Microbiome analysis of Cystic Fibrosis sputum presents higher sensitivity than the conventional bacterial culture

Microbiological communities in the airway of Cystic Fibrosis (CF) patients may be associated with clinical conditions and bacterial exacerbation. The main aim of this study was to establish the correlation between the airway microbiome and the bacteriological culture. We also correlated the microbiome data with the CFTR mutation, presence/absence of leukocytes and hospitalization status of CF patients.

To establish the correlation between the airway microbiome and the bacteriological culture. We also correlated the microbiome data with the CFTR mutation, presence/absence of leukocytes and hospitalization status of patients.

Sputum collected for routine bacteriological culture of 27 CF patients was submitted to microbiome sequencing. Library of 16S rRNA was prepared using a V3V4 region. The Amplicon Sequence Variants (ASV) obtained from sequencing were compared according with the CFTR mutation and laboratory parameters. Leukocytes in the sputum were evaluated by a differential slide counting in microscopy. The genus Staphylococcus and Pseudomonas were detected by microbiome analysis in all sputa while Staphylococcus aureus was identified in only 19 (70.4%) and Pseudomonas aeruginosa in only 9 (33.3%) sputa by bacteriological culture. In 14 specimens the genus Burkholderia (Burkholderia-Caballeronia-Paraburkholderia) was detected by microbiome analysis; however, the Burkholderia cepacia complex was identified in only 8 sputa by bacteriological culture. Lower alpha diversity was directly correlated to the leukocyte presence and hospitalized patients. There was no significant difference in alpha diversity and CFTR mutations.

The use of NSG resources has become an important tool to improve the knowledge of the microbial profile of a CF patient. Our findings contribute to a better understanding of that the evaluation of the airway microbiome of CF patients plays an important role to better understand the pulmonary microbiota and to anticipate the detection of common CF pathogens.