Ensembl 2009.

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases, and other information for chordate, selected model organism and disease vector genomes. As of release 51 (November 2008), Ensembl fully supports 45 species, and three additional species have preliminary support. New species in the past year include orangutan and six additional low coverage mammalian genomes. Major additions and improvements to Ensembl since our previous report include a major redesign of our website; generation of multiple genome alignments and ancestral sequences using the new Enredo-Pecan-Ortheus pipeline and development of our software infrastructure, particularly to support the Ensembl Genomes project (http://www.ensemblgenomes.org/).

A distinctive aphthous ileitis linked to Ancylostoma caninum.

Ileal ulceration is diagnosed commonly at colonoscopy in northeastern Australia. This observation has occurred contemporaneously with the description of a painful enteritis caused through supposedly rare infections by Ancylostoma caninum, the cosmopolitan dog hookworm. In this study, we describe the morphology and prevalence of ileal ulcers and investigate their cause. There were 182 patients with a distinctive aphthous ileitis highlighted by haemorrhage into the tips of surrounding villi. The annual rate reached 4.7% of ileal examinations. Eosinophilic enteritis was the characteristic, but inconsistent, histological appearance. Ulceration was linked to infection by A. caninum through serological testing and, in three patients, by the retrieval of single hookworms. Affected patients were also more likely to own a dog (53%) than the total colonoscopic population (43%; P < 0.02). The monthly rates of diagnosis were related to climate with fewest recordings during winter. Pain was the chief indication for colonoscopy (49%), proportionally higher than in controls (28%; P < 0.0001). Patients with ulcers had increased blood eosinophil, immunoglobulin E and serological values. These results were higher still in the subset with pain compared with the rest. Most patients, however, had colonoscopy performed for unrelated reasons, such as bowel cancer surveillance, and were identified as having subclinical ulceration (rate 3.2%). The findings establish a distinctive aphthous ileitis characterized by tissue eosinophilia. The cause has been tentatively linked to canine hookworms. It is proposed that infection in this geographic region is common and only rarely does a painful enteritis develop as a consequence of hypersensitization.

Human enteric infection with canine hookworms.

OBJECTIVE: To describe a zoonotic ancylostomiasis (canine), acquired from domestic pets by patients living in developed, urban communities. DESIGN: An 8-year, retrospective case study. SETTING: A clinical gastroenterologic practice in Townsville and a university parasitology department in Brisbane, Australia. PATIENTS: Nine patients, each with enteric hookworm infection diagnosed by finding a single organism in situ; five were treated by us, and the rest were referred to us for parasite identification. MEASUREMENTS: Clinical and demographic data, complete blood examinations, total serum immunoglobulin E assay, and serologic testing with enzyme-linked immunosorbent assay and Western blot using excretory-secretory antigens of Ancylostoma caninum. Gut biopsy specimens were examined histologically, and hookworms were identified using morphologic criteria. RESULTS: The infections in three of the patients were diagnosed during the initial 6 years and six in the last 2 years. All owned a dog and described activity potentially exposing them to infection with canine hookworm larvae. Three patients had a laparotomy for acute abdominal pain, and six had colonoscopies (five with pain and one without symptoms). Six of the nine had blood eosinophilia (mean, 0.97 x 10(9)/L), and five of eight had elevated immunoglobulin E levels (mean level, 756 micrograms/L); six of eight had eosinophilic inflammation of the gut. In six patients, the worm was identified as A. caninum, whereas in three, damage to the specimen did not allow specific identification; however, they were unlikely to be human parasite species. Although all parasites were in the adult stage, none were sexually mature. Positive serologic findings in seven of the eight patients tested confirmed presence of antibody to the parasite. CONCLUSIONS: Human enteric infections with A. caninum are being diagnosed more frequently in northeastern Australia. Although infection may be subclinical, the chief symptom is abdominal pain, sometimes sudden and severe. The pathologic finding is focal or diffuse eosinophilic inflammation caused by a type 1 hypersensitivity response to secreted antigens. Infection by sexually immature worms is scant and nonpatent, indicating poor adaptation to the human host. Serologic testing assists in identification of occult infection. Advanced hygiene and sanitation afford little protection because the parasite reservoir is a large and growing pool of infected domestic pets.

Comparative evaluation of three selective media and a nonselective medium for the culture of Helicobacter pylori from gastric biopsies.

Plating on solid media is the standard technique used in most laboratories for the isolation of Helicobacter pylori from gastric biopsies. Recently, various selective media were developed for this purpose. We compared and evaluated three selective media, Skirrow's, Dent's CP, and modified Glupczynski's Brussels campylobacter charcoal media, and chocolate agar medium for the isolation of H. pylori. Gastric biopsies taken from a total of 203 patients were plated in parallel on all four media. An isolation rate of 51% (104 of 203) was obtained with a combination of all four media. Of the 104, 92 (88%) were positive with Dent's medium and with modified Glupczynski's medium. Skirrow's medium gave the highest isolation rate, 96% (100 of 104). However, growth of H. pylori was scant (only one to five colonies) when growth occurred on Skirrow's medium alone. Overall, modified Glupczynski's medium provided significantly heavier growth. Chocolate agar medium yielded a 76% (79 of 104) positivity rate. We recommend the use of a combination of two selective media for the maximum recovery of H. pylori from antral biopsies.