title: Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients.
abstract: Gastro-Oesophageal Reflux (GOR) is a key problem in Cystic Fibrosis (CF), but the relationship between lung and gastric microbiomes is not well understood. We hypothesised that CF gastric and lung microbiomes are related. Gastric and sputum cultures were obtained from fifteen CF patients receiving percutaneous endoscopic gastrostomy feeding. Non-CF gastric juice data was obtained through endoscopy from 14 patients without lung disease. Bacterial and fungal isolates were identified by culture. Molecular bacterial profiling used next generation sequencing (NGS) of the 16S rRNA gene. Cultures grew bacteria and/or fungi in all CF gastric juice and sputa and in 9/14 non-CF gastric juices. Pseudomonas aeruginosa(Pa) was present in CF sputum in 11 patients, 4 had identical Pa strains in the stomach. NGS data from non-CF gastric juice samples were significantly more diverse compared to CF samples. NGS showed CF gastric juice had markedly lower abundance of normal gut bacteria; Bacteroides and Faecalibacterium, but increased Pseudomonas compared with non-CF. Multivariate partial least squares discriminant analysis demonstrated similar bacterial profiles of CF sputum and gastric juice samples, which were distinct from non-CF gastric juice. We provide novel evidence suggesting the existence of an aerodigestive microbiome in CF, which may have clinical relevance.
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: H
authors.initials: H
authors.lastname: Al-Momani
authors.affiliation: Department of Microbiology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK.
authors.forename: A
authors.initials: A
authors.lastname: Perry
authors.affiliation: Northumbria University, Ellison Place, Newcastle-upon-Tyne NE1 8ST, UK.
authors.forename: C J
authors.initials: CJ
authors.lastname: Stewart
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: R
authors.initials: R
authors.lastname: Jones
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: A
authors.initials: A
authors.lastname: Krishnan
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: A G
authors.initials: AG
authors.lastname: Robertson
authors.affiliation: Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: S
authors.initials: S
authors.lastname: Bourke
authors.affiliation: Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: S
authors.initials: S
authors.lastname: Doe
authors.affiliation: School of Science and Engineering, Teesside University, Middlesbrough, TS1 3BA, UK.
authors.forename: S P
authors.initials: SP
authors.lastname: Cummings
authors.affiliation: Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: A
authors.initials: A
authors.lastname: Anderson
authors.affiliation: Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: T
authors.initials: T
authors.lastname: Forrest
authors.affiliation: Adult Cystic Fibrosis Centre and Northern Oesophago-Gastric Unit, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK.
authors.forename: S M
authors.initials: SM
authors.lastname: Griffin
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: M
authors.initials: M
authors.lastname: Brodlie
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: J
authors.initials: J
authors.lastname: Pearson
authors.affiliation: Institutes of Cellular Medicine and Cell &Molecular Biosciences, Newcastle University Medical School, Newcastle University, Newcastle upon Tyne. NE2 4HH, UK.
authors.forename: C
authors.initials: C
authors.lastname: Ward
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D015373:Bacterial Typing Techniques; D001439:Bacteroides / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D003550:Cystic Fibrosis / Q000150:complications / Q000382:microbiology* / Q000473:pathology; D016002:Discriminant Analysis; D000070036:Faecalibacterium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D005750:Gastric Juice / Q000382:microbiology*; D005764:Gastroesophageal Reflux / Q000150:complications / Q000382:microbiology* / Q000473:pathology; D005774:Gastrostomy; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008168:Lung / Q000382:microbiology; D008297:Male; D064307:Microbiota / Q000235:genetics*; D008875:Middle Aged; D010288:Parenteral Nutrition; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013183:Sputum / Q000382:microbiology*; D013270:Stomach / Q000382:microbiology
chemical_list: D012336:RNA, Ribosomal, 16S