About

Alain J Benitez, MD, MSTR, is a Research Assistant Professor of Pediatrics specializing in Gastroenterology, Hepatology, and Nutrition at the Children's Hospital of Philadelphia. He serves as the Clinical Research Director at the Suzi and Scott Lustgarten Center for GI Motility and is a faculty member at the Institute for Translational Medicine and Therapeutics at the University of Pennsylvania. His educational background includes a BA in Biology from Florida International University, an MD from Universidad Iberoamericana (UNIBE), and a Master of Science in Translational Research from the University of Pennsylvania School of Medicine. His research focuses on pediatric gastrointestinal motility, dietary patterns in children with genetic syndromes such as 22q11.2 deletion syndrome, and the development of biomarkers for gastrointestinal disorders. He has contributed to studies on virtual wellness programs, micronutrient imbalances, gastric mapping, colonic manometry analysis, and the microbiome in pediatric gastrointestinal conditions. Dr. Benitez's work emphasizes translational research aimed at improving diagnosis and treatment of pediatric GI motility disorders.

Research topics

• Internal medicine
• Medicine
• Biology
• Gastroenterology
• Pathology

Selected publications

• QUANTITATIVE SMALL BOWEL MOTILITY ASSESSMENT ON MAGNETIC RESONANCE ENTEROGRAPHY IN PEDIATRIC CROHN'S DISEASE: ASSOCIATIONS WITH CLINICAL PHENOTYPE AND SURGICAL OUTCOME

  Gastroenterology · 2026-01-22

  article
  PublisherDOI

• QUANTITATIVE SMALL BOWEL MOTILITY ASSESSMENT ON MAGNETIC RESONANCE ENTEROGRAPHY IN PEDIATRIC CROHN’S DISEASE: ASSOCIATIONS WITH CLINICAL PHENOTYPE AND SURGICAL OUTCOME

  Inflammatory Bowel Diseases · 2026-01-22

  article

  Abstract The natural history of pediatric Crohn’s disease (CD) can lead to complications such as strictures and fistulae, increasing the risk of surgery. Magnetic resonance enterography (MRE) is unique in its ability to provide anatomic and functional characterization of intestinal morphological abnormalities. Prior adult studies have linked altered small bowel motility to strictures and fibrosis, but pediatric data are limited. In addition, it is unclear if motility can predict surgical risk in children with CD. Our study aims to evaluate motility in the small bowel and its association with clinical phenotype and surgical outcome in pediatric CD and compare it to patients with irritable bowel syndrome (IBS) and healthy controls (HC). In this single-center retrospective study we included pediatric CD patients with macroscopic ileal involvement (Paris classification L1 or L3) who underwent cine-MRE from 2012-2024. The images were anonymized and uploaded to the Entrolytics.io website by Motilent. Two pediatric radiologists identified the proximal, distal, and terminal ileum on dynamic cine-MRI sequences to attain GIQuant motility scores., Clinical, laboratory and additional MRE parameters were collected. GIQuant scores were collected also for patients with IBS and HC, who had radiologically normal studies. Patients who had more than one MRE for follow up were included in a subcohort to analyze longitudinal changes in intestinal motility. Descriptive and regression statistical analysis was performed. 33 pediatric CD patients (median age 14.7 years), 38 IBS patients and 9 HC were included. In the CD cohort, 79% had L3 ileocolonic and 21% L1 ileal disease, and 24% were inflammatory, 39% stricturing and 37% both stricturing and penetrating. Ileal and ileocolonic CD patients had lower mean terminal ileum GIQuant score (148.3±94.4) than IBS (271.3±112.4) and HC (269.6±74.7) (p < 0.01), while the mean proximal ileum GIQuant score was lower in CD (293.68±106.83) vs IBS (372.31±117.89) (p < 0.05). CD patients who underwent surgery showed similar terminal ileum scores to those who did not undergo surgery (median 120.3 (IQR (87.1-145.5)) vs 130.7(111.5-221.7)) but more frequently had mesenteric fatty proliferation (79% vs 29%). GIQuant scores did not differ significantly between complicated phenotypes (B2 or B2/B3) and inflammatory (B1) ones. In the longitudinal analysis (n = 12), an increase in terminal ileum GIQuant correlated with an increase in albumin. Ileal motility is reduced in children with CD compared to IBS and HC, consistent with prior studies. In our cohort, motility differences across CD phenotypes and surgical outcome were minimal. Additional studies are necessary to understand how quantitative motility assessment can provide complementary information on disease characterization in pediatric CD. Figure 1:GIQuant scores in the proximal, distal and terminal ileum of children with Crohn’s disease (CD), irritable bowel syndrome (IBS) and healthy controls (HC).

  PublisherDOI

• Clinical, manometric, genetic, and histologic associations in pediatric intestinal pseudo‐obstruction: A case series

  Journal of Pediatric Gastroenterology and Nutrition · 2026-01-01

  articleOpen access

  OBJECTIVES: Pediatric intestinal pseudo-obstruction (PIPO) is a severe bowel motility disorder characterized by impaired propulsion of gastrointestinal contents without mechanical obstruction. PIPO encompasses congenital and acquired disorders, including neuropathies, myopathies, and mesenchymopathies. PIPO presents with abdominal distension, bilious vomiting, and severe constipation. Diagnosis is based on objective measures of neuromuscular dysfunction, dilated bowel on imaging, parenteral and/or enteral nutrition dependence, and genetic or metabolic testing. Antroduodenal manometry permits objective assessment of proximal bowel neuromuscular function. Genetic testing is increasingly valuable although causes of PIPO often remain incompletely defined. Understanding genotype-phenotype correlations is essential for clarifying disease mechanisms and guiding therapies. This study aimed to characterize the clinical and genetic profiles of children with PIPO, utilizing manometric data for subtype classification. METHODS: A retrospective chart review was conducted at a tertiary care pediatric medical center, with inclusion criteria of PIPO diagnosis, completed manometry testing, and genetic evaluation. RESULTS: Nineteen children met inclusion criteria. Antroduodenal manometry classified 59% as neuropathic, 35% as myopathic, and one with mixed neuropathic and myopathic dysfunction. Genetic testing revealed pathogenic ACTG2 mutations in all myopathic cases, while neuropathic PIPO exhibited more genetic variability. Histopathology was inconsistent and often nonspecific. Therapeutic approaches focused on nutritional support and promotility agents, with surgical intervention more common in myopathic cases. CONCLUSIONS: This study highlights the association of ACTG2 mutations with a myopathic phenotype, and genetic diversity in neuropathic PIPO, emphasizing the need for further research to improve phenotyping to enhance diagnosis and treatment.

  PublisherOA PDFDOI

• Histologic Response Is Associated With Improved Esophageal Distensibility and Symptom Burden in Pediatric Eosinophilic Esophagitis

  Gastroenterology · 2025-08-18 · 3 citations

  articleOpen access
  PublisherOA PDFDOI

• 590 Differences in gastric slow wave propagation in youth and young adults with CF compared to healthy controls

  Journal of Cystic Fibrosis · 2025-10-01

  article
  PublisherDOI

• Tu2026: CAN BODY SURFACE COLONIC MAPPING DETECT THE COLONIC BISACODYL RESPONSE IN CONSTIPATED PATIENTS? RESULTS FROM A PILOT STUDY

  Gastroenterology · 2025-05-01

  articleOpen access
  PublisherDOI

• The healthcare burden imposed by children with gastroparesis and the shift imposed by COVID-19

  Frontiers in Pediatrics · 2025-07-22

  articleOpen access

  Goals: We aim in this study to report the trend of annual economic burden of children admitted with Gastroparesis (GP) over the last 10 years and evaluate the possible effect of COVID-19. Background: Inpatient healthcare utilization by children with GP was last reported between 2004 and 2013. Since then, the effect of the COVID-19 pandemic has not been evaluated. Study: We used the Pediatric Health Information System (PHIS) database to retrieve data recorded in 42 children's hospitals between January 2014 and September 2023 with GP being a primary or secondary diagnosis. Results: A total of 20,293 pediatric gastroparesis admissions were documented. The total cost was $1,323,541,518. The average admission cost was $65,222 and the median was $18,921. Reviewing the possible effect of COVID-19, we found that the highest annual mean and median costs were in 2020, and the highest annual total cost was in 2022. The costs are divided over 6 different categories: clinical, imaging, lab, pharmacy, supplies, and others, with the highest impacts resulting from these 3 categories: clinical, pharmacy, and others. The mean and median costs differ in the 4 regions, Northeast, South, Midwest and West, with the highest in the Midwest. Of all the admissions, 15.6% had a code for nasogastric tube (NG) present, 40.7% used the code for a gastrostomy tube (G-tube), 10.0% had a code for a jejunostomy tube (J-tube) and 24.6% required nutrition support via surgical feeding tubes. Conclusion: This PHIS database study confirms an upward trend in the annual healthcare utilization by children admitted with GP, resulting in an upward trend in the total economic burden on children's hospitals emphasized by the COVID-19 pandemic.

  PublisherOA PDFDOI

• Body Surface Gastric Mapping Delineates Specific Patient Phenotypes in Adolescents With Functional Dyspepsia and Gastroparesis

  Neurogastroenterology & Motility · 2025-03-19 · 10 citations

  articleOpen access

  BACKGROUND: Diagnosing pediatric patients with chronic gastroduodenal symptoms is clinically challenging, with the role of gastric emptying testing being controversial. Body Surface Gastric Mapping (BSGM) is a new diagnostic test that can identify specific patient phenotypes in adults with gastric dysfunction. This study evaluates whether BSGM can delineate specific phenotypes in adolescents and provide clinically meaningful distinctions between gastroparesis and functional dyspepsia diagnoses. METHODS: A prospective cross-sectional study recruited adolescents aged 12 to 21 between 2022 and 2024. Controls were recruited from New Zealand and patients from the Children's Hospital of Philadelphia, USA. BSGM followed a standardized protocol, including simultaneous symptom reporting and completion of validated symptom, psychometric, and physical health questionnaires. KEY RESULTS: Fifty-six subjects were recruited (31 controls, 25 patients); median age 16; 96% of patients were female. Control data showed that adult reference intervals provided an acceptable interpretation framework. Patients with FD (n = 10) and gastroparesis (n = 15) had common symptoms, mental health, quality of life, and functional disability (all p > 0.05). Three distinct BSGM phenotypes were identified: BSGM Normal (n = 10), BSGM Delay (n = 8), and Low Stability/Low Amplitude (n = 7), having spectral differences in BMI-Adjusted Amplitude 34.6 versus 39.1 versus 19.9 (p = 0.01) and Gastric Alimetry Rhythm Index: 0.45 versus 0.45 versus 0.19 (p = 0.003). BSGM phenotypes demonstrated differences in symptoms (nausea p = 0.04), physical health (p = 0.04), and psychometrics (anxiety p = 0.03). CONCLUSION AND INFERENCES: Adolescents with FD and gastroparesis have overlapping clinical profiles, making treatment challenging. Conversely, employing BSGM to categorize patients into distinct phenotypes reveals clinically relevant differences, offering avenues for individualized therapeutic pathways.

  PublisherOA PDFDOI

• Pediatric Culinary Medicine: Current Status, Challenges and Opportunities

  Current Gastroenterology Reports · 2025-12-29

  articleOpen access
  PublisherOA PDFDOI

• Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants

  Microbiome · 2025-01-24 · 10 citations

  articleOpen access1st authorCorresponding

  BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry. RESULTS: Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition. CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.

  PublisherOA PDFDOI

Frequent coauthors

• Amanda B. Muir

  Children's Hospital of Philadelphia

  79 shared

• Jonathan M. Spergel

  Children's Hospital of Philadelphia

  50 shared

• Gary W. Falk

  32 shared

• Mei‐Lun Wang

  OSE Immunotherapeutics (France)

  31 shared

• Kelly A. Whelan

  Temple University

  21 shared

• Kristin Fiorino

  Children's Hospital of Philadelphia

  20 shared

• Calies Menard‐Katcher

  19 shared

• Glenn T. Furuta

  Children's Hospital Colorado

  18 shared

Education

• B.A., Biology

  Florida International University

  2001

• M.D.

  Universidad Iberoamericana (UNIBE)

  2007

• Other, Translational Research

  University of Pennsylvania School of Medicine

  2021