Making Monsters, Renegade C. butyricum and E. coli

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Clostridium

It is common knowledge that our gut is teeming with good bacteria that we feed with prebiotic fiber to keep us healthy.  But a sick gut, caused by antibiotics or fiber deficient processed food, can make us susceptible to infection with pathogens, such as the notorious, toxin-producing strains of E. coli that cause food poisoning or Clostridium difficile, a.k.a. C. diff. of hospital infections.  What prompted me to write this post, was reading that premature babies in neonatal intensive care units are dying from gut infections caused by a pathogenic strain of C. butyricum, known as a probiotic that provides protection from C. diff.

Healthy Gut Microbiota

New Toxin-Producing, Antibiotic Superbugs are Manmade

Closer examination of the report revealed that the new strain of C. butyricum is a toxin producer.  This made a lot of sense to me.  When I started working with E. coli in the early 70’s, it was known as the safe ubiquitous lab bacterium that everyone cultivated in their colons.  Similarly, C. butyricum is present in commercial probiotics and is a hero for producing butyric acid from resistant starch, promoting immune system development and reducing inflammation.  How did these beneficial gut bacteria become converted into pathogens?

Source of Antibiotic Resistant Superbugs

Antibiotic and Drug Use in Hospitals and Farms Select for Antibiotic Resistance

C. butyricum and E. coli have been converted into toxin-producing, antibiotic resistant pathogens by common procedures of meat production and hospital treatments.  These bacteria do not normally produce toxins nor are they resistant to antibiotics.  They have been systematically selected for those pathogenic properties.

Formula Contributes to NEC

Common Practices in Neonatal Intensive Care Units Lead to NEC

Chronic inflammation is one of the common contributing factors to premature births, because labor is stimulated by a spike of inflammation, normally occurring at 40 weeks of gestation.  Chronic inflammation from autoimmune disease, infection, or obesity, can cause labor to be early and a newborn to be unprepared for life without some special care.  Unfortunately, there is not uniform enlightenment about the development of newborn gut flora, and immature newborns are exposed to antibiotics and formula, which prevent normal gut flora development.  C. butyricum is not present in low birth weight babies exclusively fed breast milk, but the combination of antibiotics and formula select for colonization by antibiotic resistant hospital strains of C. butyricum.  This sets the stage for necrotizing enterocolitis, NEC, which is as nasty and lethal as the name suggests.

Toxin Producing E. Coli are Manmade

Antibiotics Used to Make Fat Cattle Select for Toxin Production

The development of toxin producing E. coli in cattle suggests how pathogenic C. butyricum was produced in the hospital environment.  E. coli was a healthy component of the digestive system of cattle, until the gut flora community was reengineered by antibiotics, so that short chain fatty acids that were normally converted into more gut bacteria and more steer manure, were instead absorbed by the gut to produce a fatter steak.  Unfortunately, this newly designed gut flora community left no place for E. coli.  Some of the E. coli spontaneously mutated to antibiotic resistance and/or picked up multi-drug resistant plasmids from other bacteria, but that still didn’t provide a niche in the new community.  Picking up a toxin-producing gene solved that problem, because the toxin releases needed nutrients from host cells.  Thus, antibiotic use in cattle directly selected for the evolution of toxin-producing, antibiotic resistant E. coli.

Antibiotics and Formula Use Lead to NEC Bacteria

Toxin-producing C. butyricum would be expected to develop in the hospital environment, because high antibiotic use will select for multiple drug resistant C. butyricum, and the disrupted gut flora produced in the presence of antibiotics will also favor toxin producing strains.  Thus, the hospital environment selects for toxin-producing, multiple drug resistant C. butyricum.  The gut flora of newborns in a neonatal intensive care unit are acquired from the staff and relatives that handle the babies.  Since the babies are routinely treated with antibiotics and drugs, multiple drug resistant bacteria, including C. butyricum, are common in fecal samples of neonates and persist for at least two years. 

Breastmilk Prevents NEC in Newborns

Breastfeeding or Donor Bank Milk Avoids NEC Caused by Formula

Exclusive use of breastmilk from mothers, donor banks or breastmilk products, eliminates NEC.   Some hospitals respond to the scientific evidence and use only breastmilk for newborns.  Other hospitals simply stick to old practices until law suits force them to change.  They continue to use formula and cow’s milk products,  even though breastmilk is available, and as a consequence NEC is still a problem. Prejudice against breastmilk persists and there is intense promotion of commercial alternatives that contribute to NEC.  None of the alternatives containing probiotics and prebiotics have been found to be adequate.   Hospitals are slow to change, because patients are uninformed and low birthweight babies continue to die.

Breast Is Still Best, but Second Best is Donor Milk Banks

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Milk is a baby's first prebiotic and a major function of mother's milk is to prevent adult gut bacteria from inflaming a newborn's gut, before the gut is sealed up and a new immune system is developed. Formula companies scurry to get parents hooked on their expensive substitutes that promise ease of use and nutritional equivalence, but the sad truth is that these artificial milk substitutes undermine baby gut flora with tragic results.  Even in the rare cases where mothers are not able to breastfeed their babies, there is a safe alternative, donor milk banks.  This post is a plea for new parents to wise up and smell the poop.  You may need to tell hospital staff that you will be checking diapers and taking names to make sure that your baby only gets your breast milk.

Background: Up Close and Personal Birth and Breastfeeding

I have been personally and professionally concerned about the care and nurturing of babies for the past three decades.  I was introduced to breastfeeding, milk and babies by my wife.  My first faculty position was teaching premed students at Harvard and my wife was a nurse at the Harvard Medical School affiliate, Brigham and Women's Hospital.  We honeymooned near a well baby clinic in Malawi.  My three daughters were all born at home and never used formula -- they started to eat some mashed up food at about six months and continued to nurse for more than two years.  My wife worked evening shifts, she provided some pumped milk and I drove the girls back and forth, so she could nurse during her break.  She was also a La Leche League leader for more than 25 years, was co-founder of the Singapore branch of LLL and has been an International Board Certified Lactation Consultant for 20 years.  Because of our applied discussions of lactation, I also spent several years studying passive immunity and tolerance of the mucosal immune system of the gut.

First Flora

Breast milk is nutritive for the newborn, but it also establishes the baby's gut flora.  It is the quality of the gut flora, which species of bacteria, that determines if a newborn will thrive or die.  If the baby is delivered by Caesarian, then her first gut flora will resemble the nursery staff.  If she forces her way out the old fashioned way, her first flora will resemble her mother's vaginal flora.  Interestingly, as birth approaches, the mother's vaginal flora shifts toward that found in fermented dairy products, i.e. dairy probiotics.  As soon as milk starts to reach the mother's nipples prior to birth, it is colonized by lactic acid bacteria, the only bacteria that can survive in the harsh milk environment.  Thus, breast milk is the source of both food and flora, and it is not surprising that breastfed baby poop looks and smells like curds and whey.

Breast Milk Kills Adult Gut Flora

I used to enjoy watching the student perplexity when E. coli in lab experiments progressively died in contact with raw milk.  All of the ingredients in milk conspire against normal adult gut bacteria to withhold essential vitamins, minerals and macronutrients.  The baby' stomach enzymes also convert milk proteins into antimicrobial peptides, e.g. lactoferrin into lactoferricin (FKCRRWQWRMKKLGAPSITCVRRAF, note the heparin-binding domains consisting of basic amino acids, K & R.)  Human milk oligosaccharides (HMOs, bifidus factor) are abundant in breast milk and block the attachment of pathogens to the lining of the gut to prevent infection.  At the same time, milk hormones seal the intestines to prevent leakiness.

Formula Kills Pathogens with Inflammation

Formula provides macronutrients for rapid weight gain (obesity risk), but lacks the protective components of breast milk.  The result is a rapid and irreversible shift to dominant adult gut flora and the fecal smell of E. coli.  It is not surprising that the use of formula in under developed countries results in a high rate of infant mortality.  It is, however, surprising that the gut inflammation caused by formula provides enough protection to permit its use in countries with high hygiene and good water quality.

Hospital Use of Formula and Bovine Products Increases Infant Mortality

Full term babies are pretty tough and have been known to survive major calamities in addition to formula-induced inflammation.  Tiny preterm newborns are a different story and their immature GI tracts are fragile.  Unfortunately, the first line of defense for the newborn gut, newborn gut flora, is frequently ignored in neonatal intensive care nurseries, and a major killer of preterm newborns is necrotising enterocolitis (NEC), in which bacteria common to adults overruns the immature gut.  NEC is dramatically reduced by using only breast milk, but hospital nurseries change slowly and doctors, staff and parents are unaware that formula and cow's milk products put newborns at increased risk.

Night Nurses Would Rather Feed Formula

Recent studies show that newborns designated as "breast milk only" are still given bottles of formula, because night nurses don't understand the risks of formula and enjoy feeding the babies.  The mothers are not usually told that their baby received formula and inexperienced mothers fail to recognize why their baby never had normal bowel movements.  Some hospitals continue to use bovine, cow milk, products simply because they always have and they are unaware of the damage to newborn gut flora and the cause of NEC.

Donor Milk Banks

Some mothers produce more milk than their baby needs and so they arrange to donate the extra to milk banks.  The milk banks pasteurize and distribute the milk.  Many hospitals are unfamiliar with milk banks and donations have not been energetically encouraged, so both the supply and demand for donor milk are developing.  It is important to realize that newborn and premature babies have very small stomachs of only a few ounces, and some mothers can easily produce a cup of milk at each feeding.  Thus, the cost of using only breast milk by all babies for their first few days after birth is negligible compared to the risk of disease caused by formula use. 

Demand at Least Second Best

The bottom line is that parents must demand that only breast milk be used in hospitals, even if it must be from milk banks, and all parents must be able to check diapers for the yogurty smell typical of exclusively breastfed babies.

For more information see the Human Milk Banking Association of North America