Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.

The management of paediatric airway emergencies is part of ENT practice. The most common conditions are acute viral laryngotracheobronchitis (croup), acute epiglottitis and bacterial tracheitis. Management of these conditions is significantly different and accurate diagnosis is crucial. We performed a retrospective analysis of all acute airway admissions to the paediatric intensive care unit (PICU) at the Royal Belfast Hospital for Sick Children from 1990 to 2003. The results showed a gradual decrease in the number of admissions due to croup. Acute epiglottitis admissions decreased markedly after 1992 but rose again in 2000, with a peak in 2002. Bacterial tracheitis is now the most common paediatric airway emergency requiring PICU admission and its incidence has been steadily increasing since 1990, peaking in 2003. The total number of admissions showed little change over the 14-year period audited. The significant shift in the nature of these conditions and these findings confirm the ongoing requirement for caution in dealing with a suspected airway emergency.

Haemophilus somnus (‘Histophilus somni’) is a Gram-negative bacterium and opportunistic pathogen associated with multisystemic diseases of bovines. Some strains of H. somnus are relatively avirulent, but are biochemically and antigenically similar to the virulent strains. Several virulence factors have been identified in H. somnus, of which lipo-oligosaccharide phase variation, induction of apoptosis, intraphagocytic survival and immunoglobulin Fc binding proteins have been well studied. The sequencing of the genomes of two strains of H. somnus has facilitated the identification of genes responsible for distinctive attributes within this species and related bacteria. The genetic characterization of this bacterium will enhance our understanding of H. somnus virulence factors and facilitate the development of new and improved vaccines. This review presents an overview of H. somnus virulence factors, their role in resistance to host defenses and pathogenesis, and the host immune response to this bacterium. Current areas of investigation in the post-genomic era and recent insights into new pathogenic mechanisms are also discussed.