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Improving the quality of microbiome studies – STORMS

/in ISAPP Science Blog /by KC

By Mary Ellen Sanders, PhD, ISAPP Executive Science Officer

In mid-March I attended the Gut Microbiota for Health annual meeting. I was fortunate to participate in a short workshop chaired by Dr. Geoff Preidis MD, PhD, a pediatric gastroenterologist from Baylor College of Medicine and Dr. Brendan Kelly MD, MSCE, an infectious disease physician and clinical epidemiologist from University of Pennsylvania. The topic of this workshop was “Designing microbiome trials – unique considerations.”

Dr. Preidis introduced the topic by recounting his effort (Preidis et al. 2020) to review evidence for probiotics for GI endpoints, including for his special interest, necrotizing enterocolitis (NEC). After a thorough review of available studies testing the ability of probiotics to prevent morbidity and mortality outcomes for premature neonates, he and the team found 63 randomized controlled trials that assessed close to 16,000 premature babies. Although the effect size for the different clinical endpoints was impressive and clinically meaningful, AGA was only able to give a conditional recommendation for probiotic use in this population.

Why? In part, because inadequate conduct or reporting of these studies led to reduced confidence in their conclusions. For example, proper approaches to mitigate selection bias must be reported. Some examples of selection bias include survival bias (where part of the target study population is more likely to die before they can be studied), convenience sampling (where members of the target study population are not selected at random), and loss to follow-up (when probability of dropping out is related to one of the factors being studied). These are important considerations that might influence microbiome results. If the publication on the trial does not clearly indicate how these potential biases were addressed, then the study cannot be judged as low risk of bias. It’s possible in such a study that bias is addressed correctly but reported incompletely. But the reader cannot ascertain this.

With an eye toward improving the quality and transparency of future studies that include microbiome endpoints, Dr. Preidis shared a paper by a multidisciplinary team of bioinformaticians, epidemiologists, biostatisticians, and microbiologists titled Strengthening The Organization and Reporting of Microbiome Studies (STORMS): A Reporting Checklist for Human Microbiome Research.

Dr. Preidis kindly agree to help the ISAPP community by answering a few questions about STORMS:

Dr. Preidis, why is the STORMS approach so important?

Before STORMS, we lacked consistent recommendations for how methods and results of human microbiome research should be reported. Part of the problem was the complex, multi-disciplinary nature of these studies (e.g., epidemiology, microbiology, genomics, bioinformatics). Inconsistent reporting negatively impacts the field because it renders studies difficult to replicate or compare to similar studies. STORMS is an important step toward gaining more useful information from human microbiome research.

One very practical outcome of this paper is a STORMS checklist, which is intended to help authors provide a complete and concise description of their study. How can we get journal editors and reviewers to request this checklist be submitted along with manuscripts for publication?

We can reach out to colleagues who serve on editorial boards to initiate discussions among the editors regarding how the STORMS checklist might benefit reviewers and readers of a specific journal.

How does this checklist differ from or augment the well-known CONSORT checklist?

Whereas the CONSORT checklist presents an evidence-based, minimum set of recommendations for reporting randomized trials, the STORMS checklist facilitates the reporting of a comprehensive array of observational and experimental study designs including cross-sectional, case-control, cohort studies, and randomized controlled trials. In addition to standard elements of study design, the STORMS checklist also addresses critical components that are unique to microbiome studies. These include details on the collection, handling, and preservation of specimens; laboratory efforts to mitigate batch effects; bioinformatics processing; handling of sparse, unusually distributed multi-dimensional data; and reporting of results containing very large numbers of microbial features.

How will papers reported using STORMS facilitate subsequent meta-analyses?

When included as a supplemental table to a manuscript, the STORMS checklist will facilitate comparative analysis of published results by ensuring that all key elements are reported completely and organized in a way that makes the work of systematic reviewers more efficient and more accurate.

I have been struck through the years of reading microbiome research that primary and secondary outcomes seem to be rarely stated up front. Or if such trials are registered, for example on clinicaltrials.gov, the paper does not necessarily focus on the pre-stated primary objectives. This approach runs the risk of researchers finding the one positive story to tell out of the plethora of data generated in microbiome studies. Will STORMS help researchers design more hypothesis driven studies?

Not necessarily. The STORMS checklist was not created to assess study or methodological rigor; rather, it aims to aid authors’ organization and ease the process of reviewer and reader assessment of how studies are conducted and analyzed.  However, if investigators use this checklist in the planning phases of a study in conjunction with sound principles of study design, I believe it can help improve the quality of human microbiome studies – not just the writing and reporting of results.

Do you have any additional comments?

One of the strengths of the STORMS checklist is that it was developed by a multi-disciplinary team representing a consensus across a broad cross-section of the microbiome research community. Importantly, it remains a work in progress, with planned updates that will address evolving standards and technological processes.  Anyone interested in joining the STORMS Consortium should visit the consortium website (www.stormsmicrobiome.org).

See related blog:   ISAPP take-home points from American Gastroenterological Association guidelines on probiotic use for gastrointestinal disorders

 

Can dietary supplements be used safely and reliably in vulnerable populations?

/in ISAPP Science Blog /by KC

By Dr. Greg Leyer, Sr. Director – Scientific Affairs, Chr. Hansen, Inc., Madison, WI and Prof. Dan Merenstein, Department of Family Medicine, Georgetown University Medical Center, Washington DC

What is it that doctors look for when recommending or prescribing therapies to patients? If it is a drug, a supplement, a new diet, or even a new exercise regimen, they look for safety and efficacy. There are of course other things to consider, including cost, ease of administration, and patient compliance, among others. But safety and efficacy are their foremost concerns.

A recently published clinical report from the American Academy of Pediatrics (AAP) (Poindexter 2021) examined the evidence for probiotics to prevent morbidity and mortality in preterm infants. They concluded that probiotics could not be recommended. This differs from conclusions of the American Gastroenterological Association (AGA) (Su et al. 2020), which recommended specific probiotic strains for preterm (less than 37 weeks gestational age) and low birth weight infants. The AAP report also differs from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) (Van den Akker et al. 2020), which recommends specific strains for this use, although their recommendations are not fully aligned with AGA’s (see What’s a Clinician to do When the Probiotic Recommendations from Medical Organizations Do Not Agree?).

The AAP report does a thorough job of reviewing data on use of probiotics in the NICU, including conflicting studies, lack of confirmatory studies of efficacious strains, and safety and cross contamination inside the NICU. However, the overriding theme of the report is “clinicians must be aware of the lack of regulatory standards for commercially available probiotic preparations manufactured as dietary supplements and the potential for contamination with pathogenic species.” Therefore, at the heart of the AAP failure to recommend probiotics is the concern that the quality of available products is insufficient. Because of the absence of a pharmaceutical-grade probiotic product for use in the United States, they posit, they cannot recommend usage. It is noteworthy that the trials performed on premature infants resulting in multiple conclusions of safety and efficacy have thus far utilized probiotic products manufactured as dietary supplements.

Probiotics can be marketed as drugs if they follow that regulatory pathway, but generally in the US they are sold under the regulatory classification of dietary supplements. Is the AAP correct that no dietary supplement is of sufficient quality to recommend for use in preterm infants?

Quality of probiotic dietary supplement probiotics. Dietary supplements were a category of product developed to supplement the diet of the generally healthy population, not to treat or prevent disease. In practice this is an important distinction, because while the safety standard is high for dietary supplements for healthy individuals (see comments by food safety expert Jim Heimbach here), such supplements do not need to be established as safe for patient populations. But in the case of probiotics, many clinical trials have evaluated safety and efficacy for prevention or treatment of disease, more aligned with drug uses. Yet probiotic products supported by these data are not marketed in the US as drugs.

It is a common misperception that dietary supplements are “not regulated”. However, the FDA has clear good manufacturing practices (GMP’s) and regulations dedicated to dietary supplement manufacturing.  The onus is on manufacturers to establish appropriate product specifications based on intended use and risk. Reputable manufactures establish rigorous purity, strength, and identity quality standards consistent with the intended population and sufficient for that use. Products intended for infants, including premature infants, should be manufactured under quality standards more rigorous than those intended for a healthy adult population. For example, Chr. Hansen bases the enhanced specifications for products aimed at infants, and preterm infants, on elements of Codex standards for infant formula, amongst other stringent microbiological criteria. This would include manufacturing the probiotic strain to an “infant” grade, employing stricter environmental monitoring, sanitation, and airflow control throughout the process, careful selection of raw ingredients for infant compatibility, and enhanced testing and purity standards using validated methods at every step. The internal manufacturing standards that Chr. Hansen applies for products intended for infants, and preterm infants, are much stricter than typical dietary supplement standards, and are appropriate for their intended use.

Therefore, there are high quality, safe probiotic products produced under dietary supplement regulations even though such products do not carry any label statement claiming this added level of quality. However, products sourced for hospitals to stock in formularies could work with the supplier to demand this extra level of product testing specifications. Pharmacies can institute quality agreements with vendors that would delineate their expectations for the strains present, the levels of live microbes acceptable in the final product, etc. This agreement could also mandate that any product change – as defined in the agreement – would require the vendor to notify the customer. Such an agreement might be burdensome for a hospital pharmacist, but a sophisticated dietary supplement company should be able to assure the hospital formulary of their quality.

Products made using strict specifications, geared towards infant and premature infant applications, are on the market and are safely being used in this patient population in many NICUs and as part of infant formulas. We disagree with AAP’s position that a pharmaceutical approach is needed, as long as a product of sufficient quality can be provided. To deny preterm infants probiotics, which have a significant chance of improving their clinical outcomes, is not in line with other medical recommendations. Instead, the hospital formularies should stock products that have been scrutinized for sufficient evidence of safety and efficacy. Suppliers of stocked products should provide product testing results, a description of the quality standards employed during production, and a rationale for the suitability of the standards for preterm infants. Third party verification of adherence to these quality standards would assure medical professionals regarding the safety of these products for use.

References

CAC/RCP 66-2008. Code of hygienic practice for powdered formulae for infants and young children. Codex.

Poindexter, B. 2021. Use of Probiotics in Preterm Infants. Pediatrics 147 (6): e202 1051485.

Su et al. 2020. AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology 159:697-705.

Van den Akker et al.  2020. Probiotics and Preterm Infants: A Position Paper by the European Society for Paediatric Gastroenterology Hepatology and Nutrition Committee on Nutrition and the European Society for Paediatric Gastroenterology Hepatology and Nutrition Working Group for Probiotics and Prebiotics. Journal of Pediatric Gastroenterology and Nutrition. 70(5):664-680.

 

 

What’s a Clinician to do When the Probiotic Recommendations from Medical Organizations Do Not Agree?

/in ISAPP Science Blog /by KC

By Prof. Hania Szajewska, MD, Department of Paediatrics, The Medical University of Warsaw, Poland

The scientific literature on probiotics is growing rapidly, with newly published studies continually adding to the sum of information about the probiotic strains that confer health benefits in specific populations.

In research, we make hypotheses. Eventually, they are resolved by collecting data or they are replaced by more refined, or entirely new, hypotheses. This process usually unfolds over an extended period of time. Along the way, medical and scientific organizations may decide to take ‘snapshots’ of the evidence to-date and develop guidelines based on available published studies. Unfortunately, disagreements can occur about the meaning of the data, sometimes leading to differences in the guidelines developed by various organizations.

But clinicians cannot always wait for the data to provide a crystal-clear picture. They want answers to guide their clinical practice. Hence the question: Should probiotics be used if guidelines do not agree on the use of probiotics for a certain indication, or on the strains to be used?

Take, for example, the current situation relevant to pediatric practice. Here I discuss two recommendation documents: one developed by the European Society of Pediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN), and another developed by the American Gastroenterological Association (AGA).

Acute diarrhea

In 2020, the ESPGHAN Working Group (WG) on Probiotics identified 16 systematic reviews and meta-analyses published since 2010, which included more than 150 RCTs. The WG made weak (also known as conditional) recommendations for (in descending order in terms of the number of trials evaluating any given strain):

  • S boulardii (low to very low certainty of evidence);
  • L rhamnosus GG (very low certainty of evidence); L reuteri DSM 17938 (low to very low certainty of evidence);
  • L rhamnosus 19070-2 & L reuteri DSM 12246 (very low certainty of evidence).

The WG made a strong recommendation against L helveticus R0052 & L rhamnosus R0011 (moderate certainty of evidence) and a weak (conditional) recommendation against Bacillus clausii strains O/C, SIN, N/R, and T (very low certainty of evidence)1.

In contrast, also in 2020, the AGA, based on the evaluation of 89 trials, made a conditional recommendation against the use of probiotics in children from North America with acute infectious gastroenteritis (moderate quality of evidence)2. The rationale for the negative AGA recommendation was that the majority of the studies were performed outside North America. Moreover, two large, high-quality null trials, performed in Canada and US, questioned the efficacy of the probiotics evaluated in these studies, for the management of children with acute gastroenteritis 3,4.

Prevention of necrotizing enterocolitis

Another example of discordant guidelines relates to necrotizing enterocolitis (NEC) in preterm infants. NEC is one of the most severe and life-threatening gastrointestinal diseases to occur in preterm infants, particularly those with a birth weight <1,000 g. The factors involved in the pathogenesis of NEC include formula feeding rather than breastfeeding, intestinal hypoxia–ischemia, and colonization of the gut with pathogenic microbiota5.

In 2020, both ESPGHAN6 and AGA2 published their recommendations on the use of probiotics for preventing NEC. While both were based on pair-wise systematic reviews and network meta-analyses7, their conclusions differed. The only probiotic strain that was recommended by both societies was L rhamnosus GG ATCC 53103. With regard to L reuteri DSM 17938, the ESPGHAN did not formulate a recommendation for or against it, while the AGA conditionally recommends it.

Why do guidelines differ?

Many factors contribute to the discrepancy in guidelines developed by various organizations. In the case of probiotics, they may be due to these differences:

  • Study methods. Although dozens of studies involving thousands of patients have been conducted in many indications, studies are subject to bias resulting from incorrect randomization, non-confidentiality, non-masking, or lack of intention-to-treat analysis.
  • Targeted population. The effectiveness of probiotics in different populations may vary, for example, due to differences diet or in microbiota at the start of treatment.
  • Probiotics are a heterogeneous intervention. Even if the rules for assessing individual strains, and not probiotics as a group, are followed, the effectiveness of probiotics is influenced by factors such as product quality, storage conditions, dose, timing of administration, and the duration of the intervention.
  • Outcome measures (endpoints). Studies use different outcomes to measure efficacy, and even if the same outcomes are used, their definition may differ (e.g. diarrhea duration may be defined as time to the last diarrheal stool or time to the first normal stool). Such heterogeneity in the reported outcomes, combined with the lack of standardized definitions, pose a challenge in meta-analyses and should be considered when interpreting the results.

What should clinicians do when the guidelines are not consistent?

Back to the question asked earlier: Should probiotics be routinely used if guidelines from the scientific or medical organizations do not agree on the use of probiotics?

One approach may not fit all. However, in the case of acute infectious diarrhea in children, both the AGA and ESPGHAN formulated a conditional recommendation: in the first case, it is negative; in the second, positive. It is important to note that the interpretation of a conditional recommendation for and a conditional recommendation against is similar. For clinicians, both mean that different choices will be appropriate for different people. Clinicians should help each patient make decisions consistent with the patient’s preferences. For patients, it means that the majority of individuals in this situation would want the suggested course of action, but many would not8.

Taken together, the recommendations communicate that probiotics may be beneficial, although not essential, in the treatment of acute diarrhea in young children.  The use of certain probiotics with documented efficacy may be considered in the management of acute diarrhea in young children.

With regard to the prevention of NEC, the AGA and ESPGHAN guidelines agree that certain probiotics reduce the risk of NEC in preterm infants. However, based on their analyses and the included / excluded studies they differ in the recommended strains; additionally, not all of the strain combinations are available everywhere. Therefore, it seems reasonable to choose a probiotic that is included in the recommendations of both societies (if available). One example is L. rhamnosus GG.

In general, organizations should be commended for taking on the daunting task of evaluating the probiotic evidence – both the quality of the studies and the positive or negative results – in order to generate recommendations. Until further well-conducted studies make the answer clearer, clinicians must live with some ambiguity and use the recommendations in the best way possible to inform their daily decisions with individual patients.

REFERENCES

  1. Szajewska H, Guarino A, Hojsak I, et al. Use of Probiotics for the Management of Acute Gastroenteritis in Children. An Update. J Pediatr Gastroenterol Nutr. 2020.
  2. Su GL, Ko CW, Bercik P, et al. AGA Clinical Practice Guidelines on the Role of Probiotics in the Management of Gastrointestinal Disorders. Gastroenterology. 2020.
  3. Schnadower D, Tarr PI, Casper TC, et al. Lactobacillus rhamnosus GG versus Placebo for Acute Gastroenteritis in Children. The New England journal of medicine. 2018;379(21):2002-2014.
  4. Freedman SB, Williamson-Urquhart S, Farion KJ, et al. Multicenter Trial of a Combination Probiotic for Children with Gastroenteritis. The New England journal of medicine. 2018;379(21):2015-2026.
  5. Neu J, Walker WA. Necrotizing enterocolitis. The New England journal of medicine. 2011;364(3):255-264.
  6. van den Akker CHP, van Goudoever JB, Shamir R, et al. Probiotics and Preterm Infants: A Position Paper by the European Society for Paediatric Gastroenterology Hepatology and Nutrition Committee on Nutrition and the European Society for Paediatric Gastroenterology Hepatology and Nutrition Working Group for Probiotics and Prebiotics. Journal of pediatric gastroenterology and nutrition. 2020;70(5):664-680.
  7. van den Akker CHP, van Goudoever JB, Szajewska H, et al. Probiotics for Preterm Infants: A Strain-Specific Systematic Review and Network Meta-analysis. Journal of pediatric gastroenterology and nutrition. 2018;67(1):103-122.
  8. Andrews J, Guyatt G, Oxman AD, et al. GRADE guidelines: 14. Going from evidence to recommendations: the significance and presentation of recommendations. J Clin Epidemiol. 2013;66(7):719-725.

 

See here for a published comment on this topic in The American Journal of Gastroenterology.

ISAPP ha estado trabajando en colaboración con la Sociedad de Enterocolitis Necrotizante

/in Consumer Blog, News /by KC

La Asociación Científica Internacional para Probióticos y Prebióticos (ISAPP, por sus siglas en inglés), ha estado trabajando en colaboración con la Sociedad de Enterocolitis Necrotizante (NEC Society) en el desarrollo de una infografía sobre el rol de los probióticos en la prevención de la Enterocolitis Necrotizante (ECN).

La ECN es una enfermedad intestinal que puede poner en peligro la vida principalmente en bebés prematuros. Esta enfermedad produce un proceso inflamatorio que puede provocar daños en el tejido intestinal e incluso la muerte.

La leche materna de la madre del bebé es la forma más importante de ayudar a disminuir el riesgo de ECN. La leche pasteurizada de madres donantes es la segunda mejor opción. Adicionalmente, suministrar probióticos a bebés prematuros, junto con la leche materna, puede reducir el riesgo de ECN.

Los probióticos son microorganismos vivos que, cuando se administran en cantidades adecuadas, confieren un beneficio para la salud del huésped.

Los padres con hijos con riesgo de desarrollar ECN pueden consultar a los responsables de la Unidad de Cuidados Intensivos, sobre la posibilidad de utilizar probióticos para contribuir a prevenir el desarrollo de ECN.

ISAPP ha preparado una infografía en español con mayor información sobre este tema, la cual se puede encontrar aquí.

Probiotics to Prevent Necrotizing Enterocolitis: Moving to Evidence-Based Use

/in ISAPP Science Blog /by KC

By Ravi Mangal Patel, MD, Msc, Associate Professor of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta. rmpatel@nullemory.edu Twitter: @ravimpatelmd

Necrotizing enterocolitis (NEC) is one of the most lethal neonatal diseases, yet most people have never heard about it. The disease primarily affects preterm infants and is characterized by the development of intestinal inflammation. Clinically, the disease often manifests with an infant developing feeding intolerance or abnormal abdominal exam findings. The diagnosis is confirmed by abdominal x-ray or ultrasound. One of the key diagnostic radiographic findings is pneumatosis, which is air in the lumen of the bowel caused by gas-producing bacteria.

Dr Ravi Mangal Patel

NEC accounts for 1 out of every 10 deaths in US neonatal intensive care units. Among extremely preterm infants (those born at 22-28 weeks’ gestation) in the US, NEC is the most common single cause of death between 2 weeks and 2 months of age. Many infants with NEC undergo surgery to remove diseased bowel and those who recover and survive are at risk for long-term neurodevelopmental impairment and short bowel syndrome.

Decades of research into NEC have identified several key risk factors, including formula feeding, inconsistent feeding, abnormal intestinal oxygenation and [gut microbiota] dysbiosis. Studies have shown that dysbiosis, or abnormal intestinal colonization, is an important antecedent risk factor for the development of NEC. These studies have found that infants who develop NEC have an increase or bloom in the relative abundance of proteobacteria, compared to those who do not develop NEC. These proteobacteria, which contain a lipopolysaccharide coating, may lead to inflammation through their interaction with Toll-like receptor 4.

Given the role of dysbiosis in NEC, efforts to intervene by provision of probiotics to prevent NEC is a rational and extensively studied intervention, with over 63 randomized trials enrolling ~15,000 infants to date. The aforementioned meta-analysis, along with several others (Table 1), show probiotic supplementation results in large magnitude reductions in the risks of NEC and death and more modest reductions in the risks of late-onset sepsis. However, there is more limited data on extremely preterm infants and the quality or certainty of evidence for probiotics for the prevention of NEC was low in a recent Cochrane review.

 

Source: https://doi.org/10.1053/j.sempedsurg.2017.11.008

In the United States, an increasing number of centers have begun to routinely provide probiotics, with the greatest increase in use beginning in 2015. Observational studies evaluating routine probiotic use show benefits that are similar in magnitude to those from randomized trials, supporting the external validity of the results from the trials. This includes a large recent evaluation of probiotic use in the United States. Around the world, probiotic use is highly variable, from 100% of NICUs in New Zealand, 68% of NICUs in Germany, to 12% in the UK, 21% in Canada and 14% in the United States. Some of the variability in clinical use may be related to the uncertainty regarding the quality of commercially available probiotic products and need for clarity regarding strain-specificity of effects. There are many considerations both for and against routine use of probiotics to prevent NEC (Table 2). Current probiotic dietary supplements do not undergo FDA’s premarket review and approval requirements for safety and effectiveness or have to meet manufacturing and testing standards for drugs, and the potential risks were highlighted by a case of an infant death from a contaminated supplement. There is currently no FDA-approved live biotherapeutic product to prevent NEC.

Source: doi: 10.1016/j.earlhumdev.2019.05.009

Recent recommendations and guidance from ESPHGAN and the AGA also demonstrate that some medical organizations recognize the strength of the data in support of probiotic use to prevent NEC. It has been over two decades since the first study demonstrating the benefit of probiotic supplementation to prevent NEC in preterm infants. Now, more than ever, the evidence continues to accumulate regarding the beneficial effects of probiotic use in preterm infants as a compelling strategy to reduce the risks of both NEC and death. Therefore, considering the balance of potential risks and benefits including data from both randomized trials and routine implementation studies, my opinion is that the cumulative evidence to date supports routine probiotic use to prevent NEC and death in preterm infants.

As important is considering the parent voice regarding probiotic use. The NEC Society is a non-profit focused on NEC that has worked to incorporate the voice of the patient-family in clinical decisions.

Disclosures: Dr. Patel serves on the data-safety monitoring board of the Connection Study, which is a trial examining the use of an investigational probiotic to decrease the risk of NEC.

For further information, see this seminar by Dr. Patel: Practical Consideration for Probiotics in the NICU