Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis

Cystic fibrosis (CF) manifests in the lungs resulting in chronic microbial infection. Most morbidity and mortality in CF is due to cycles of pulmonary exacerbations—episodes of acute inflammation in response to the lung microbiome—which are difficult to prevent and treat because their cause is not well understood. We hypothesized that longitudinal analyses of the bacterial component of the CF lung microbiome may elucidate causative agents within this community for pulmonary exacerbations. In this study, 6 participants were sampled thrice-weekly for up to one year. During sampling, sputum, and data (antibiotic usage, spirometry, and symptom scores) were collected. Time points were categorized based on relation to exacerbation as Stable, Intermediate, and Treatment. Retrospectively, a subset of were interrogated via 16S rRNA gene sequencing. When samples were examined categorically, a significant difference between the lung microbiota in Stable, Intermediate, and Treatment samples was observed in a subset of participants. However, when samples were examined longitudinally, no correlations between microbial composition and collected data (antibiotic usage, spirometry, and symptom scores) were observed upon exacerbation onset. In this study, we identified no universal indicator within the lung microbiome of exacerbation onset but instead showed that changes to the CF lung microbiome occur outside of acute pulmonary episodes and are patient-specific.囊性纤维化（Cystic fibrosis, CF）会累及肺部，引发慢性微生物感染。囊性纤维化患者的绝大多数发病与死亡，均源于肺部急性加重的反复循环——即针对肺部微生物组的急性炎症发作；由于其致病机制尚未明确，此类发作难以预防与治疗。本研究假设，对囊性纤维化肺部微生物组的细菌组分进行纵向分析，或可阐明该微生物群落中引发肺部急性加重的致病因子。本研究中，我们对6名受试者进行了为期最长1年、每周三次的采样。采样期间，我们收集了受试者的痰液样本以及相关数据，包括抗生素使用情况、肺量测定结果与症状评分。采样时间点根据其与急性加重的关联被划分为稳定期（Stable）、中间期（Intermediate）与治疗期（Treatment）。后续我们通过16S核糖体RNA（16S rRNA）基因测序技术，对部分样本进行了分析检测。当对样本进行分类别分析时，在部分受试者中，我们观察到稳定期、中间期与治疗期的肺部菌群存在显著差异。然而，当对样本进行纵向分析时，在急性加重发作时，并未观察到菌群组成与收集到的各项数据（抗生素使用情况、肺量测定结果与症状评分）之间存在关联。本研究未发现肺部微生物组中存在可预测急性加重发作的通用标志物，反而证实囊性纤维化肺部微生物组的变化发生于急性肺部发作之外，且具有受试者个体特异性。