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Primary Care Corner by Geoffrey Modest MD: Risks and benefits of longterm PPIs

26 Apr, 17 | by gmodest

​by Dr Geoffrey Modest

The American Gastroenterological Association (AGA) just published a clinical practice update on the risks and benefits of long-term use of proton pump inhibitors (see  ).



RISKS: (these are the authors’ assessment of the quality of the evidence and the effect sizes)

kidney disease: 2 retrospective observational studies found a modest effect size (10-20%) of CKD in those on PPIs, with very low quality of evidence. Mechanism, unclear: ? if those on PPIs had more comorbidities which predispose them to kidney disease?

dementia: retrospective observational studies finding a modest effect size (4-80%), with very low quality of evidence. Presumed mechanism: microglial cells use certain ATPases to degrade beta-amyloid, and PPIs may block these ATPases (which does increase beta-amyloid in mice)

bone fracture: many observational studies, data inconsistent, modest effect size (39% to 4-fold increase), with low to very low quality of evidence. Presumed mechanism: hypochlorhydria-related malabsorption of calcium or vitamin B12, gastrin-induced parathyroid hyperplasia, and/or osteoclast vacuolar proton pump inhibition.

myocardial infarction: though a very small effect was found in an observational study, none found in RCTs. Presumed mechanism: omeprazole decreasing clopidogrel levels and its anti-platelet effect, but a randomized controlled trial comparing those on clopidogrel versus those on clopidogrel plus omeprazole had no difference in cardiovascular event rates.

small intestinal bacterial overgrowth: small studies have found that PPIs lead to bacterial overgrowth in the duodenum/small intestine, only some of which were symptomatic, modest effect size (2-fold to 8-fold increase), low quality of evidence. Presumed mechanism is loss of the bactericidal effects of gastric acid by taking PPIs

non-typhoidal salmonella and Campylobacter infections: increase found in 1 study, not confirmed. modest effect size (2-fold to 6-fold increase). Presumed mechanism: achlorhydria (and studies show that those with pernicious anemia or gastric surgery-induced achlorhydria do seem to have increases in these infections)

spontaneous bacterial peritonitis: observational studies suggest a 2-fold increased risk of SBP (50% to 3-fold increase), very low quality of evidence. Proposed mechanism: achlorhydria leading to gut bacteria changes, leading to changes in intestinal permeability and translocation of bacteria across the intestinal wall

C. diff infections: observational studies suggest 50% increased risk of C diff infection; and changes in bacterial taxa associated with C diff were increased in healthy volunteers after 4-8 weeks of high-dose PPIs. (the risk still pales compared to the rate of C diff with antibiotics). Risk may be higher in children, modest effect size (no increase to 3-fold increase), quality of evidence: low. Proposed mechanism: downstream effects of PPIs on colonic microbiota (see comment below)

pneumonia: seems to be more frequent soon after starting PPIs than after longer-term treatment.   Raises question of perhaps the PPIs were erroneously started for early misdiagnosed pneumonia. pneumonia is not a consistent finding in other studies, modest effect size (though no association in RCTs), very low quality of evidence. Proposed mechanism: upstream effects of PPIs on oropharyngeal microbiome

micronutrient deficiencies (overall 60-70% increase), low or very low quality of evidence:

–Calcium: may be decreased absorption, but not of water-soluble calcium salts or calcium from milk or cheese.

–Iron:  inconsistent data. No association in some Zollinger-Ellison patients on 6 years of PPIs, some association in other studies

–Magnesium: rare cases of profound hypomagnesemia. Observational data on modest positive association

–vitamin B12: most studies finding around 2.4-fold increased risk.

gastrointestinal malignancies: data also mixed. Suggestive data of increased risk in those with untreated H pylori infections, and concern about the profound hypergastrinemia (which has trophic effects on colonic epithelial cells in mice and on human colorectal cancers in vitro),  but population-based retrospective studies have failed to confirm a relationship. (No association in RCTs), modest effect size, very low quality of evidence.



In terms of benefits of PPIs, there are basically moderate to high quality studies supporting their use in:

— GERD with esophagitis or structure (though may not be necessary with non-severe esophagitis, and no long-term data)

— GERD without esophagitis or stricture (though may not be necessary with relatively mild symptoms, and no long-term data)

— Barrett’s esophagus with GERD (no long-term data)

— NSAID bleeding prophylaxis (no long-term data)

— Barrett’s esophagus without GERD (this has low quality of evidence from observational studies only: no RCT, mostly mechanistic thinking that chronic inflammation may lead to esophageal adenocarcinoma and some observational data. But I would also be concerned that these data are based an unusual subset of patients who are asymptomatic yet have had endoscopy that documents Barrett’s, and even observational studies are therefore a tad suspect).



–It is not surprising that the quality of these studies on benefit is higher than the above studies of adverse effects, since these were designed explicitly as intervention trials to look for benefit, probably all supported by drug companies, and controlling for co-morbidities, etc.

–I am also a little concerned that the AGA may be biased towards PPIs, perhaps because gastroenterologists tend to see patients with more severe conditions requiring PPIs, or perhaps financial conflicts-of-interest (as with all specialty societies, since the top academic specialists who often write the guidelines tend to be involved in drug-company-sponsored research).  My real concern with PPIs is that many many outpatients are put on PPIs for marginal reasons, and that very few patients are stepped-down to less aggressive therapy. As mentioned in prior blogs, given the limitations of time a primary care clinician has with patients, when their stomach problem is better with PPIs, it is time to deal with the myriad of other problems, keeping up with standard health maintenance issues, etc etc. The issue of the above potential complications of PPIs are very probably less important clinically than the need for PPIs for those with very clear indications (though I am a bit concerned that these studies are all short-term and it is a bit tenuous to extrapolate to long-term harms). But, the preponderance of studies finding some association of potentially serious adverse effects from PPIs, whether the studies are great or not, reinforces the imperative to avoid using PPIs unless clearly indicated, and, when appropriate, to step-down therapy as soon as possible. My experience is that patients who have endoscopy for dyspepsia are essentially invariably put on PPIs by the gastroenterologists independent of endoscopic findings. And, I have had pretty good success in getting some patients off of them, sometimes just onto prn calcium tablets or H2 blockers. But this may be a time-consuming issue to deal with. And I certainly have many patients for whom either I do not have the time to pursue or who are resistant to stepping down on therapy.

–To me, there is also the perhaps significant general omission in the above article of the effects of PPIs on the microbiome (see here). My guess is that these effects do not necessarily translate clinically into disease, which is not so surprising given the complexity of this process, the multiple variables involved, and the length of time necessary to develop detectable disease (and the studies are too short). But, PPIs are associated with changes in the colonic microbiome to a less healthy one: with significant increases in Enterococcus, Streptococcus, Staphylococcus, and potentially pathogenic E coli species, as well as oral bacteria of the genus Rothia. And decreased Clostridiales.  These changes have been thought to lead to the association with C diff infections, but perhaps with other even unsuspected long-term harms. Though not mentioned specifically in the above article, these microbiome changes do add further credence to the imperative (I think) to minimize PPI usage.

So, my bottom line: PPIs are way overused for marginal indications (it is easy to jump to PPIs for dyspepsia, since they work so well…), but we should really discourage the use of PPIs unless they meet a clear criterion as above, or try to use the step-up approach: start with calcium or H2 blockers, then increase to PPIs when needed, and still try to step-down later; and try to get patients off of PPIs when they have been on them for awhile, unless there is a clear indication to continue.  Though a complicating factor here is that they are available OTC….

for another recent blog on PPI risks and benefits and some additional concerns, see here.


Primary Care Corner with Geoffrey Modest MD: Penicillin Allergy???

8 Mar, 17 | by EBM

By Dr. Geoffrey Modest

A large concern in treating patients with infections is the very high prevalence of “penicillin allergy”, leading to the use of broad-spectrum antibiotics as well as 2nd or 3rd line medications, which are usually more toxic, along with their attendant effects on antimicrobial resistance as well as secondary infections such as C. difficile­­­­. A recent article looked at 2 methodologies to determine the safety of using beta-lactams in these “penicillin allergic” patients (see 10.1016/j.jaci.2017.02.005).


  • Of 1000 medicine in-patients with a noted penicillin allergy in a single Boston hospital, 625 were admitted with a presumed infection: mean age 66, 60% female, 70% white/16% black, reported penicillin allergy was rash or hives in 60%/angioedema 15%, anaphylaxis 8%
  • Patients were assessed during 3 different time periods: 148 patients in a standard-of-care group (SOC), 278 in a penicillin skin testing group (ST), and 199 in a group using a computerized guideline-based management app (APP) to predict real allergy
  • ST group: excluded patients with penicillin intolerance (such as GI upset), patients taking medications that might interfere with skin testing (such as antihistamines), and also patients with multiple beta-lactam allergies, penicillin anaphylaxis in the last 5 years, or type II-IV hypersensitivity reactions to penicillin
  • APP group: the clinical support basically divided people into low risk (benign delayed maculopapular rash); medium-to high-risk (urticaria, angioedema, anaphylaxis, recent or severe delayed maculopapular rash; and those who should avoid a beta-lactam (history of Stevens-Johnson syndrome, toxic epidermal necrolysis or exfoliative dermatitis; DRESS syndrome or acute interstitial nephritis; or serum sickness-like reaction)
  • Primary outcome was the actual use of penicillin or cephalosporin during the hospitalization


  • ST group: 179 (64%) were felt to be skin test eligible, but only 43 (24%) actually receive skin testing and none of those were allergic, defined as negative skin test and tolerance of an oral amoxicillin 250 mg test dose. As compared to the SOC group,
    • Nonsignificant 30% increased odds of use of penicillin or cephalosporin overall, adjusted OR 1.3 (0.8-2.0), but a highly-significant 5.7-fold increased use in a per protocol analysis, adjusted OR 5.7 (2.6-12.5), p<0.001 [the per protocol analysis limited the analysis to those few who actually got the skin test]
    • Of the ST per protocol patients, there was increased odds of penicillin or cephalosporin prescriptions for discharge treatment, with OR 2.5 (1.04-6.2)
  • APP group: 292 unique website views (averaging 26 seconds only), 112 users (38%) completed clinical decision support. Patients in the low or moderate-to-high risk groups as above were given test doses of beta-lactam antibiotics with an initial dose of 1/10 of an IV dose or 1/4 of an oral dose. The 2nddose was administered 30 minutes later, comprising the remainder of the therapeutic dose. Nurses assessed patients every 30 minutes for the duration of the challenge. As compared to the SOC group,
    • Significant 80% increased odds of use of penicillin or cephalosporin, adjusted OR 1.8 (1.1-2.9), p=0.03


  • Penicillin allergy is remarkably common, up to 15% of all inpatients are recorded as having a penicillin allergy, and 5-25% of inpatients who are treated for infections. Three quarters of patients with an alleged penicillin allergy would otherwise use a beta-lactam antibiotic in other studies, but in the SOC group only half of them received one.
  • Not using a beta-lactam antibiotic when that would otherwise be indicated leads to more treatment failures, adverse events, and antibiotic resistant organisms such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus.
  • There were few patients who actually had skin testing, mostly because of difficulty in coordinating the testing for those felt to be eligible, which the authors note would have been different if they hired an on-site clinician for that purpose (some patients also refused skin testing).
  • Another concern about skin testing is that fewer than 15% of US hospitals have the appropriate reagent on formulary. The per protocol analysis of the ST arm may be open to bias (vs the intention-to-treat analysis looking at the overall group), however the low numbers of patients getting skin testing clearly biased the results to negative.
  • However, it is quite remarkable how much effect the pretty simple computerized guideline and decision support provided. It should, however, be pointed out that this was not a clean randomized-controlled trial, so there are potential inherent biases (including the possibility that there were different sensibilities and approaches to treating infections, perhaps related to the different time periods above, or proclivities of the ID departments, ward attendings, residents, etc.)
  • These results parallel those in a prior blog regarding skin testing. See found that of 146 patients with history suggestive of IgE-mediated penicillin allergy (but excluding those with history of anaphylaxis), only one patient had a positive skin test, and the remaining 145 did fine with oral penicillin. Of note, as opposed to the prior blog, those with Type I (IgE- mediated) hypersensitivity reactions were excluded from the above study.
  • Why is “penicillin allergy” so rampant?? as a singular anecdote, 25 years ago one of my children had otitis media in the middle of the night when he was less than a year old, and as a really tired parent I decided to watch him instead of getting antibiotic treatment (he wasn’t really very sick appearing, and at that point in Europe most otitis media was not being treated with antibiotics), he remained relatively stable for the next day or 2, then developed a maculopapular rash. If he had been given a beta-lactam antibiotic, he would have been labeled as penicillin allergic perhaps for the rest of his life. I do realize that there are negatives to treating family members, however my tiredness won out….
  • So, what does this all mean? The combination of the current and prior blog strongly suggest that true penicillin allergy is really quite unusual (the number quoted is <5% of those with listed penicillin allergy). And the ability to use beta-lactams for common outpatient (and inpatient) infections is really useful, especially as we are trying so hard to protect our microbiome and decrease resistance. [And, by the way, adverse reactions, need for hospitalization, costs…]. It would be really great to have a large study looking at the computer-assisted app to see the real incidence of bad allergic reactions to beta-lactams in each of the low and moderate-to-high risk groups, with an eye to using beta-lactams, perhaps initially in a monitored setting (depending on the actual incidence of severe reactions in these cohorts in subsequent studies).

Primary Care Corner with Geoffrey Modest MD: Thumb Sucking and Immunity

25 Jan, 17 | by EBM

By Dr. Geoffrey Modest

Another microbiome article (I realize this is the third in a series of two, but can’t help myself). This one looked at the “hygiene hypothesis”, which is basically that kids exposed to more microbes early in life have fewer allergies or asthma. This article looked at thumb-sucking, nail-biting and atopic sensitization, also finding that the more the fingers went into the mouth, the fewer had atopic sensitization (see DOI: 10.1542/peds.2016-0443).


  • The Dunedin Multidisciplinary Heath and Development Study, a population-based birth cohort study of 1037 people (52% male) born in Dunedin (the second largest city in the South Island of New Zealand with 120,000 inhabitants), with follow-up at ages 3,5,7,9,11,13,15,18,21,26,32, and 38
  • At age 5,7,9,11 the parents were asked about the kid’s thumb-sucking and nail-biting, along with an estimate of frequency
  • Skin-prick testing was done at age 13 on 724 of the 1031 kids (70%), including testing for house dust mites, grass, cat, dog, horse, aspergillus, penicillium, and a few others; a positive test was a wheal >2mm larger than the negative saline control
  • Detailed respiratory reviews were done since age 9
  • The researchers controlled for potential confounders of sex and parental history for asthma or hayfever; breastfeeding; exposure to cat or dog in childhood (a prior analysis of this cohort showed that this exposure led to lower risk of atopic sensitization); parental smoking history, household crowding (total number of kids divided by number of rooms), socioeconomic status


  • Overall 31% of children were frequent thumb-suckers or nail-biters at age >1yo
    • Nail-biting or thumb-sucking were each found in 20% of girls and 17% of boys
  • Incidence of atopy:
    • ​Atopic sensitization in 38% of girls/52% of boys age 13; 58% of girls/61% of boys at age 32
    • ​Asthma in 10% of girls/16% of boys age 13; 18% of girls/18% of boys at age 32
    • ​Hayfever in 28% of girls/32% of boys age 13; 42% of girls/37% of boys at age 32
  • For atopic sensitization, as compared to those without thumb-sucking or nail-biting:
    • At age 13:
      • There was an adjusted 36% lower likelihood of atopic sensitization: OR 0.64 (0.45-0.90) for either thumb-sucking or nail-biting
      • A 36% lower likelihood if only thumb-sucking, OR 0.64 (0.42-0.97)
      • A 30% lower likelihood if only nail-biting, OR 0.70 (0.47-1.10), nonsignificant
    • At age 32:
      • There was a 38% adjusted lower likelihood of atopic sensitization: OR 0.62 (0.45-0.86) for either thumb-sucking or nail-biting
      • A 31% lower likelihood if only thumb-sucking, OR 0.69 (0.47-1.00), borderline significant
      • A 29% lower likelihood if only nail-biting, OR 0.71 (0.49-1.02), nonsignificant
    • The only significant difference for specific allergens was for house dust mites in those aged 32, though all of the others had trends that were almost significant
  • For asthma or hayfever:
    • None were significantly associated, at either ages 13 or 32
  • A dose-response curve (doing both thumb-sucking and nail-biting vs either one of them) was only evident at age 13


  • This study further supports the “hygiene hypothesis”, though it was notable that the dramatic difference in atopy was only in the objective measurement of sensitization (but, one might argue that these clinical manifestations of atopy are what really matters….). Why not with asthma or hayfever?
  • Is it just that these were by report and therefore less “reliable” than the objective measure of atopic sensitization?
  • Asthma, also, is more complicated, given that atopy is only part of the issue playing into it
  • Or, my guess, is that they were looking at kids who were already too old (there were no data on thumb-sucking and nail-biting during the preschool years), that immune tolerance largely develops earlier in life, and other studies showing a relationship between “hygiene” and atopic conditions (e.g. hayfever or asthma) included much younger children (see blogs listed below)
  • The study does support the results of a prior study finding that in kids using pacifiers, there seemed to be fewer allergies later in life when the mothers sucked the pacifiers to clean them
  • The proposed mechanism here is that exposure to bacteria and other microorganisms early changes the gut microbiome (and, see blog below about the respiratory microbiome); and the microbiome can change the function of helper T cell (TH) subsets, increasing the helper T cell type 1 (TH-1, which produce interferon-g, IL-2, TNF-b and leads to cell-mediated immunity) and decreasing helper T cell type 2 (TH-2, which produces a slew of interleukins which lead to strong antibody responses), with these changes promoting the development of immune tolerance to allergen exposures.
  • But overall this study does support the concept that early exposure to some microbes leads to more immune tolerance. And thumb-sucking or nail-biting certainly increases exposure to a diverse variety of microbes.

See​ which includes an article on the microbiome and type 1 diabetes, and two more on the “hygiene hypothesis”: one on the increased incidence of autoimmune disease in kids in those born in North Karelia Finland (more automated, advanced technologically) vs the Russian side (same gene pool but more natural environment/exposures); and the other being the recent NEJM article finding the same type of difference for asthma in the Hutterites (industrialized farming) vs the Amish (traditional farming)​

See which is a Canadian longitudinal study finding that early infancy microbiome changes increase the risk of childhood asthma; or which looks at 4 US cities and similarly finding that early allergen exposure leads to more asthma

There was a blog I sent out 8/27/2014 (which did not make it into the BMJ blogs) which looked at the lung microbiome, showing that diet leads to changes in the TH1 and TH2 cells in the lung itself (i.e., there is more than one microbiome, not just the gut one). For the article, see doi:10.1038/nm.3444. With regards to asthma: there is evidence of increased prevalence of chlamydia and mycoplasma with asthma exacerbations. Also, the respiratory microbiome is different in asthmatic vs nonasthmatic patients, even in asymptomatic asthmatic patients, with abundance of Proteobacteria. There is also some evidence that airway hyperresponsiveness tracks with bacterial diversity and composition (esp. increase in Proteobacteria).

Primary Care Corner with Geoffrey Modest MD: Microbiome 2

24 Jan, 17 | by EBM

By Dr. Geoffrey Modest

This is the second of two blogs on the microbiome, inspired by a recent review that highlighted several other health-related data besides the non-caloric artificial sweeteners (see Lynch SV. N Engl J Med 2016;375:2369).


  • ​The microbiome is huge, with 9.9 million microbial genes represented, as found from studying 1200 people in the US, China, and Europe. And it has >1000 species of microbes
  • Although the microbiome was previously felt to develop after birth, bacteria are found in the placentas of healthy mothers, in the amniotic fluid of preterm infants, and in meconium. And, the mode of infant delivery does influence postnatal microbial exposure: intravaginal delivery does seem to confer an infant microbiome taxonomically similar to the maternal gut and vaginally microbiota. Also the infant microbiome does become more similar to the adult one with the cessation of breast-feeding, and over the years bacterial diversity and functional capacity expand. The microbiome becomes less diverse in elderly, which could reflect coexisting conditions and age-related declines in immunocompetence.
  • Things that affect the microbiome include sex, age, diet, exposure to antimicrobial agents, changes in stool consistency, PPIs and other meds, travel, malnutrition, exercise (the effect of exercise on the microbiome is pretty clear in mice, not so clear in humans, since it is hard to sort out the effect of exercise vs different diets in those who exercise more). Also, host genetic features, host immune response, xenobiotics (including antibiotics), other drugs, infections, diurnal rhythms (see below), and environmental microbial exposures.
  • Clostridium difficile infections
    • This is probably the most advanced and practicable microbiome application. See for many studies and analyses. However about 90% of patients affected with severe, recurrent antibiotic-resistant C. difficile infections respond to fecal microbial transplants
  • Effects on immunity:
    • There are data that the infant microbiota at one month of age is significantly related to allergy in two-year-old children and to asthma in four-year-old children. Several of the products of the higher risk microbiota are associated with subclinical inflammation, which precedes childhood disease. Also other studies have found that children born by cesarean section, who do have differences in their microbiota, are more likely to develop type I diabetes, celiac disease, asthma, hospitalizations for gastroenteritis, and allergic rhinitis.
  • Obesity/metabolic syndrome/insulin resistance/diabetes
    • There are several studies finding that there are significant differences in the microbiome between obese and lean human subjects, with a decrease in Bacteroidetes and an increase in Firmicutes species in obese individuals. Studies have shown that taking microbiome samples from pairs of identical human twins, one lean and one obese, and placing them into genetically identical baby mice, have found that the mice with the microbiota from the obese twin develops more weight gain and more body fat, along with a less diverse microbiome, than those from the lean twin. Also, interestingly, women in their third trimester of pregnancy have an altered microbiome, which, when transplanted into mice, leads to more obesity, and that pro-obesity microbiome is more efficient in extracting energy from food [one common clinical issue with overweight/obese patients is that they may often eat much less than others but still do not lose weight, which has been shown in several studies, and attributed to their being more efficient in metabolizing foods. But perhaps this is mediated through the microbiome???]
    • Some proteins elaborated by E. coli stimulate glucagon-like peptide-1 (GLP-1) secretion, which could augment glycemic control in diabetics, where this hormone is less active than in nondiabetics. In addition, E. coli can elaborate peptide YY (produced in the ileum in response to feeding), which can activate anoxeretic pathways in the brain, mediating satiety.
  • Atherosclerosis/cerebral artery occlusion
    • There are pretty convincing studies that eating red meat leads to changes in the gut microbiota, which leads to increase production of trimethylamine-N-oxide (TMAO), which is a very strong risk factor for human atherosclerotic disease. And feeding meat to vegetarians does not increase TMAO until there are these microbiota changes from recurrent red meat diets. See blogs listed below for more details. Also, experimental data on mice show that cerebral arterial occlusion leads to 60% less damage in those with microbiota which are sensitive to antibiotics; mice given probiotics have less impairment after spinal cord injury.
  • Cancer
    • In mice, specific gut bacteria (most clearly shown for Bifidobacterium) enhance the efficacy of cancer immunotherapy, delaying melanoma growth. Human data has shown that certain microbiota species (B. Thetaiotaomicron or B. fragilis) can improve the effects of anti-tumor therapy targeting cytotoxic T-lymphocytes-associated antigen 4.
  • Autism
    • There are even some suggestive data that the microbiome may play a role in autism spectrum disorders. MIA mice, a maternal immune activation mouse model, exhibits autistic-like behavior, gut microbiome dysbiosis, increased gut mucosal permeability, and an increase in 4-ethylphenylsulfate (4EPS, a metabolite of gut bacteria). Injection of 4EPS into healthy, normal mice results in anxiety. And, feeding the MIA strain of mice a strain of Bacteroides fragilis normalized these adverse gut changes and decreased behavioral abnormalities, associated with decreasing circulating 4EPS levels. There are other neuropsych issues potentially related to the microbiome: gut bacteria can produce several neurotransmitters (eg norepinephrine, serotonin, dopamine, GABA, acetylcholine), and can change emotional behavior of mice (which seems to be related to central GABA receptor expression).
  • Other diseases with suggestive data of a linkage to microbiome dysbiosis include inflammatory bowel disease, kwashiorkor, juvenile rheumatoid arthritis, and multiple sclerosis. Also, in mice, stress leads to altered microbiota (less Bacteroides and more Clostridia), and in humans undergoing bariatric surgery, there are huge differences in the microbiome by either the Roux-en-Y gastric bypass or vertical banded gastroplasty, and this microbiome transplanted into germ-free mice leads to reduced fat deposition, suggesting that these microbiome changes themselves might play a direct role in decreasing adiposity (see Tremaroli V. Cell Metabolism2015; 22:228)​. And perhaps the changes in the microbiome, through the gut-brain relationship is part of the reason for the documented improvement in memory noted after bariatric surgery.
  • Diurnal rhythms (see Thaiss CA. Cell. 2014; 159: 514): the gut microbiota has diurnal variations that reflect feeding rhythms; humans with jet lag have dysbiosis; this jet lag leads to microbiome changes promoting glucose intolerance and obesity and are transferable to germ-free mice.


  • We should approach these studies on the microbiome with caution: some of the most impressive studies were done in animals in highly controlled conditions, and predictions in humans based on the studies is always fraught. For example, in general the use of probiotics in human adults has not shown as dramatic a response as found in rodents. (Although an interesting study of human neonatal probiotic supplementation in the first month of life was associated with a 60% reduction in the risk of pancreatic islet cell autoimmunity, a precursor to type 1 diabetes, before school-age). In addition, a stool sample may not be an adequate proxy for the microbial content of the entire GI tract. And, most of these studies have focused primarily on bacterial species in the microbiota, not taking into account the many other types of microorganisms found or their complex interactions.
  • One concern I have in general is our tendency towards reductionism. The microbiome appears to be a quite complex organ, composed of many different varieties of organisms which undoubtedly interact with each other in complex ways, and which are influenced by many known and undoubtedly unknown external cues (diet, antibiotic use, etc., etc.). So, for example, simply attempting to manipulate that microbiome through the introduction of one species or another of probiotics (i.e., our usual medical fix) may not deal with the complexity of this situation.
  • There have been a slew of other blogs on the microbiome over the years. See . One particularly interesting finding in one of the blogs was that one of metformin’s major action might be in its effects on the microbiome (see, which also reviews some of the TMAO data.
  • So, although I am pretty convinced of the importance of a healthy microbiome, it does seem to me that the major initiative should be around lifestyle changes overall: a healthy diet (and specifically one which is predominantly vegetarian), adequate exercise, perhaps adequate sleep (would be great to have more data on the effect of sleep patterns overall on the microbiome and if changing those patterns changes the microbiome), and minimizing exposure to unnecessary antibiotics (both in humans and in animals that make it into our food chain).

Primary Care Corner with Geoffrey Modest MD: Artificial Sweeteners Microbiome1

23 Jan, 17 | by EBM

By Dr. Geoffrey Modest

As mentioned in prior blogs, I think that the microbiome represents a very important mediator between the external environment and health/disease. A few recent articles supplement and strengthen this understanding. The first in a series of two is a study reinforcing the potentially deleterious effects of non-caloric sweeteners on the microbiome and health outcomes. The second (to be sent tomorrow) is a broader description of our understanding of the microbiome overall and its potential relationship to health.

​Non-caloric artificial sweeteners (NAS) were developed from the biological perspective that these potent sweeteners (more than 100 times sweeter than sucrose) are non-caloric and  are excreted unchanged; they should therefore be an important sugar alternative to help people lose weight and control glucose intolerance. Although a study done in the 1980s, prior to DNA sequencing capabilities, did show that saccharin could alter the rat microbiome, it is only relatively recently that we understand the fuller effects of NAS on both the microbiota as well as clinical outcomes. Many of the clearest studies were done on animals, since it is easier to control the environment completely and isolate the effects attributable to NAS. A recent study looked further into the relationship between NAS, the microbiome, and the clinical effects (see Suez J. Gut Microbes 2015; 6(2), 149). This is an update of a prior article in Nature (see prior blog:​ )


  • The human weight control studies here are a bit mixed. However it should be noted that most of the comparisons were between individuals consuming NAS to those consuming caloric sweeteners, with very few comparing NAS consumption to avoiding all sweeteners.
  • Several studies have shown NAS leads to weight gain in rats (including saccharin, sucralose, aspartame and Stevia), and are associated with increased adiposity
  • NAS can also induce hyperinsulinemia, impaired insulin tolerance, impaired glucose homeostasis, and worsened atherosclerosis in genetically susceptible mice
  • It should be noted that there are some genetically-altered mice where there are some discordant defects: some with decreasing glucose and insulin levels but increasing adiposity, and in some cases hyperinsulinemia

Details of the current study:

  • Mice drinking water supplemented with high doses of commercial saccharin, sucralose, or aspartame, after 11 weeks had marked glucose intolerance, as compared to controls drinking water, sucrose, or glucose.
  • Further studies of saccharin showed that mice on different baseline diets (e.g. high-fat or other) and at different doses of saccharin had increased glucose intolerance
  • The glucose intolerance induced by NAS was ameliorated by prior dosing with antibiotics (ciprofloxacin and metronidazole, in an attempt to sterilize the gut)
  • There were specific changes in the microbiome associated with NAS, including enrichment of Bacteroides and some Clostridiales and decreases in Lactobacilli and some other members of Clostridiales, several of the microbiota changes previously associated with type II diabetes in humans
  • Fecal microbiomes from mice consuming either water or commercial saccharin were then transplanted into germ-free mice, finding that those germ-free mice receiving the saccharin-associated microbiome developed glucose intolerance
  • In 381 nondiabetic humans, NAS consumption was associated with increases in BMI, blood pressure, hemoglobin A1c, and fasting glucose levels. Also there were changes in microbial taxa in the microbiome: more Actinobacteria, Enterobacteriales, and certain Clostridiales.
  • A preliminary small-scale human study found that supplementing the regular diet with higher doses of saccharin led to elevated glycemic responses in four of the seven volunteers, those 4 had microbiome alterations. And when these microbiomes were transplanted into germ-free mice, these mice also developed the same abnormal glycemic responses. Of note, in two of these 4 volunteers, their microbiome changes reverted to normal within 2 to 8 weeks.


  • NAS is consumed by approximately 32% of adult Americans.
  • The microbiome can be rapidly altered by diet, as noted in diets rich in fat (for example, see
  • There are a remarkable number of largely unregulated food additives in the current food supply, many added for purely commercial ends, such as preservatives to extend the shelf life of some foods. I believe this NAS data challenges the concept that even those ingredients that are not absorbed and internalized could conceivably adversely affect the human microbiome. The main point here is not that all additives or chemicals are necessarily bad, but that we should be very circumspect about assuming that they are probably benign based on our often incomplete models (i.e. It did make intuitive sense at the time that a non-absorbed sweetener would lead to less obesity and diabetes; but as our understanding and models have expanded/become more complex, our “intuitive” sense has changed). But, I think all of this reinforces what Michael Pollan (author or many books, including The Omnivore’s Dilemma) has suggested: it really does make sense to eat natural foods, especially ones which our bodies have evolutionarily adapted to, and avoid foods with ingredients that your grandmother would not know.

In my practice, I have focused on trying to get patients to decrease their consumption of sodas, and with some reasonable success. I think this is often the low-hanging fruit (though less healthy than other fruits), and at least most of my patients say they have dramatically decreased or eliminated sodas by either substituting water (best) or water slightly flavored by fruit juice. For regular sodas, the attempt is to decrease the consumption of high-fructose corn syrup (a bad actor with multiple bad effects, including increasing uric acid levels), was well as “diet” sodas (commenting on the fact that they really are not benign, non-sugar alternatives, as above). I think my patients have been able to change this soda habit by our regularly and repeatedly targeting this issue (with motivational interviewing) over the past several years, especially with my patients who are overweight, glucose intolerant/diabetic or hyperuricemic.

Primary Care Corner with Geoffrey Modest MD: Fluoroquinolone Warning

16 Dec, 16 | by EBM

By Dr. Geoffrey Modest

There was another FDA warning recently, this time regarding systemic fluoroquinolones (ciprofloxacin, levofloxacin, etc.), leading to a boxed warning, the FDA’s strongest warning (see for the summary, and for the full report).


  • Fluoroquinolones are associated with disabling and potentially permanent adverse effects on tendons (tendinitis, tendon rupture), muscles (muscle weakness or pain), joints (joint pain or swelling), peripheral nerves (peripheral neuropathy), and the central nervous system (anxiety, depression, hallucinations, suicidal thoughts, psychosis, confusion). Other adverse effects include worsening of myasthenia gravis, skin rash, sunburn (photosensitivity/phototoxicity), irregular heartbeat (including prolonged QT interval), severe diarrhea (they are the leading cause of Clostridium difficile-associated diarrhea). Multiple problems can occur in the same patient. The peripheral neuropathy may be irreversible.
  • Therefore, fluoroquinolones should only be used in patients where no other treatment options are available for acute bacterial sinusitis, acute bacterial exacerbation of chronic bronchitis, and uncomplicated urinary tract infections. Also for serious bacterial infections where the benefits outweigh the risks.
  • The prior warnings for tendinitis, tendon rupture, and worsening of myasthenia gravis has been extended by the above problems.
  • Side effects may occur within hours to weeks after starting the fluoroquinolone and continue an average of 14 months to as long as nine years after stopping the medicines. (Though, as noted, some may be irreversible)
  • The majority (74%) of reported cases were in patients 30 to 59 year-olds, some with severe resulting disabilities. Most of the adverse reactions involve the musculoskeletal system, peripheral nervous system, and central nervous system. Long-term pain was most commonly reported symptoms, 97% of all cases reporting pain associated with musculoskeletal adverse effects
  • And one should stop treatment at the first sign of an adverse reaction


  • Although many of the musculoskeletal and central nervous system effects have been known for many years, the above update includes many other conditions. And some of the newly included conditions (e.g. peripheral neuropathy) can last forever.
  • My sense locally is that fluoroquinolones are still being used quite frequently for uncomplicated urinary tract infections and other relatively minor infections. Hopefully the above warning will further discourage their potentially unnecessary usages.
  • I’m also very concerned about antibiotic resistance overall, as many of you know. Please see for many blogs highlighting in rather scary detail the increasing antibiotic resistance in general, both in the US and worldwide. And I am also concerned about the effect of broad-spectrum antibiotics in particular and fundamental changes in the gut microbiome which can lead to many known, and probably many more unknown, health complications (see many blogs in )

Primary Care Corner with Geoffrey Modest MD: Microbiome and Type 1 Diabetes, etc

19 Sep, 16 | by EBM

By Dr. Geoffrey Modest

The NY Times had a recent story looking at the role of the microbiome (sorry to those microbiome-phobic) in the development of type 1 diabetes (T1D), see . This article was based on a recent clinical study (see

  • 33 infants genetically predisposed to T1D through specific HLA alleles, following changes in their gut microbiota frequently
  • Though microbiota varied greatly between individuals, it remained stable throughout infancy in each individual
  • After 3 years, 4 of the children developed T1D
  • At the time of T1D diagnosis, there was a marked 25% drop in diversity of the microbiome occurring after anti-islet cell autoantibody development/seroconversion (not found in those who did not seroconvert) but 1 year before clinical T1D, along with spikes in inflammation-favoring organisms, gene functions and serum plus stool metabolites.


  • Initial colonization of the human gut begins in utero, is influenced by microbial exposure at birth, then gets gradual increase in diversity in part related to the introduction of table foods. The microbiome largely stabilizes at approximately 3 years of age
  • T1D: an autoimmune disorder resulting from T cell-mediated destruction of insulin-producing pancreatic b-cells. 70% of T1D cases carry HLA high risk alleles for T1D, yet only 3-7% of children with those alleles develop T1D. The incidence of T1D has been increasing rapidly over the past few decades. All of this suggests that there are important non-genetic factors influencing the development of clinical T1D. In Finland, the incidence of T1D is particularly high: 1 in 120 children develop T1D before age 15 (the US is about 1 in 300).
  • Mouse data show that in those susceptible to T1D, changing the gut microbiota can lead to protection from T1D.
  • Other studies have found a decreased intestinal microbial diversity in children with long-lasting b-cell autoimmunity, as well as in inflammatory bowel disease and C difficile-associated diarrhea (in mice, decreased diversity is associated with increased in IgE levels and predisposition to immune-mediated disorders).
  • The probability of progression to T1D after positivity of 2 islet autoantibodies is >80% after 15-year followup, though there is significant variability as to when this happens. so even though in the above study the microbiome seemed to influence the development of clinical T1D but not the autoantibody seroconversion, it does suggest that the effect of an adverse microbiome is associated at least with earlier development of clinical disease.


A follow-up of the above but now larger study looked the “hygiene hypothesis” in general, which posits that early exposure to specific microorganisms/parasites in infancy benefits the development of the immune system, leading to protection from the development of allergic and immunologic disease. This study looked at microbiome changes in North Karelia, Finland, where those from the same genetic pool but living on the Russian side have about 1/5 the development of early-onset autoimmune diseases as the European side, and noting important microbiome changes, which might explain these clinical differences (see Vatanen T. Cell 2016; 165: 842).

  • Background:
    • Several studies have shown that improved sanitation seems to be associated with increased incidence of type 1 diabetes (T1D), multiple sclerosis, and early childhood infections
    • Rates of asthma, hayfever and allergic sensitization are decreased in kids growing up on traditional farms
    • Mice with their gut colonized by with protective microbiota have decreased risk of autoimmune diabetes and allergies
    • There is a 2- to 6-fold increase in allergies and 5- to 6-fold increase in T1D and other autoimmune disorders in the Finnish vs Russian sides of North Karelia; in nearby Estonia, the incidence of T1D and atopy are transitioning with economic development from rates historically similar to the Russian side to the Finnish side
  • The study:
    • Approx 1000 infants in the three areas (Russian Karelia, Finnish Karelia, and Estonia) were followed from birth to 3 yo with monthly stool samples, with metagenomic characterization of 785 gut microbial communities. These 3 areas have similar genetic makeup as well as similar climate and latitude.
    • 74 kids were selected from each country based on similar HLA risk class distribution and gender, getting monthly stool samples and information on breastfeeding, diet, allergies, infections, family history, etc.
  • Results:
    • The resident country was the major source of variation of gut microbiome, especially during the first year of life. The diversity of the microbiome overall increased with age. The specific microbiome findings below are corrected for major confounding factors or birth mode, breastfeeding and other dietary factors, antibiotic use and age
    • The Finnish and Estonian kids harbored more Bacteroides species and enrichment in lipopolysaccharide (LPS) biosynthesis-encoding genes; Russian kids had more Bifidobacterium species (esp B. bifidum)
    • The abundance of Bacteroides correlated with serum insulin autoantibody levels
    • More lipopolysaccharides (endotoxins) were produced in Finnish and Estonian kids,
    • This LPS differed from that in the Russian kids, which developed almost exclusively from E coli. (And, the Bacteroides LPS inhibits immune stimulation and inflammatory cytokine responses to E coli LPS in human cells.) This Russian-side LPS, unlike that from Bacteroides as in the Finnish and Estonian kids, elicits endotoxin tolerance (further studies in mice of the specific endotoxins found that the LPS from E coli, as in the Russian kids, also increased their immune tolerance and decreased diabetes): i.e., different LPS produce different constituents in the human gut microbiome, with either stimulatory or inhibitory activity on components of the immune system (though, of note, the specific LPS differences are quite different in mice and human gut microbiomes)
    • Assessment of T1D anti-b cell autoantibody seropositivity revealed a gradient: 16 in Finland, 14 in Estonia and 4 in Russia


  • This article and the NY Times commentary reinforce that the microbiome is a major mediator of the environment into human disease. Colonization by different bacteria in the first year of life leads to changes in attendant lipopolysaccharides, which seem to have a direct effect on immune tolerance/susceptibility, and seems to be related to diabetes autoantibody seropositivity (not found in the first study) and potentially to the increased incidence in T1 diabetes in certain areas. One of the important components of this study is that the potential genetic differences between these communities is pretty much mitigated, since they all derive from a common gene pool and only recently had such dramatic differences in environmental exposures.
  • Again, this type of study reinforces that what seems intuitive: it makes sense that being brought up in a natural environment with natural exposures, as in farming, allows for evolutionary adaptation; recent human changes, which do not allow for evolutionary accommodation, in farming and hygiene have the potential to disrupt the complex interaction between us and nature.
  • Some unresolved issues: is it just the microbiome? Are there undetected viruses which either promote or protect from T1D development? Is it when one is exposed to the virus (e.g. it seems that several diseases such as EBV seem to confer less likelihood of developing MS if the EBV infection happens earlier. same with the clinical results from polio infection). Though the very well-controlled mice experiments seem to suggest an important role for the microbiome itself, and the effect of specific bacterial changes.
  • This does not mean that modernization has no benefits: Russian Karelia has life expectancy 66.6 years, 13 yrs less than Finns.
  • The hygiene hypothesis does not mean personal cleanliness. It refers to specific environmental exposures. So, eating food off the ground is not necessarily protective….

—————————————————————————————————                                     The Amish of Indiana and the Hutterites of South Dakota are groups of farmers who emigrated from Europe in the 1700s and 1800s during the Prostestant Reformation, have similar genetic ancestries, but very different prevalences of asthma: the Amish schoolchildren have a prevalence of 5.2% vs 21.3% in the Hutterites; and the prevalence of allergic sensitization is 7.2% vs 33.3%. This is despite similarities in many of the risk factors for asthma, including: large sibship size; high rates of childhood immunization; diets rich in fat, salt and raw milk; low rates of childhood obesity; long duration of breast-feeding; minimal exposure to tobacco and air pollution; and taboos against indoor pets. But they have very different farming styles: the Amish practice traditional farming using horses for fieldwork and transportation, and live on single-family dairy farms; the Hutterites live on large communal industrialized farms. The current study (see Stein MM. N Engl J Med 2016; 375:411) assessed environmental exposures, genetic ancestry, and immune profiles of 60 Amish and Hutterite children, measuring levels of antigens and endotoxins, and the microbial composition of indoor dust samples. They also looked at the effect of dust extracts from each grouping on the immune and airway responses in a mouse model of experimental allergic asthma. Results:

  • Of the 30 children from each group, mean age 11, 30% girls, 14 sibs, but they found: no asthma in the 30 Amish kids and 6 cases in the Hutterites, similarly much higher allergen-specific IgE  and total serum IgE levels in the Hutterites. No other immunoglobulin differences. Also decreased peripheral eosinophils in the Amish children
  • Genome-wide SNPs revealed “remarkable genetic similarities” between the 2 groups of children (confirming that these groups are from similar genetic backgrounds)
  • Median endotoxin levels were 6.8 times as high in the Amish house dust; common allergens (cats, dogs, house dust-mites, cockroaches) were 4 times as high in the Amish homes
  • There were profound differences in the microbial composition of mattress dust samples
  • There were profound differences in the proportions, phenotypes, and functions of innate immune cells of the 2 groups of kids
  • Intranasal instillation of dust extracts from Amish but not Hutterite houses significantly inhibited airway hyperreactivity and eosinophilia in the mice


  • Unfortunately they did not assess microbiome changes (both in the gut and in the respiratory tract) in these children. This study does suggest that there are profound effects of the environment (likely related to the differing farming techniques) which translate into quite dramatic differences in immune responses and ultimately into clinical allergic asthma.
  • The tie-in with microbiome is a bit opaque (at least translucent) in this article, but was addressed in a Canadian study, which looked at the effect of microbiome changes associated with antibiotic exposure and the development of asthma, along with comments on other studies about T1D, gluten-sensitivity, etc. (see prior blog
  • So, the bottom line: there are pretty clearly very important associations between the human microbiome and an array of disorders (see; the microbiome is sometimes referred to as the “missing organ”, but seems quite susceptible to external/environmental stimuli. Preserving a healthy microbiome relies on a healthy diet and exercise (and reducing the barriers to them…). And there are even some data finding that stress itself leads to changes in the microbiome and conversely that changes in the microbiome lead to changes in how the body reacts to stress through the hypothalamic-pituitary axis (e.g. see Gur TL. Front Psychiatry 2015; 6:1, or the whole issue of Science from June 08, 2012, including the article by Nicholson JK. Science. 2012; 336: 1262). So, to me, this issue really does reinforce some of the current initiatives: reducing the use of antibiotics both in humans and especially in farming where farm animals get antibiotics to increase their weight; and increasing a healthier lifestyle with better nutrition, exercise, and decreasing stress (though these last ones are not really getting better….).



Primary Care Corner with Geoffrey Modest MD: Microbiome Changes and Severity of NAFLD

18 Mar, 16 | by EBM

By Dr. Geoffrey Modest

There is not a great understanding as to which patients with non-alcoholic fatty liver disease (NAFLD), the most common liver disorder in the US/Western countries, are among the 20-30% who progress to nonalcoholic steatohepatitis (NASH), or those who progress even further to fibrosis and cirrhosis. Certain genetic polymorphisms have been identified which predispose people to more aggressive disease: there are some data that the I148M variant of the PNPLA3 gene confers a 3.5-fold increased risk of NASH and a 3.2-fold increased risk of fibrosis. And there may be roles for epigentics, gender/hormone status, and nutrition as well. This article looked at the potential role of the gut microbiome (see HEPATOLOGY 2016;63:764), since as noted in several blogs (see below), there may also be a role of microbiome changes in some related conditions (e.g., obesity, metabolic syndrome, diabetes).


  • 30 patients with no/only periportal F0/F1 fibrosis (10 with NASH) and 27 patients with significant F≥2 fibrosis (25 with NASH) had 16S ribosomal RNA gene sequencing of stool samples. All patients had liver biopsy diagnosis, did not drink alcohol >210 g/week for men or >140 g/week for women, did not have chronic hepatitis B or C, and did not have evidence of other chronic liver diseases on biopsy.
  • Mean age 57, 34 males/23 females, BMI 31, 40% with diabetes, 50% elevated triglycerides, 75% depressed HDL, 81% with metabolic syndrome, mean AST of 40 and ALT of 64.


  • Bacteroides was significantly more abundant in those with NASH and F≥2 fibrosis; Prevotella was decreased (these two genera are competitors with an inverse abundance relationship). Also, Ruminococcus  was increased.
  • On multivariate analysis (adjusting for BMI, BP, triglycerides, HDL, metabolic syndrome), Bacteroides was independently associated with NASH, and Ruminococcus with F≥2 fibrosis.
  • ​There was a dose-response curve: both the rate of NASH and F≥2 fibrosis tracked with increasing abundance of Bacteroides and Ruminococcus, respectively
  • ​In the subgroup with metabolic syndrome (overall a group with higher risk of more severe NAFLD lesions), those with more abundant Bacteroides and Ruminococcus had more severe NAFLD lesions. This was also found in those with diabetes and several of the components of metabolic syndrome
  • In assessing the presumed functional effects of these bacterial changes, those with NASH had a microbiome enriched in ability to metabolize carbohydrates, lipids, and amino acids.
  • This study adds to the potential role of microbiome changes in causing clinical diseases. The study itself cannot imply causality, just an association: for example, did the microbiome cause the changes in the microbiome, or vs vice versa? Were there other nonetiologic factors that caused both the microbiome changes in these patients and the NAFLD/NASH changes in the liver,such as eating too much pâté (this was a French study, after all)? But, arguments in favor of the microbiome changes being causal:
    • Animal studies show that manipulating the gut microbiome can lead to changes in the liver lesions of NAFLD, including steatosis, NASH, fibrosis and liver cancer
    • ​Bacteroides is associated with increased fecal content of deoxycholic acid, D-pinitol, choline, farrrinose, and stachyose (the last 2 containing glucose and fructose), and lower amounts of short-chain fatty acids (SFCAs) and amino acids. And deoxycholic acid induces apoptosis in the rat liver and is increased in NASH patients, fructose is associated with increased liver inflammation and fibrosis in NAFLD patients, and decreased SCFAs (esp. butyrate, propionate and acetate — see Curr Opin Clin Nutr Metab Care 2014, 17:139) may be detrimental to NAFLD
    • Bacteroides is favored overall in the gut when people eat western diets (high in fat, animal proteins, and sugar), vs Prevotella being favored in those eating foods rich in fiber, starch and plant polysaccharides. In fact changing the diet to an animal-based one leads to a rapid shift in the gut microbiome to Bacteroides, and promotes insulin resistance.

So, what are the implications of this study:

  • This study and others on the microbiome (for example, see blogs:​ ) reinforce that there seems to be a dynamic interrelationship between the gut microbiome and human disease, and that the changes in the microbiome lead to changes in bacterial metabolism and byproducts, which may be the mediators/abettors of disease processes.
  • There are several key players affecting the composition of the gut microbiome, including diet [see above microbiome blogs for articles on red meat and heart disease, medications (including one on metformin suggesting that much of its hypoglycemic role is as a promoter of healthy changes in the microbiome) as well as on antibiotics, and exercise]
  • And, I think that the associations with NAFLD above (even if not clearly causal) will expand my approach to patients with NAFLD to include reinforcing a vegetable-based diet, as well as my usual approach of weight loss, lipid control, and exercise.

Primary Care Corner with Geoffrey Modest MD: Antibiotic Resistant Bugs in Gut Microbiome of Kids

22 Dec, 15 | by EBM

By Dr. Geoffrey Modest

Ciprofloxacin​-resistant e. coli are increasingly found worldwide and are capable of causing extraintestinal infections, especially urinary tract infections. A report in 2006 found that 1.5% of healthy Seattle children excreted cipro-resistant e coli in their stool, without prior fluoroquinolone exposure. A new study looked at 80 healthy children and their mothers​ who were part of the St Louis twin cohort, assessing stool samples from 2010-2013 semiannually from mothers, and monthly from their twins til age 2 yo and then bimonthly, analyzing for e coli resistance (see J Infect Dis. (2015) 212 (12): 1862-1868).


  • 15 kids (19%) and 8 mothers (20%) excreted ciprofloxacin-resistant e coli at least once, and 11 of 23 colonized subjects had multiple and usually consecutive positive samples
  • Overall 33% of 40 families had at least 1 member with a positive culture for cipro-resistant e coli
  • For the kids, the median day-of-life for the first positive specimen was 341
  • Stools specimens positive for cipro resistance correlated with length of hospital stay after birth (p=0.002), where the median was 6 days longer (10 vs 4 days) than for those with no resistance, and with maternal colonization (p=0.001); antibiotic use in the first 2 months of life, acid suppression, sex, mode of delivery or maternal perinatal antibiotic use were not correlated. and only 2 of the 15 kids with a positive stool specimen received any antibiotics at all in the first 9 months of life
  • In 6 families, both kids had positive stool samples
  • Cipro-resistant e coli were often resistant to other antibiotics: of 57 cipro-resistant e coli, 1 sample was resistant to 5 other antibiotics (ampicillin/cefazolin, tmp/smx, piperacillin/tazobactam, gentamicin, doxycycline), 5 were resistant to 4 of the other antibiotics, 16 to 3 antibiotics, 21 to 2 antibiotics, 8 to 1 antibiotic, and only 6 were resistant only to cipro
  • The cipro-resistant e coli had genotypes typical of extraintestinal pathogenic e coli.

So, some points:

  • Antibiotic-resistance is pretty common and may be increasing, even without the selection pressure of prescribed antibiotics
  • The cipro-resistant e coli found have the genetic profile of potential human pathogens (not just for urinary tract infections but also for soft-tissue and bone infections)
  • In this study they used a very small stool sample for inoculation, raising the issue of underestimating the actual presence of cipro-resistant e coli​ (and 1/2 the kids had only one positive stool sample, which may be because of the small inoculum and low levels of colonization)
  • Though there was a correlation between the length of hospital stays for the infants and subsequent positive stools, suggesting hospital-acquired colonizatons, the median date of the first positive culture was almost a year later​. One possible explanation is that these infants were in fact colonized in the hospital but their level of colonization was below what was detectable. Or, perhaps kids who stayed 6 days longer were more premature and there was something either developmentally or posthospitalization specific to these kids which led to more likelihood of acquiring the resistant bug. Not sure from the data.
  • So, how does this all fit together? Clearly the issue is common, probably increasing, and potentially quite profound, especially since the cipro resistance was almost always associated with resistance to other antibiotics, and we don’t have a slew of new, great antibiotics in the wings. The presence of resistance in kids without antibiotic exposure suggests, I think most likely, that there was community-acquired colonization, potentially from food (e.g. from animals or plants treated with antibiotics. Fyi, 80% of antibiotics used is for food production, and quinolones have been heavily used in agriculture and aquaculture for years). So, the canary in the mine whispers in my ear that we really try to understand the mode of spread of these resistant organisms (whether from food or community or hospital), to look at ways of restoring a healthy gut microbiome (through lifestyle interventions of diet/exercise — esp in adults, avoiding use of antibiotics or meds which put the microbiome at risk of pathologic changes), and largely to eliminate the unnecessary use of antibiotics in animals/plants and us.

For an array of prior blogs on antimicrobial resistance, see .

Primary Care Corner with Geoffrey Modest MD: Microbiome and Cancer

15 Dec, 15 | by EBM

By Dr. Geoffrey Modest

Well, here is yet another microbiome blog, but this one suggests that the gut microbiome and associated immunologic changes could affect cancer development and therapy. There were 2 articles in an issue of the journal Science which assessed this (002)

  1. One study looked at how changes in the microbiome affect host immunity and the natural response to implanted cancer (see Science 2015; 350 (6264): 1084). Prior studies have found a role for the intestinal microbiome in human systemic immune responses.


  • 2 genetically-similar mice from 2 different suppliers (JAX and TAC) with 2 different intestinal microbiomes (257 different bacterial taxa) had different responses to implanted melanoma, with the JAX mice having higher tumor-specific T-cell responses, intratumor CD8 T-cell accumulation, and improved survival
  • Cohousing the JAX and TAC mouse eliminated the difference, as did transferring fecal specimens from the JAX mice into the TAC mice (but not if gavage saline or TAC fecal material into TAC mice)
  • The clinical effect of having the JAX microbiome was equivalent to using a specific antibody immunotherapy (PD-L1), though the combo of this immunotherapy with the more immunogenic JAX microbiome was even better (human patients with evidence of endogenous T cell response also do better with immunotherapies)
  • In assessing the genus-level taxa of the differences in the microbiomes of JAX and TAC mice, the presence of Bifidobacterium species in particular showed the positive association with antitumor T-cell responses (400-fold). And Bifidobacterium species (including B. breve and B. longum) administered to TAC mice led to improved tumor control, which was abrogated in CD-8 depleted mice, suggesting that the effect of this bacterial species was not direct but was mediated through modifying endogenous immunologic responses
  • The same basic finding was found with bladder cell implants
  • Lactobacillus had no effect on tumor growth
  • Further experiments suggested that the antitumor effect of Bifidobacterium was not related to indirect effects of the Bifidobacterium​ on other bacterial species but was acting on its own. In addition, Bifidobacterium was shown to alter lymphocytic dendritic cell activation and improved tumor-specific CD8 T-cell function.
  1. Another study (which I will not summarize much) found that antibodies targeting a regulator of T cell activation (ipilimumab, a human monoclonal antibody useful in patients with metastatic melanoma) only worked if the gut microbiome had Bacteroides species present, especially B. fragilis (see Science 2015; 350 (6264): 1079)

So, I am continually amazed at both the extent of the rather profound impacts of the microbiome in preserving many health-related outcomes as well as its remarkable fragility. And, I really do not want to be reductionist — the Bifidobacterium seems to be protective in a few studies, along with other bugs such as Bacteroides. But there are undoubtedly complex interactions between the different species, some known and some not, which are essential for a healthy microbiome. And some of these commensals may be important for some functions and others for other functions. I.e., the answer is not simply to take certain probiotics (which may be helpful), but to do everything we can to preserve the microbiome naturally. As noted in several of themicrobiome blogs, the issue is to emphasize a healthy life style (esp. diet and exercise), eat good foods (e.g. avoid many of the artificial stuff around us, such as artificial sweeteners), and avoid toxins as much as we can (antibiotics, both given unnecessarily in the medical setting, and especially in use in agriculture and in animals).  No doubt, the microbiome is often able to regenerate (and we are lucky that many of our natural systems, including the environment are able to repair themselves from natural and human interruptions), but as with all such systems, there may be tipping points beyond which there is no return….

For other blogs on the microbiome: associates PPI use and C diff infections showing short term salivary and long-term gut microbiome changes after a single dose of antibiotics​ noting increased asthma in kids with early antibiotic exposure, as well as some data on celiac disease (also highlights possible protective effect of Bifidobacterium)​ showing microbiome changes with international travel and use of antibiotics looked at the effect of red meat on the microbiome (increasing TMAO levels, which are strongly pro-atherogenic) and showing that metformin induces positive changes in the microbiome which decrease insulin resistance finding that non-caloric artificial sweeteners induce microbiome changes causing increased insulin resistance and, several additional articles in on recommendations to limit antibiotic use or to use the most targeted and specific antibiotic when necessary in order to inflict the least harm on the microbiome

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