Lasting Effects of Antibiotics

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Baldanzi, G., Larsson, A., Sayols-Baixeras, S. et al.  Nat Med (2026). https://doi.org/10.1038/s41591-026-04284-y. Open Access! Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals.

This is a highly-detailed and lengthy report (25 pages).

Methods: The authors combined individual-level data from the Swedish Prescribed Drug Register with fecal metagenomes of 14,979 adults to examine the association between oral antibiotic use over 8 years and gut microbiome. The authors used several microbiome diversity metrics.

Key findings:

  • Antibiotic use <1 year before fecal sampling was associated with the greatest reduction in species diversity, but significant associations were also observed for use 1–4 and 4–8 years earlier. 
  • Clindamycin, fluoroquinolones and flucloxacillin accounted for most of the associations with the abundance of individual species. Use of these antibiotics 4–8 years earlier was associated with altered abundance of 10–15% of the species studied

My take: Clindamycin, fluoroquinolones and flucloxacillin had the largest and most persistent effects on the microbiome. The significance of these microbiome disruption is not clear; though, there have been reports of an association of increase use of antibiotics with cardiovascular disease, inflammatory bowel disease, celiac disease, type 2 diabetes, and colorectal cancer. An association with these disorders, however, does not prove causality.

From the authors: “the primary reason for a restrictive use of antibiotics is the risk of resistance development. Still, our study adds another argument for reducing antibiotic use: namely, gut microbiome alterations that may persist for many years. As the microbiome field advances, our understanding of the long-term impact of antibiotic treatment beyond infections and resistance may reveal additional health implications.”

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AAP & NASPGHAN: Practice Guideline for Faltering Weight

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HB Kersten, PS Goday et al. PEDIATRICS Volume 157, Issue 4, April 2026:e2025075764. Open Access! PDF: Clinical Practice Guideline for Diagnosis and Management of Faltering Weight

The AAP in partnership with the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN) has published its first clinical practice guideline on diagnosis and management of “faltering weight,” a condition formerly described as “failure to thrive” that affects 5%-10% of young pediatric patients in the primary care setting.

  • The clinical practice guideline (CPG) explains that the prior term, failure to thrive (FTT), has never been well-defined. In addition, “the term FTT has also been fraught with controversy that has contributed to the difficulty in determining the criteria used to define it. The word “failure” has led caregivers to feel blamed for their child’s condition. The term has also
    been inconsistently applied, which may exacerbate existing health care inequities.”
  • “When evaluating a child who has been hospitalized for faltering weight, consider the 5 most-common co-occurring conditions…congenital heart disease, gastroesophageal reflux disease (GERD), swallow dysfunction, neurologic disease, genetic abnormalities/congenital syndrome.”
  • “When evaluating a child in the outpatient setting for faltering weight, consider the 5 most-common co-occurring conditions….gastrointestinal disease, pulmonary disease, food allergy, genetic abnormalities/congenital syndrome, neurologic disease.”

My take: Overall, this is a useful guideline. A couple comments:

  1. For several decades I have avoided the term ‘failure to thrive’ (for the reasons given in the CPG) and typically have used terms like poor weight gain or growth failure.
  2. Most pediatric patients with faltering weight need to ingest more calories and do not need extensive testing. I agree that endoscopy should not be part of the routine workup for faltering weight in the absence of other indications
  3. “Gastroesophageal reflux disease” is often attributed as a reason for faltering weight as well as choking. However, isolated reflux is unlikely to cause these presentations in the absence of other factors (e.g. pyloric stenosis, malrotation, swallow dysfunction)

Additional Links:

Clinical Practice Guideline

Technical Reports

AAP News coverage

Information for Families from HealthyChildren.org

  • Faltering Weight in Children: Parent FAQs, in English and Spanish
  • Understanding Growth Charts: A Parent’s Guide to Percentiles & Z-Scores, in English and Spanish

Further reading

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Dr. Danielle Wendel: Management of Short Bowel Syndrome

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Two years ago, Dr. Wendel gave our group a great lecture on short bowel syndrome (SVS). One of the neonatologists in attendance invited her back to provide a state of the art update. While this 2026 lecture covered some of the same issues, there were important updates and insights.

My notes below may contain errors in transcription and in omission. In addition, the information provided is based on what is done in Seattle. However, there is not a lot of evidence for much of what is done in intestinal rehabilitation. Thus, there is variation in practice at different centers and what works for one patient might not work for another. Following my notes, I have included many of her slides.

Diet:

  • Enteral feedings promote intestinal adaptation. Pediatric patients with SBS require much higher calories with enteral nutrition and may have hyperphagia as a compensatory mechanism
  • Breastmilk and/or Standard formula likely help promote intestinal adaptation better than hydrolysates and elemental formulas. In addition, it may help reduce the development of food allergies which are increased in children with SBS
  • Oral feedings have many advantages over NG or GT feedings when feasible. The ability to consume solid foods is quite helpful in reducing diarrhea. Also, encouraging oral feedings may help reduce feeding aversions. As such, GT placement is avoided if possible in Seattle
  • Key diet advice: avoid sweet tasting food/drink, especially in the first few years of life while they are developing their palate/food preferences
  • Feed osmolarity/caloric density: Most children with SBS tolerate lower caloric density (15-20 cal/oz) and more volume orally rather than higher caloric density/lower volume feeds

Parenteral Nutrition:

  • Lipid emulsions: SMOFlipid at 2 gm/day can help prevent essential fatty acid deficiency (EFA). Omegaven may need to be dosed at 1.5 gm/day to prevent EFA. If used for short-term and low dose, standard intralipid can be useful
  • HAL (aka TPN): Typically weaning calories is done before weaning volume. Cycling HAL (delivering over fewer hours) can be started prior to discharge. Watch for tolerance of the glucose infusion rate (JH: I prefer the terms HAL = hyperalimentation or PN=parenteral nutrition. TPN =total parenteral nutrition. Most patients are receiving parenteral nutrition but not total parenteral nutrition.)

Ostomy/Stool Output:

  • Output goals: Most pediatric patients can tolerate output of 50 mL/kg/day of ostomy output  (if being supported by PN), though less than 30 mL/kg/day is more physiologic
  • Iron: Parenteral iron is typically needed. Seattle team prefers ferric carboxymaltose as it may deliver enough iron for 6-12 months in one infusion
  • Acid suppression: While acid suppression can sometimes be beneficial by lowering gastric output, if possible avoid long-term use as it may increase risk of bacterial overgrowth along with other infections
  • Excessive stool output (via stoma or per rectum) is when it is more than the patient’s baseline. This should prompt investigation for potential causes including diet/osmotic agent, bacterial overgrowth and infections
  • Pancreatic enzymes: It is unclear if pancreatic enzymes (PERT, Relizorb) will improve stool output due to lack of data
  • Teduglutide can reduce the need for HAL. It is a hormone (like insulin) and sustained effects are generally not seen when it is stopped. However, especially in patients close to coming off HAL, it may be beneficial

Monitoring:

  • Nutrient deficiencies: Close monitoring for nutrient deficiencies is needed and often even more important when no longer receiving HAL
  • Urine sodium more than 30 is a goal. Sodium depletion interferes with growth and can contribute to other electrolye disturbances (eg. hypokalemia)

CLABSI:

  • Antibiotics: Treatment starts with a broad-spectrum antibiotic and wait to add specific gram-positive coverage unless ill-appearing or gram-positive organism starts growing. Vancomycin is not used frequently in Seattle due to concerns of renal toxicity. In patients with gram-positive infection, linezolid is often used
  • Minimum of 48 Hours For All Fevers: Everyone with SBS and with fever (greater than or equal to 100.4) stays for at least 48 hrs on broad spectrum IV antibiotics
  • Locks: Sodium bicarb locks help prevent CLABSI and appear to have similar infection prevention as ethanol locks. Ethanol locks have been difficult to get coverage.

SIBO:

  • Medications: Metronidazole is generally 1st line agent and gentamicin (IV formulation given enterally) is a 2nd line agent in Seattle. Rifaximin would be potentially their 1st line agent if it were easier to get covered

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Disclaimer: This blog, gutsandgrowth, assumes no responsibility for any use or operation of any method, product, instruction, concept or idea contained in the material herein or for any injury or damage to persons or property (whether products liability, negligence or otherwise) resulting from such use or operation. These blog posts are for educational purposes only. Specific dosing of medications (along with potential adverse effects) should be confirmed by prescribing physician.  Because of rapid advances in the medical sciences, the gutsandgrowth blog cautions that independent verification should be made of diagnosis and drug dosages. The reader is solely responsible for the conduct of any suggested test or procedure.  This content is not a substitute for medical advice, diagnosis or treatment provided by a qualified healthcare provider. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a condition.

Endoscopic Closure of Tracheoesophageal Fistulas in Pediatric Patients

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A Corcoran et al. J Pediatr Gastroenterol Nutr. 2026;82:828–839. Endoscopic tracheoesophageal fistula closure—Electrocautery combined with esophageal clip application in pediatric patients

This retrospective study with 15 patients shows the feasibility of endoscopic closure of tracheoesophageal fistulas (TEFs) in pediatric patients by a highly-specialized multidisciplinary team.

Background: Surgical repair of esophageal atresia (EA) is usually completed in infancy, yet TEF can still be identified later in life. These late-presenting fistulas fall into three general categories .5 First, true recurrences arise when the original site of TEF ligation breaks down, resulting in reformation of the fistula at the prior repair site. These occur in approximately 5%–10% of patients. Second, missed congenital fistulas were present at birth but went undetected during the initial evaluation or operation…Third, acquired fistulas can develop de novo in children without a history of EA, typically resulting from chronic inflammation and tissue breakdown due to an inciting injury, prolonged infection, or a retained foreign body. In children with repaired EA, similar fistulas may develop along a new tract months or years after surgery, often arising from the same underlying mechanisms.

Open repair of TEF can be a technically challenging operation, and depending on the location, it requires re-do thoracotomy or neck dissection. Given the morbidity and mortality associated with these open surgical approaches, there has been a growing trend toward endoscopic repair of recurrent, acquired and missed congenital TEF.4–9 

Key findings:

  • in 14 patients, 14 of 15 fistulas were closed successfully
  • Ten TEF were closed with electrocautery and esophageal clip placement while five were closed with cautery alone

Discussion Points:

  • Repeated procedures are often necessary to both achieve and ensure closure for endoscopically treated TEFs.

My take (borrowed from authors): Endoscopic closure using “electrocautery with or without esophageal clip application is a safe, minimally invasive, and effective treatment for all types of TEFs…While especially valuable for patients who are poor surgical candidates due to comorbidities, this approach may also be considered as a first-line option prior to surgical intervention in select cases.”

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View from Victoria Island near Bariloche, Argentina

Humor: MAHAspital

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This satire is particularly amusing for those who have watched “The Pitt.” Unfortunately, many of the health care policy changes under this administration will cause harm here and throughout the world for decades.

3/14/26 SNL: MAHAspital

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Reimbursement Reduction for Gastroenterology Practices

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JA Busam, ED Shah. Clin Gastroenterol Hepatol 2026; 24: 281-284. A Decade of Decreasing Reimbursement Strains Gastroenterology Practices and Threatens Their Independence

Background: “Over the past decade, a remarkable number of independent community gastroenterologists became part of larger groups, primarily due to financial concerns. Although the number of gastroenterologists increased between 2012 and 2020, the number of associated practices decreased by more than 650 (14%), with the number of physicians practicing in groups of less than 10 decreasing by nearly 1500 (35%).1 Simultaneously, the number of self-employed physicians decreased,2 while the number of hospital-employed and private equity affiliated physicians increased.3,4 Surveys of practices engaged in such consolidative behavior most often cite financial uncertainty given increased costs, decreased revenues, and continuing regulatory pressures, along with personal financial gains, as important motivations.5,6“

Methods: The authors examine how “Medicare reimbursement has affected independent, community practices over time, with a particular emphasis on hourly rates to account for any efficiencies in endoscopic procedure times over the past decade…[using] multiple datasets from the Centers for Medicare and Medicaid Services (CMS).”

Key finding:

  • “All major endoscopic procedures investigated brought in decreased associated professional revenue between 2014 and 2024 per unit billed. Most procedures saw a reduction between 30% and 40% in the amount of cash brought into the practice per procedure”
  • “Although independent practices faced tough decisions due to these trends, other health care stakeholders benefited. Concurrently, facility revenues, medical complexity,13 overall health expenditures,14 drug prices,15 and pharmacy benefit manager profits16 all increased, the latter by approximately 80%”

My take: This small study shows how “independent gastroenterology practice reimbursement decreased substantially since 2014 despite increasing patient complexity and capital flows into health care, threatening the viability of many community practices.” 

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Baby-Led Weaning and Less Picky Eaters

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FDMG Layug-Dionglay et al. J Pediatr Gastroenterol Nutr. 2026;82:801–811. Open Access! The association of baby‐led weaning and picky eating in children aged 2–5 years

Background: Baby‐led weaning (BLW) has emerged over the past decade as an alternative approach to traditional spoon‐feeding. BLW encourages infants to self‐feed nutritious whole foods during family mealtimes, without any pressure. It emphasizes infant autonomy over what, how much, and how quickly to eat from the foods offered.

Methods: A retrospective cross-sectional study was conducted in Metro Manila, Philippines (n=284)

Key findings:

  • Children who underwent strict BLW had a 95.4% lower likelihood of picky eating versus traditionally spoon-fed peers (p < 0.01)

Discussion points:

  • “In this study, picky eaters demonstrated a similar profile: Higher Food Avoidance traits (slowness in eating, satiety responsiveness, emotional undereating), and lower Food Approach traits (enjoyment of food, food responsiveness).”
  • “Strict BLW showed the lowest likelihood of picky eating, suggesting that the positive outcomes of the BLW approach requires consistent self-feeding of at least 90% of the time to experience its best effects. Meanwhile, BLW 51%–90% of the time (Predominant BLW) showed 55% lower likelihood.”
  • Limitation: “This study’s cross-sectional research design limits causal inference. Reverse causation is possible.”

My take: Allowing infants to self-feed likely reduces the tendency towards picky eating.

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A small section of Iguazu Falls

Variance with Guidelines in Hepatic Hemangiomas

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TL Mosher et al. J Pediatr Gastroenterol Nutr. 2026;82:765–769. Guidance adherence in the evaluation and management of hepatic hemangiomas in infants and children

Background: Hepatic hemangiomas are one of the visceral hemangiomas that can be seen and are categorized as infantile or congenital.1, 2 Infantile hepatic hemangiomas (IHH) develop in the first weeks-to-months of life, reach peak size typically by 3 months and often spontaneously involute without medical management within 1–2 years.3 Congenital hepatic hemangiomas (CHH) are present at birth and may rapidly involute, partially involute, or remain static for life.

Guidelines for screening with imaging and laboratory evaluation have been previously published and highlight differences between IHH and CHH.2 (Reference: Iacobas I, Phung TL, Adams DM, et al. Guidance document for hepatic hemangioma (infantile and congenital) evaluation and monitoring. J Pediatr. 2018; 203: 294-300 e2).” Screening with blood counts, fibrinogen, liver function tests, alpha-fetoprotein (AFP), thyroid function tests (TFTs), should be performed at diagnosis for both types of hemangiomas with frequency of repeat testing depending on whether IHH or CHH is diagnosed.2 Echocardiogram at diagnosis should be considered in both if patients have symptoms of cardiac failure. Serial monitoring with liver ultrasounds for at least 1 year or until stable size and vascularity twice in a row is recommended for CHH whereas continued monitoring with ultrasound until complete involution is recommended for IHH.2“

Methods: This study was a retrospective chart review with 64 patients

Key findings:

  • 29 (46%) had CHH and 34 (54%) had IHH
  • In those 47 patients who were monitored clinically, 62% (n = 29/47) had ALT/AST collected whereas only 51% (n = 24/47) TSH/FT4, 55% (n = 26/47) AFP, and only 26% (n = 12/47) had an INR drawn. Only about one-third (28%, n = 13/47) had a screening echocardiogram performed during evaluation
  • When comparing across hemangioma type, patients with CHH were significantly less likely than those with IHH to have TSH/FT4 (26% vs. 75%, p < 0.001) or AFP (39% vs. 71%, p = 0.002) drawn
  • Sixteen patients (25%), 6 with CHH and 10 with IHH, required active management.
    • Among CHH patients, one (17%) received propranolol prior to transfer to our institution, two (33%) underwent embolization, one (17%) surgical resection, and two (33%) required multiple modalities (i.e., surgery plus embolization). Two patients with CHH receiving multiple treatment modalities developed multi-system organ failure and died.
    • Among IHH patients, most patients (90%) received propranolol and one (10%) underwent surgical resection.

Discussion Points:

“Current guidance recommends screening for the complications of hepatic hemangiomas, particularly in patients with diffuse or multifocal hemangiomas, as they are at increased risk for heart failure and hypothyroidism.”

“Current guidance recommends monitoring of hepatic hemangiomas until complete involution of the hemangioma is documented.2, 10 These recommendations are in place given the devastating sequelae that can develop in patients with proliferation of hemangiomas that may be missed when not evaluated with serial abdominal imaging.”

My take: This study shows that about 25% of these patients require medical intervention and is a good reminder of the recommended evaluations.

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Disclaimer: This blog, gutsandgrowth, assumes no responsibility for any use or operation of any method, product, instruction, concept or idea contained in the material herein or for any injury or damage to persons or property (whether products liability, negligence or otherwise) resulting from such use or operation. These blog posts are for educational purposes only. Specific dosing of medications (along with potential adverse effects) should be confirmed by prescribing physician.  Because of rapid advances in the medical sciences, the gutsandgrowth blog cautions that independent verification should be made of diagnosis and drug dosages. The reader is solely responsible for the conduct of any suggested test or procedure.  This content is not a substitute for medical advice, diagnosis or treatment provided by a qualified healthcare provider. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a condition.

Noncirrhotic Portal Hypertension

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C Jarasvaraparn, et al. J Pediatr Gastroenterol Nutr. 2026;82:751–759. Clinical presentation, management, and outcomes for noncirrhotic portal hypertension in children

Background: Noncirrhotic portal hypertension (NCPH) is a rare condition marked by elevated portal venous pressure in the absence of cirrhosis and is caused by intrahepatic and extrahepatic pathways. NCPH is more common in Eastern countries than in Western countries. In the East, infectious diseases, particularly schistosomiasis in Africa, and poor socioeconomic conditions leading to chronic abdominal infections, are significant contributing factors. On the other hand, Western countries see a higher prevalence of NCPH linked to hypercoagulable disorders and potential genetic predispositions.

Methods: This was a  single-center retrospective study of 63 pediatric patients form 2000-2024.

Key findings:

  • The three most common etiologies included extrahepatic portal vein obstruction (EHPVO) in 27 (42.8%), congenital hepatic fibrosis (CHF) in 17 (27%), and nodular regenerative hyperplasia (NRH) in 10 (15.9%). 6 (9.5%) patients had idiopathic noncirrhotic portal hypertension
  • Most patients presented with incidental splenomegaly (20; 32%) or gastrointestinal (GI) bleeding (20; 32%)
  • Mortality was seen in 5% of children in this series

My take: More than two decades ago, a patient was referred to me with dyspnea as the pulmonologist suspected that this was due to portal hypertension/hepatopulmonary syndrome. Ultimately, after evaluation by a colleague, she was diagnosed with idiopathic noncirrhotic portal hypertension and underwent a successful liver transplantation. This condition is very difficult to diagnose if you are unaware of its existence.

Fatigue in Pediatric Inflammatory Bowel Disease

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MD Stutvoet et al. J Pediatr Gastroenterol Nutr. 2026;82:699–707. Open Access! Fatigue in pediatric inflammatory bowel disease: Explained by transdiagnostic and disease-focused factors

Methods: “The PROactive cohort is a longitudinal study that collects transdiagnostic patient-reported outcomes on fatigue, daily life participation, and psychosocial well-being in children with chronic conditions. It is based at the Wilhelmina Children’s Hospital in the Netherlands.” this study enrolled 127 patients with IBD.

Key findings:

  • Fatigue is highly prevalent in pediatric IBD, with 29% of patients reporting severe fatigue—despite most being in clinical remission
  • 78% of variance in fatigues explained by transdiagnostic lifestyle, psychological and social factors
Fatigue prevalence in pediatric IBD. For reference, fatigue prevalence measured using the same “general fatigue” subscale of the MFS-GCS is also shown for other chronic childhood diseases15 and the general Dutch population.19 

Discussion Points:

  • “Clinical disease activity was significantly associated with fatigue in univariate analysis (p < 0.01). This is consistent with earlier studies showing modest associations between clinical disease activity and fatigue2–4, 33–35 and no association with biochemical markers such as FC, CRP, and anemia.2–4, 11, 35 The discrepancy between clinical and biological markers may reflect the inclusion of functional limitations in the clinical disease activity scores, and their weak correlation with measures of biological disease activity as FC.36… Taken together, the association with clinical disease activity shows that fatigue may be closely linked to perceived disease-related limitations rather than inflammatory activity alone.”
  • “Transdiagnostic factors—including depressive symptoms, poor sleep, and social functioning—were strongly associated with fatigue, consistent with previous findings in pediatric IBD cohorts,3, 4, 33 and other chronic diseases.14, 16…Our results emphasize the complex interactions among psychosocial factors and support a more integrative approach to fatigue assessment. “

My take (borrowed in part from the authors): “While disease activity may initially precipitate fatigue, other factors—such as poor sleep or school pressure—can perpetuate it, even after inflammation resolves.”

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