Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

Abstract

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (107 vs. 105 CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.

High Blood Eosinophil Count at Stable State is Not Associated with Airway Microbiota Distinct Profile in COPD

“…Patients with mild to severe COPD were included prospectively in the RINNOPARI cohort (Recherche et INNOvation en PAthologie Respiratoire Inflammatoire; University Hospital of Reims, France; NCT02924818) as described previously 6 The regional ethics committee approved the study (Comité de Protection des Personnes-Dijon EST I, no. 2016-A00242 -49).…”

“…Previous studies performed in a stable state identified associations between the sputum microbiome and COPD phenotypes. [4][5][6] Associations with COPD inflammatory phenotypes including eosinophils have been recently investigated, suggesting that different profiles of bacteria phyla might be associated with different profiles of inflammation: low sputum eosinophil count in the presence of potential pathogenic microorganism (PPM), 7,8 more diverse respiratory microbiome in subjects with BEC ≥2%. 9 However, the relationships between BEC and airway microbiota and its clinical implications remain to be determined.…”

“…We previously described an extended conventional culturebased approach, allowing the identification of bacteria restricted to viable strains. 6,10 In this study, we applied this culture technique and compared viable airway microbiota in COPD patients at a stable state with high and low BEC.…”

The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises

“…Using a combination of multiple culture conditions and media, Whelan et al showed that an average of 82.13% of bacterial OTUs from sputum of cystic fibrosis patients can be cultured [44] . Through a comprehensive cultivation effort, Muggeo et al found an enrichment of Enterobacterales was associated with deteriorated clinical symptom in COPD patients [45] . Sun et al have characterized the lung and oral microbiota using culturomics and 16S rRNA gene sequencing and found site and pathology-dependent alterations in patients with lung cancer [46] .…”

Profile of the Lower Respiratory Tract Microbiome in Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome and Lung Disease

“…In the past, based on culture-dependent techniques, it was thought that the lungs of healthy individuals were sterile. The primary tool for identifying pathogens responsible for lung infections was bacteriology-based culture ( Muggeo et al, 2021 ). With advances in next-generation sequencing technology, researchers have found that, even in healthy individuals, the lungs are not as sterile as was once thought.…”