Lower airway microbiota associates with inflammatory phenotype in severe preschool wheeze

• Published in: Journal of allergy and clinical immunology Vol. 143; no. 4; pp. 1607 - 1610.e3
• Main Authors: Robinson, Polly F.M., Pattaroni, Céline, Cook, James, Gregory, Lisa, Alonso, Aldara Martin, Fleming, Louise J., Lloyd, Clare M., Bush, Andrew, Marsland, Benjamin J., Saglani, Sejal
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.04.2019; Elsevier Limited
• Subjects: Age; Asthma; Atopy; Bacteria; Blood; Child, Preschool; Children; Coefficient of variation; DNA sequencing; Female; Genotype & phenotype; Humans; Immunoglobulin E; Inflammation; Inflammation - immunology; Inflammation - microbiology; Lung - immunology; Lung - microbiology; Lung diseases; Lymphocytes; Male; Microbiota; Neutrophils; Pediatrics; Phenotype; Phenotypes; Polymerase chain reaction; Preschool children; Respiratory Sounds; Respiratory tract; rRNA 16S; Skin tests; Streptococcus infections
• ISSN: 0091-6749; 1097-6825
• DOI: 10.1016/j.jaci.2018.12.985

Any surplus BAL fluid was stored at −80°C for microbiota analysis. Because BAL fluid was first sent for clinically indicated tests, only BAL fluid that was left over after cytospin had been prepared, and samples sent for bacterial culture and viral PCR could be used for microbiota profiling. Atopy was defined as more than 1 positive specific IgE level (≥0.35 kU/L) or more than 1 positive skin prick test response. Because children were undergoing a clinically indicated procedure, not all recruited patients had blood or BAL fluid samples taken, and thus the sample size for each parameter is stated.Bacterial DNA isolation and 16S rDNA sequencing Bacterial DNA was isolated from BAL fluid supernatants, as previously described.E8 In addition, DNA extraction and PCR-negative controls were added. A subset of samples was counted by a minimum of 2 investigators, and interobserver variability was analyzed with Bland-Altman plots for 2 observers or as the coefficient of variation for 3 observers. Because participants were undergoing clinically indicated tests, not all patients had blood and BAL fluid samples taken. [...]the sample size for each parameter is stated in the table or figure legend.Extended Fig 1 legend Fig 1.