BACKGROUND Cystic fibrosis (CF) is characterised by reduced airway clearance, microbial accumulation, inflammation, and lung function decline. Certain bacterial species may contribute disproportionately to worsening lung disease. However, the relative importance of these microorganisms compared to the absolute abundance of all bacteria is uncertain. We aimed to identify the characteristics of lower airway microbiology that best reflect CF airway inflammation and disease in children. METHODS Analysis was performed on bronchoalveolar lavage (BAL) fluid from 78 participants of the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial, aged 4.5-5.5 years. Universal bacterial quantitative PCR (qPCR), species-specific qPCR, and 16S rRNA gene sequencing were performed on DNA extracts to determine total bacterial load, species-specific load and taxa relative abundance. Quantification of pre-specified pathogens was performed by culture-based methods. Bacteriological data were related to neutrophil counts, interleukin-8, lung function, and two computed-tomography based measures, CF-CT (as the primary measure) and PRAGMA. RESULTS Of all bacteriological measures assessed, total bacterial load determined by qPCR correlated most strongly with structural disease (CF-CT total score, rs=0.30, P=0.0095). Specifically, total bacterial load correlated with bronchiectasis, airway wall thickening, mucus plugging and parenchymal disease sub-scores. In contrast, culture-based quantification, microbiota-derived measures, and pathogen-specific qPCR-based quantification were weakly associated with total CF-CT. Regression analyses supported correlation findings, with total bacterial load explaining the greatest variance in total CF-CT (R2=0.097, P=0.0061). Correlations with PRAGMA score were comparable to CF-CT total score. CONCLUSIONS Within the ACFBAL trial, culture-independent quantification of total bacteria provided the most clinically-informative bacteriological measure in 5-year-old CF patients.

中文翻译：

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小儿囊性纤维化中的总细菌负荷、炎症和结构性肺病

背景囊性纤维化（CF）的特征在于气道清除率降低、微生物积累、炎症和肺功能下降。某些细菌种类可能会导致肺部疾病恶化。然而，与所有细菌的绝对丰度相比，这些微生物的相对重要性尚不确定。我们旨在确定最能反映儿童 CF 气道炎症和疾病的下呼吸道微生物学特征。方法 对来自澳大利亚 CF 支气管肺泡灌洗 (ACFBAL) 临床试验的 78 名参与者的支气管肺泡灌洗 (BAL) 液进行分析，年龄为 4.5-5.5 岁。对 DNA 提取物进行通用细菌定量 PCR (qPCR)、物种特异性 qPCR 和 16S rRNA 基因测序，以确定总细菌载量，物种特异性负荷和分类群相对丰度。通过基于培养的方法对预先指定的病原体进行定量。细菌学数据与中性粒细胞计数、白细胞介素 8、肺功能和两种基于计算机断层扫描的测量值、CF-CT（作为主要测量值）和 PRAGMA 相关。结果 在评估的所有细菌学指标中，qPCR 确定的总细菌载量与结构性疾病的相关性最强（CF-CT 总分，rs=0.30，P=0.0095）。具体而言，总细菌负荷与支气管扩张、气道壁增厚、粘液堵塞和实质疾病子评分相关。相比之下，基于培养的量化、微生物群衍生的措施和基于病原体特异性 qPCR 的量化与总 CF-CT 的相关性较弱。回归分析支持相关性发现，总细菌载量解释了总 CF-CT 的最大差异（R2=0.097，P=0.0061）。与 PRAGMA 评分的相关性与 CF-CT 总分相当。结论 在 ACFBAL 试验中，不依赖培养的总细菌定量为 5 岁 CF 患者提供了最具临床信息量的细菌学指标。