Evaluation of the airway microbiome in nontuberculous mycobacteria disease

Abstract

Aspiration is associated with nontuberculous mycobacterial (NTM) pulmonary disease and airway dysbiosis is associated with increased inflammation. We examined whether NTM disease was associated with a distinct airway microbiota and immune profile.297 oral wash and induced sputum samples were collected from 106 participants with respiratory symptoms and imaging abnormalities compatible with NTM. Lower airway samples were obtained in 20 participants undergoing bronchoscopy. 16S rRNA gene and nested mycobacteriome sequencing approaches characterised microbiota composition. In addition, inflammatory profiles of lower airway samples were examined.The prevalence of NTM cultures was 58%. Few changes were noted in microbiota characteristics or composition in oral wash and sputum samples among groups. Among NTM samples, 27% of the lower airway samples were enriched with A mycobacteriome approach identified in a greater percentage of samples, including some nonpathogenic strains. In NTM lower airway samples, taxa identified as oral commensals were associated with increased inflammatory biomarkers.The 16S rRNA gene sequencing approach is not sensitive in identifying NTM among airway samples that are culture-positive. However, associations between lower airway inflammation and microbiota signatures suggest a potential role for these microbes in the inflammatory process in NTM disease.

The microbiome in bronchiectasis

“…These organisms, particularly fungi and Mycobacteria, present difficulties related to DNA extraction, as well as the lack of agreement on appropriate methods for sequencing and databases to identify micro-organisms. The widely used 16S rRNA sequencing methods used for microbiome studies do not identify Mycobacteria accurately [72]. SULAIMAN et al [72] studied a cohort of patients with NTM infection using 16S rRNA sequencing, and despite these patients being culture-positive for NTM, few mycobacteria were identified by sequencing.…”

“…The widely used 16S rRNA sequencing methods used for microbiome studies do not identify Mycobacteria accurately [72]. SULAIMAN et al [72] studied a cohort of patients with NTM infection using 16S rRNA sequencing, and despite these patients being culture-positive for NTM, few mycobacteria were identified by sequencing. There was an association between oral commensals and inflammatory responses, suggesting a modulating effect of other microbiota in NTM lung disease.…”

The Lung Microbiota in Korean Patients with Non-tuberculous Mycobacterial Pulmonary Disease

“…As most NTM infections involve the MAC, previous studies evaluating the NTM-PD microbiome focused on the MAC. [20,28] We found that 16S rRNA sequencing identified mycobacteria in only 54.5% of bronchial washings and 27.3% of PSBs from NTM-PD patients (Supplementary Table 2). Previous studies reported that 16S…”

“…rRNA gene sequencing is not adequately sensitive, and technical improvements are needed. [28,29] Respiratory samples (especially PSBs) from NTM-PD patients tended to exhibit lower alpha diversities compared with those from control subjects. In a previous study, the alpha diversities of sputum samples from females with NTM-PD and those with both NTM-PD and breast cancer were significantly lower than those of samples from healthy females, consistent with our results.…”

“…The BMI was lower in those whose sputa were positive, compared with negative, for NTM cultures. [28] Most NTM that we detected belonged to the Mycobacterium avium complex (MAC), including M. avium and M. intracellulare. M. kansasii was cultured from one subject only, and NTM from another patient were not identified.…”