of children with autism.”

Although it was not specifically stated that these children had C. diff infections or elevated markers of HPHPA and/or 4-Cresol, it is known that vancomycin is often an effective antibiotic against these pathogens. I will discuss more about this research and its findings, along with other therapeutic information and intervention options for certain Clostridia bacterial infections in Part 3 of this series.


There are other pathogenicity mechanisms linked to Clostridia bacterial infections such as propionic acid interference with mitochondrial function (8) and spore degradation linked to poor digestive-system calcium absorption (9). However, the toxins listed in this article highlight some of the more common testable problems linked to these pathogens.

In Part 2 of this series I will go into more detail regarding different test options, i.e., stool analysis, Organic Acids Test for Clostridia bacterial toxins of A, B, HPHPA, and others.


  1. Leesa FC, Mu Y, Bamberg WM, et al. “Burden of Clostridium difficile infection in the United States.” N Engl J Med. 2015; 372: 825-834.
  2. Kuehne SA, Cartman ST, Heap JT, Kelly ML, Cockayne A, Minton NP; October 2010. “The role of toxin A and toxin B in Clostridium difficile infection.” Nature 467 (7316): 711–3).
  3. Shaw, W. “Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of Clostridia spp. in the gastrointestinal tract, in urine samples from patients with autism and schizophrenia.” Nutr. Neurosci. 2010. 13(3):135-43.
  4. Goodhart, PJ, et al. “Mechanism-based inactivation of dopamine beta-hydroxylase by p-cresol and related alkylphenols.” Biochemistry. 1983 Jun 21; 22(13):3091-6.
  5. Robert D. Hunt. “Functional Roles of Norepinephrine and Dopamine in ADHD: Dopamine in ADHD.” Medscape Psychiatry. 2006;11(1).
  6. Linan Chen, et al. “Unregulated cytosolic dopamine causes neurodegeneration associated with oxidative stress in mice.” J. Neurosci. 2008 28, 425–433
  7. Sandler RH et al. “Short-term benefit from oral vancomycin treatment of regressive-onset autism” J Child Neurol. 2000. 15(7):429-35.
  8. Richard E. Frye, Shannon Rose, John Slattery, and Derrick F. MacFabe. “Gastrointestinal dysfunction in autism spectrum disorders - the role of the mitochondria and the enteric microbiome.” Microb Ecol Health Dis. 2015.
  9. Travis J Kochan, et al., “Intestinal calcium and bile salts facilitate germination of Clostridium difficile spores.” PLoS Pathog. 2017 Jul 13;13(7).