The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

International audienceCurrent sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans

Spontaneous resolution of a large caustic tracheo-esophageal fistula following multimodal esophageal rest: A case report

Background: Esophageal ulceration is the most common complication of button battery (BB) ingestion. This can progress to development of tracheo-esophageal fistula (TEF). Operative intervention is the standard, as spontaneous healing is not expected. We describe a patient who had complete spontaneous resolution of caustic TEF by multimodal “complete” esophageal rest without operative repair. Case: A 20-month-old girl ingested a BB which resulted in TEF with mediastinitis. After 8 days, endoscopy demonstrated a large (1.5cm) TEF. “Complete” esophageal rest was imposed with a multimodal approach: nothing by mouth; pharmacologic suppression of oral secretions and gastric acid; and placement of a gastrojejunostomy tube for gastric venting and jejunal feeding.She was discharged home 14 days later, continuing esophageal rest. One month later, endoscopy revealed complete resolution of the TEF. Oral feeding was resumed 3 months following the initial ingestion when vocal fold dysfunction (and aspiration) resolved. There was no suggestion of recurrent fistula or diverticulum on the last endoscopy and exam at 15, 19, and 49 months post injury. Conclusion: A few prior reports of non-operative management of TEF following disc battery ingestion have been published, with length of stays between 28 and 82 days. We report a case suggesting that even with a large caustic TEF, multimodal “complete” esophageal rest can allow complete spontaneous resolution, and with shorter duration of hospitalization. This experience prompts consideration of a novel non-operative approach. Even if complete resolution is not achieved, eventual operation would benefit from partial contracture, resolution of mediastinitis, and time for planning and preparation

Successful treatment of eosinophilic esophagitis with ciclesonide

The abstract is included in the text

CT imaging features of eosinophilic colitis in children

Background Eosinophilic colitis (EC) is a gastrointestinal disease of undetermined etiology whose clinical features overlap with those of the inflammatory bowel diseases. To the best of our knowledge, the CT imaging features of EC have not been described in children. Objective To report and analyze the clinical, imaging and histological findings in seven children with EC. Materials and methods Children with EC were identified in a pediatric pathology database, and those with CT imaging within 2 months of diagnosis were included, totaling seven children. Clinical, imaging and pathological features were reviewed and analyzed. Results The most common presenting symptoms were abdominal pain, bloody diarrhea and rectal bleeding. EC was characterized as a dense and predominantly eosinophilic inflammatory infiltrate in the lamina propria or epithelium without granulomas. CT scans were abnormal in six children (86%), demonstrating colonic wall thickening, predominantly cecal, in five (71%), mild to moderate terminal ileal thickening in two (29%), and pneumatosis in one (14%). Right colonic involvement was greater than terminal ileal involvement. Conclusion CT imaging findings in children with EC include right colonic wall thickening of variable extent downstream and absent or mild involvement of the terminal ileum. EC should be considered in the differential diagnosis in children presenting with abdominal pain and bloody diarrhe

Effect of Proton Pump Inhibitor on Esophageal Eosinophilia

Objective: Differentiation between the common etiologies of dense esophageal eosinophilia such as gastroesophageal reflux disease (GERD) and eosinophilic esophagitis can be difficult. We hypothesized that histologic features may provide diagnostic clues concerning the etiology of esophageal eosinophilia. Methods: We performed a retrospective chart review of 204 children with the diagnosis of esophagitis characterized by 15 eosinophils (eos) per highpower field (HPF) in at least 1 biopsy. We then restricted our analysis to subjects who had received at least 8 weeks of only proton pump inhibitors (PPIs) followed by endoscopy and who had a clinicopathologic response to this treatment. Symptoms, endoscopic findings, and pathologic descriptions were reviewed and an eosinophil peroxidase (EPX) index was determined to assess for degranulation/eosinophil activation. Results: Of the 204 identified charts, 7 subjects identified met the inclusion criteria. Five of these 7 patients showed a clinicopathologic response to PPIs after their follow-up endoscopy, (mean peak eosinophil count: 92 vs 5 eos/HPF, and EPX index: 39.2 vs 14.6, pre- and posttreatment, respectively). Two patients experienced initial resolution of symptoms and esophageal eosinophilia with PPI therapy; however, within 17–23 months they redeveloped symptoms and esophageal eosinophilia while receiving PPI therapy at the time of a third endoscopy (mean peak eosinophil count: 40 vs 11 vs 36 eos/HPF, and EPX index: 44 vs 21 vs 36.5, pre-, post- and posttreatment, respectively). No clinicopathologic features or degranulation patterns differentiated subjects with GERD/PPI responsive esophageal eosinophilia from those who had transient response to PPI treatment. Conclusions: No clinicopathologic features differentiated subjects who responded to PPI treatment. PPI treatment can be helpful to exclude GERD and PPI responsive esophageal eosinophilia but long-term followup is critical in the management of esophagitis

Esophageal human β-defensin expression in eosinophilic esophagitis.

Background: Defensins are antimicrobial peptides expressed on mucosal surfaces that contribute to maintaining intestinal homeostasis by providing innate defense mechanisms for the epithelia. Defensin expression is altered in a number of diseases that affect mucosal surfaces, such as atopic dermatitis, allergic rhinitis, and inflammatory bowel disease. Similar to atopic dermatitis, eosinophilic esophagitis (EoE) is a chronic disease in which the squamous epithelial surface is affected by a similar TH2 microenvironment and eosinophilpredominant inflammation. Therefore, we hypothesized that defensin expression would be decreased in EoE. Methods: To address this, we measured defensin expression invitro in cell lines derived from patients with EoE (EoE1-T) or gastroesophageal reflux disease (GERD) (NES-G4T cells) and ex vivo in esophageal mucosal biopsy samples from children with EoE or GERD and control children without esophageal disease. Results: Interleukin-5 induced a decrease in human β-defensin (hBD) -1 and hBD3 expression in EoE1-T but not in NES-G4T cells. Compared with esophageal biopsy specimens from GERD and control children, specimens from EoE pediatric patients revealed a significant decrease in mRNA and protein expression for hBD1 and hBD3. Conclusion: Diminished expression of hBD1 and hBD3 may make the esophageal epithelium more susceptible to the development and/or perpetuation of EoE

Novel Device to Sample the Esophageal Microbiome— The Esophageal String Test

A growing number of studies implicate the microbiome in the pathogenesis of intestinal inflammation. Previous work has shown that adults with esophagitis related to gastroesophageal reflux disease have altered esophageal microbiota compared to those who do not have esophagitis. In these studies, sampling of the esophageal microbiome was accomplished by isolating DNA from esophageal biopsies obtained at the time of upper endoscopy. The aim of the current study was to identify the esophageal microbiome in pediatric individuals with normal esophageal mucosa using a minimally invasive, capsule-based string technology, the EnterotestTM. We used the proximal segment of the Enterotest string to sample the esophagus, and term this the ‘‘Esophageal String Test’’ (EST). We hypothesized that the less invasive EST would capture mucosal adherent bacteria present in the esophagus in a similar fashion as mucosal biopsy. EST samples and mucosal biopsies were collected from children with no esophageal inflammation (n = 15) and their microbiome composition determined by 16S rRNA gene sequencing. Microbiota from esophageal biopsies and ESTs produced nearly identical profiles of bacterial genera and were different from the bacterial contents of samples collected from the nasal and oral cavity. We conclude that the minimally invasive EST can serve as a useful device for study of the esophageal microbiome

Esophageal Microbiome in Eosinophilic Esophagitis

Objective: The microbiome has been implicated in the pathogenesis of a number of allergic and inflammatory diseases. The mucosa affected by eosinophilic esophagitis (EoE) is composed of a stratified squamous epithelia and contains intraepithelial eosinophils. To date, no studies have identified the esophageal microbiome in patients with EoE or the impact of treatment on these organisms. The aim of this study was to identify the esophageal microbiome in EoE and determine whether treatments change this profile. We hypothesized that clinically relevant alterations in bacterial populations are present in different forms of esophagitis. Design: In this prospective study, secretions from the esophageal mucosa were collected from children and adults with EoE, Gastroesophageal Reflux Disease (GERD) and normal mucosa using the Esophageal String Test (EST). Bacterial load was determined using quantitative PCR. Bacterial communities, determined by 16S rRNA gene amplification and 454 pyrosequencing, were compared between health and disease. Results: Samples from a total of 70 children and adult subjects were examined. Bacterial load was increased in both EoE and GERD relative to normal subjects. In subjects with EoE, load was increased regardless of treatment status or degree of mucosal eosinophilia compared with normal. Haemophilus was significantly increased in untreated EoE subjects as compared with normal subjects. Streptococcus was decreased in GERD subjects on proton pump inhibition as compared with normal subjects. Conclusions: Diseases associated with mucosal eosinophilia are characterized by a different microbiome from that found in the normal mucosa. Microbiota may contribute to esophageal inflammation in EoE and GERD

Microbiome phylum-level diversity is similar in esophageal, oral and nasal microenvironments.

<p>Microbiome diversity was measured from DNA samples taken from the esophageal mucosa, oral and nasal samples as identified using 454 pyrosequencing. Each point represents the number of Taxa present in each sample. The mean ± standard error of the mean are presented.</p