Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients.

H Al-Momani,T Forrest,C Ward,M Brodlie,S P Cummings,C J Stewart,R Jones,J Pearson,S M Griffin,A Anderson,A Perry,S Doe,S Bourke,A Krishnan,A G Robertson

doi:10.1038/srep26985

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.

Highlights

Background disease OesophagitisOesophagitis and Pyloroplasty Barrett’s Oesophagus and Hiatus Hernia Hiatus Hernia Oesophagitis and Hiatus Hernia Gastritis and Hiatus Hernia Oesophagitis and Hiatus Hernia Not known Gastric ulcer Gastritis and Hiatus Hernia Barrett’s Oesophagus Not known Duodenal ulcer Gastritispump inhibitor esomeprazole (PPI) yes/no* yes yes no yes n/a yes yes n/a yes n/a yes n/a n/a n/aGastric juice pH 2.4 6.6μL of homogenised sputum and gastric juice were plated for bacterial and fungal cultures
We sampled over 80% of all the percutaneous endoscopic gastrostomy (PEG) patients potentially available in the North East Region of England
The loading plot from the partial least squares discriminant analysis (PLS-DA) of the overall bacterial community revealed that Prevotella, Rothia, Streptococcus, Staphylococcus, Herminiimonas and Pseudomonas were closely associated with Cystic Fibrosis (CF) samples while Faecalibacterium, Roseburia, Bacteroides, and Lactobacillus were more associated with non-CF gastric juices. We believe this is the first study directly comparing microorganisms isolated from the airways and gastric juice in the same PEG fed CF patients

Summary

Introduction

ΜL of homogenised sputum and gastric juice were plated for bacterial and fungal cultures. The following media were used: Columbia blood agar supplemented with 5% horse blood, chocolate agar supplemented with 70 mg/L bacitracin, Burkholderia selective agar (for CF sputa and gastric juice, CEP bioMérieux UK), Cysteine lactose electrolyte deficient agar (CLED) and fastidious anaerobic agar (FAA). Plates were incubated according to standard protocol, CEP cultures were incubated for 10 days at 30 °C for isolation of Burkholderia cepacia complex and rapidly growing mycobacterium. Plates were examined daily for evidence of microbial growth and assessment of the number of distinct colonial variants was recorded. Mycobacterium was identified by rpoB, sodA and hsp[65] gene sequencing and strain typed using variable number tandem repeat (VNTR), (Colindale, UK15). All isolates of Pa were typed via VNTR profiling[16]

Methods

Results

Conclusion