Lucas R. Hoffman

Three Clinically Distinct Chronic Pediatric Airway Infections Share a Common Core Microbiota

RATIONALEnDNA-based microbiological studies are moving beyond studying healthy human microbiota to investigate diverse infectious diseases, including chronic respiratory infections, such as those in the airways of people with cystic fibrosis (CF) and non-CF bronchiectasis. The species identified in the respiratory secretion microbiota from such patients can be classified into those that are common and abundant among similar subjects (core) versus those that are infrequent and rare (satellite). This categorization provides a vital foundation for investigating disease pathogenesis and improving therapy. However, whether the core microbiota of people with different respiratory diseases, which are traditionally associated with specific culturable pathogens, are unique or shared with other chronic infections of the lower airways is not well studied. Little is also known about how these chronic infection microbiota change from childhood to adulthood.nnnOBJECTIVESnWe sought to compare the core microbiota in respiratory specimens from children and adults with different chronic lung infections.nnnMETHODSnWe used bacterial 16S rRNA gene pyrosequencing, phylogenetic analysis, and ecological statistical tools to compare the core microbiota in respiratory samples from three cohorts of symptomatic children with clinically distinct airway diseases (protracted bacterial bronchitis, bronchiectasis, CF), and from four healthy children. We then compared the core pediatric respiratory microbiota with those in samples from adults with bronchiectasis and CF.nnnMEASUREMENTS AND MAIN RESULTSnAll three pediatric disease cohorts shared strikingly similar core respiratory microbiota that differed from adult CF and bronchiectasis microbiota. The most common species in pediatric disease cohort samples were also detected in those from healthy children. The adult CF and bronchiectasis microbiota also differed from each other, suggesting common early infection airway microbiota that diverge by adulthood. The shared core pediatric microbiota included both traditional pathogens and many species not routinely identified by standard culture.nnnCONCLUSIONSnOur results indicate that these clinically distinct chronic airway infections share common early core microbiota, which are likely shaped by natural aspiration and impaired clearance of the same airway microbes, but that disease-specific characteristics select for divergent microbiota by adulthood. Longitudinal and interventional studies will be required to define the relationships between microbiota, treatments, and disease progression.

Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis

Cystic fibrosis gastrointestinal disease includes nutrient malabsorption and intestinal inflammation. We show that the abundances of Escherichia coli in fecal microbiota were significantly higher in young children with cystic fibrosis than in controls and correlated with fecal measures of nutrient malabsorption and inflammation, suggesting that E. coli could contribute to cystic fibrosis gastrointestinal dysfunction.

Pseudomonas aeruginosa Phenotypes Associated with Eradication Failure in Children with Cystic Fibrosis

BACKGROUNDnPseudomonas aeruginosa is a key respiratory pathogen in people with cystic fibrosis (CF). Due to its association with lung disease progression, initial detection of P. aeruginosa in CF respiratory cultures usually results in antibiotic treatment with the goal of eradication. Pseudomonas aeruginosa exhibits many different phenotypes in vitro that could serve as useful prognostic markers, but the relative relationships between these phenotypes and failure to eradicate P. aeruginosa have not been well characterized.nnnMETHODSnWe measured 22 easily assayed in vitro phenotypes among the baseline P. aeruginosa isolates collected from 194 participants in the 18-month EPIC clinical trial, which assessed outcomes after antibiotic eradication therapy for newly identified P. aeruginosa. We then evaluated the associations between these baseline isolate phenotypes and subsequent outcomes during the trial, including failure to eradicate after antipseudomonal therapy, emergence of mucoidy, and occurrence of an exacerbation.nnnRESULTSnBaseline P. aeruginosa isolates frequently exhibited phenotypes thought to represent chronic adaptation, including mucoidy. Wrinkly colony surface and irregular colony edges were both associated with increased risk of eradication failure (hazard ratios [95% confidence intervals], 1.99 [1.03-3.83] and 2.14 [1.32-3.47], respectively). Phenotypes reflecting defective quorum sensing were significantly associated with subsequent mucoidy, but no phenotype was significantly associated with subsequent exacerbations during the trial.nnnCONCLUSIONSnPseudomonas aeruginosa phenotypes commonly considered to reflect chronic adaptation were observed frequently among isolates at early detection. We found that 2 easily assayed colony phenotypes were associated with failure to eradicate after antipseudomonal therapy, both of which have been previously associated with altered biofilm formation and defective quorum sensing.

Cystic Fibrosis: Microbiology and Host Response.

The earliest descriptions of lung disease in people with cystic fibrosis (CF) showed the involvement of 3 interacting pathophysiologic elements in CF airways: mucus obstruction, inflammation, and infection. Over the past 7 decades, our understanding of CF respiratory microbiology and inflammation has evolved with the introduction of new treatments, increased longevity, and increasingly sophisticated laboratory techniques. This article reviews the current understanding of infection and inflammation and their roles in CF lung disease. It also discusses how this constantly evolving information is used to inform current therapeutic strategies, measures and predictors of disease severity, and research priorities.

WS21.2 Sequence–function analysis of clinical LasR variants of Pseudomonas aeruginosa

Objectives: Advances in genome sequencing have made it feasible to sequence multiple genomes of the same lineage of bacterial pathogens as they evolve in their human hosts. Nonetheless, only little is known about how evolution processes compare between genotypic different lineages of the same pathogenic species when they evolve within their human hosts. Methods: Here, we analyze the genomes of 474 isolates of P. aeruginosa sampled from 34 young Danish CF patients. Our phylogenetic analysis reveals the patients to be infected by 53 different clone types of P. aeruginosa, and for 36 of the clone types we sequenced multiple longitudinal isolates, enabling us to decipher the within-host evolutionary history of each of these lineages. Results: We found the 36 lineages to exhibit mutational convergence in 56 pathoadaptive genes (genes mutated in >5 clone types), in which the host environment imposed a selection for mutations. The pathoadaptive genes were related to motility, antibiotic resistance, remodeling of regulatory networks, biofilm formation, and extracellular virulence factors. Furthermore, our results show that mutation of downstream transcriptional regulators was contingent upon the mutation of upstream regulators in the same regulatory network. Conclusion: In conclusion, we have identified adaptive trajectories generic to P. aeruginosa in the CF environment, and elucidated how early mutations predict later evolutionary events. Knowledge of pathoadaptive mutations and evolutionary contingency may help prediction of bacterial persistence and development of future therapeutic targets against the infection.

136 Impact of propidium monoazide treatment on CF bacterial community pyrosequencing analysis

136 Impact of propidium monoazide treatment on CF bacterial community pyrosequencing analysis L. Cuthbertson1,2, G. Rogers2, L. Hoffman3, A. Oliver1, P. Wing3, M. Carroll4, K. Bruce2, A. Walker5, C. van der Gast1. 1NERC Centre for Ecology and Hydrology, McLean Building, Wallingford, United Kingdom; 2King’s College London, Pharmaceutical Science Division, London, United Kingdom; 3University of Washington, Department of Pediatrics, Seattle, United States; 4Southampton University Hospitals NHS Trust, Cystic Fibrosis Unit, Southampton, United Kingdom; 5Wellcome Trust Sanger Institute, Cambridge, United Kingdom