Steven L Taylor1, Lex E X Leong2, Kerry L Ivey3, Steve Wesselingh4, Keith Grimwood5, Claire E Wainwright6, Geraint B Rogers7. 1. SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia. Electronic address: steven.taylor@sahmri.com. 2. Microbiology and Infectious Diseases, SA Pathology, South Australia, Australia. 3. Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia; Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States; Department of Nutrition and Dietetics, College of Nursing and Health Sciences Flinders University, Adelaide, SA. 4. Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia. 5. School of Medicine and Menzies Health Institute Queensland, Griffith University Gold Coast Campus and Departments of Infectious Diseases and Paediatrics, Gold Coast Health, Gold Coast, Queensland, Australia. 6. Respiratory and Sleep Medicine, Queensland Children's Hospital, South Brisbane, Queensland, Australia; Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia. 7. SAHMRI Microbiome Research Laboratory, Flinders University College of Medicine and Public Health, Adelaide, SA, Australia; Microbiome and Host Health, South Australia Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.
Abstract
BACKGROUND: Cystic fibrosis (CF) is characterised by reduced airway clearance, microbial accumulation, inflammation, and lung function decline. Certain bacterial species may contribute disproportionately to worsening lung disease. However, the relative importance of these microorganisms compared to the absolute abundance of all bacteria is uncertain. We aimed to identify the characteristics of lower airway microbiology that best reflect CF airway inflammation and disease in children. METHODS: Analysis was performed on bronchoalveolar lavage (BAL) fluid from 78 participants of the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial, aged 4.5-5.5 years. Universal bacterial quantitative PCR (qPCR), species-specific qPCR, and 16S rRNA gene sequencing were performed on DNA extracts to determine total bacterial load, species-specific load and taxa relative abundance. Quantification of pre-specified pathogens was performed by culture-based methods. Bacteriological data were related to neutrophil counts, interleukin-8, lung function, and two computed-tomography based measures, CF-CT (as the primary measure) and PRAGMA. RESULTS: Of all bacteriological measures assessed, total bacterial load determined by qPCR correlated most strongly with structural disease (CF-CT total score, rs=0.30, P=0.0095). Specifically, total bacterial load correlated with bronchiectasis, airway wall thickening, mucus plugging and parenchymal disease sub-scores. In contrast, culture-based quantification, microbiota-derived measures, and pathogen-specific qPCR-based quantification were weakly associated with total CF-CT. Regression analyses supported correlation findings, with total bacterial load explaining the greatest variance in total CF-CT (R2=0.097, P=0.0061). Correlations with PRAGMA score were comparable to CF-CT total score. CONCLUSIONS: Within the ACFBAL trial, culture-independent quantification of total bacteria provided the most clinically-informative bacteriological measure in 5-year-old CF patients.
BACKGROUND:Cystic fibrosis (CF) is characterised by reduced airway clearance, microbial accumulation, inflammation, and lung function decline. Certain bacterial species may contribute disproportionately to worsening lung disease. However, the relative importance of these microorganisms compared to the absolute abundance of all bacteria is uncertain. We aimed to identify the characteristics of lower airway microbiology that best reflect CF airway inflammation and disease in children. METHODS: Analysis was performed on bronchoalveolar lavage (BAL) fluid from 78 participants of the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial, aged 4.5-5.5 years. Universal bacterial quantitative PCR (qPCR), species-specific qPCR, and 16S rRNA gene sequencing were performed on DNA extracts to determine total bacterial load, species-specific load and taxa relative abundance. Quantification of pre-specified pathogens was performed by culture-based methods. Bacteriological data were related to neutrophil counts, interleukin-8, lung function, and two computed-tomography based measures, CF-CT (as the primary measure) and PRAGMA. RESULTS: Of all bacteriological measures assessed, total bacterial load determined by qPCR correlated most strongly with structural disease (CF-CT total score, rs=0.30, P=0.0095). Specifically, total bacterial load correlated with bronchiectasis, airway wall thickening, mucus plugging and parenchymal disease sub-scores. In contrast, culture-based quantification, microbiota-derived measures, and pathogen-specific qPCR-based quantification were weakly associated with total CF-CT. Regression analyses supported correlation findings, with total bacterial load explaining the greatest variance in total CF-CT (R2=0.097, P=0.0061). Correlations with PRAGMA score were comparable to CF-CT total score. CONCLUSIONS: Within the ACFBAL trial, culture-independent quantification of total bacteria provided the most clinically-informative bacteriological measure in 5-year-old CFpatients.
Authors: Maria T Nelson; Daniel J Wolter; Alexander Eng; Eli J Weiss; Anh T Vo; Mitchell J Brittnacher; Hillary S Hayden; Sumedha Ravishankar; Gilbert Bautista; Anina Ratjen; Marcella Blackledge; Sharon McNamara; Laura Nay; Cheryl Majors; Samuel I Miller; Elhanan Borenstein; Richard H Simon; John J LiPuma; Luke R Hoffman Journal: Thorax Date: 2020-07-06 Impact factor: 9.139
Authors: Daan Caudri; Lidija Turkovic; Nicholas H de Klerk; Tim Rosenow; Conor P Murray; Ewout W Steyerberg; Sarath C Ranganathan; Peter Sly; Stephen M Stick; Oded Breuer Journal: Pediatr Pulmonol Date: 2021-10-12